http://2014.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=500&target=R.hanke2014.igem.org - User contributions [en]2024-03-29T01:43:14ZFrom 2014.igem.orgMediaWiki 1.16.5http://2014.igem.org/Team:Aachen/AttributionsTeam:Aachen/Attributions2015-09-09T13:47:08Z<p>R.hanke: /* Members */</p>
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# Thanks and acknowledgements for all other people involved in helping make a successful iGEM team.<br />
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=Members=<br />
<span class="anchor" id="members"></span><br />
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A core concept of iGEM is the collaboration within an interdisciplinary student team. Accordingly, students of different age, gender and field of study came together to found our team in Aachen, in order to realize our project with joint forces and enthusiasm for the overall goal. Working closely together, we therefore not only have the chance to learn from each other, but also to excel ourselves. Using our collective creativity and common responsibility, we will create something special in order to make our contribution to synthetic biology.<br />
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<a href="https://2014.igem.org/User:Mosthege" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Michael Osthege </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Man for Everything<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Aachen_team_member_Michael_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<a href="https://2014.igem.org/User:Fgohr" style="color:black"><br />
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<b> Florian Gohr </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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King Gibson<br />
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<a href="https://2014.igem.org/User:AZimmermann" style="color:black"><br />
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<b> Arne Zimmermann </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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The Patience himself<br />
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<a href="https://2014.igem.org/User:Nbailly" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Nina Bailly </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Flask Prep Princess<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/48/Aachen_team_member_Nina_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<a href="https://2014.igem.org/User:VeraA" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Vera Alexandrova </b><br />
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<i> Biology </i><br />
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Goddess of Plasmid Prep<br />
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<a href="https://2014.igem.org/User:Pdemling" style="color:black"><br />
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<b> Philipp Demling </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Prince of Bad Puns<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/7/77/Aachen_team_member_Philipp_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:R.hanke" style="color:black"><br />
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<b> René Hanke </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Chief of Communication<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_team_member_Rene_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:PatrickO" style="color:black"><br />
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<b> Patrick Opdensteinen </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Graphics God<br />
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<a href="https://2014.igem.org/User:Bpeeters" style="color:black"><br />
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<b> Björn Peeters </b><br />
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<i> Computational Engineering Science </i><br />
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Hardware Master<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/8d/Aachen_team_member_Bjoern_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<a href="https://2014.igem.org/User:Eshani.sood" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Eshani Sood </b><br />
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<i> Biomedical Engineering </i><br />
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Sunshine<br />
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<a href="https://2014.igem.org/User:Mjoppich" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Markus Joppich </b><br />
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<i> Computer Science </i><br />
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Software Expert & Travel Assistant<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/83/Aachen_team_member_Markus_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<a href="https://2014.igem.org/User:Ansgar" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Ansgar Niemöller </b><br />
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<i> Computational Engineering Science </i><br />
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GUI Master<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/4e/Aachen_team_member_Ansgar_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<a href="https://2014.igem.org/User:J.plum" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Julia Plum </b><br />
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<i> Biology and Business Administration </i><br />
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Fundraising & Balancing<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c9/Aachen_team_member_Julia_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:StefanReinhold" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Stefan Reinhold </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Treasurer<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0c/Aachen_team_member_Stefan_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Aschechtel" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Anna Schechtel </b><br />
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<i> Biology </i><br />
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Chip Queen<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/a/a4/Aachen_team_member_Anna_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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= Advisors =<br />
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'''Dr.-Ing. Suresh Sudarsan'''<br />
<br />
I'm working as a post-doc with Prof. Blank at RWTH Aachen University. In my Ph.D. I worked under the guidance of Prof. Andreas Schmid (2008-2012) at TU Dortmund, and Prof. Matthias Reuss (2009-2011) at the University of Stuttgart, with a focus on elucidating the link between the central and aromatic metabolism of ''P. putida'' using a systems biology approach.<br />
<br />
I'm fascinated about understanding the collective behavior of microorganisms and their metabolic potential in different niches. In my research, I use tools in ''metabolic engineering & systems biology'' such as metabolomics, fast sampling, kinetic/dynamic modeling and metabolic flux analysis. <br />
<br />
In iGEM, I enjoy working with a group of young scientists from Aachen to achieve our common goal of detecting ''Pseudomonas aeruginosa'' on hard surfaces. Besides science, I try to get myself involved in adventurous sports...but honestly... I just like to relax my day with a delicious meal and a good sci-fi movie!<br />
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<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/c/c8/Aachen_team_member_Ljubica.jpg" width="200px" /></html><br />
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'''Dr. rer. nat. Ljubica Vojcic'''<br />
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I am working as a Subgroup Leader in Prof. Schwaneberg research group at the Institute of Biotechnology, RWTH Aachen. The research area of the Schwaneberg group focuses on directed protein evolution by developing novel methods for generating diversity at the gene level, analyzing consequences of mutational biases on the protein level and developing novel high-throughput screening systems that will lead to improved biocatalysts for prominent applications in industry. In particular, my core expertise is development of high throughput screening systems for different enzyme classes in order to redefine the screening step no longer as bottleneck in directed evolution. <br />
<br />
In iGEM, I enjoyed very much to work with highly motivated and ambitious young scientists from RWTH Aachen University. I truly believe that our collaboration has just started and that we will enjoy jointly solving the scientific challenges in the near future. <br />
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=Instructors=<br />
<span class="anchor" id="instructors"></span><br />
== Prof. Dr.-Ing. Lars M. Blank ==<br />
==== RWTH Institute for Applied Microbiology (iAMB) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/4/42/Aachen_LarsBlank.jpg" width="150px" /></html> <br />
Prof. Blank focuses his research on fundamental and applied aspects of microbial metabolism. Of specific interest is the interaction between the metabolic network and the introduced genetic and environmental perturbations. The research on in silico/in vivo metabolic network operations is aimed at a deeper understanding of cell function, with the ultimate goal of rational cell engineering.<br />
<br />
In his teaching, Prof. Blank focuses on the integration of biological concepts with the tools from bioinformatics and engineering. He believes that a sound knowledge base in life sciences is the key for creative and thus successful work in the areas of Metabolic Engineering and Synthetic Biology. Read more about Prof. Blank's work on the [http://www.iamb.rwth-aachen.de/html/members.php?s=det&id=3 iAMB's website].<br />
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== Prof. Dr. Wolfgang Wiechert ==<br />
==== Forschungszentrum Jülich, Institute of Bio- and Geosciences (IGB-1) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/8/88/Aachen_WolfgangWiechert.jpg" width="150px" /></html> <br />
Prof. Wiechert's main area of work lies within the field of applied systems bio(techno)logy of microorganisms with a special focus on methodological developments for quantitative biology. Characteristics of his research work are a close integration of experimental and theoretical work within multi disciplinary projects. As the head of the Systems Biotechnology research division at Forschungszentrum Jülich, he is developing methods for quantitative metabolomics, fluxomics and proteomics including model based mathematical methods for experimental design, parameter estimation, and process optimization in biotechnological systems. Future work will also incorporate micro fluidic methods for single cell analysis. In general, all research results are used to drive forward the process of gaining knowledge in the course of an iterative improvement of industrial production systems. This proceeds in close cooperation of all working groups at the IBG-1. Together with industrial partners also diverse examples from industry are investigated and further developed. Read more about Prof. Wiechert's work on the [http://www.fz-juelich.de/SharedDocs/Personen/IBG/IBG-1/EN/Research_groups/general/wiechert.html/ IBG-1 website].<br />
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== Prof. Dr. Ulrich Schwaneberg ==<br />
==== RWTH Institute for Biotechnology, Leibniz Institute for Interactive Materials (DWI) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/f/fe/Aachen_UlrichSchwaneberg.jpg" width="150px" /></html> <br />
The Schwaneberg Group seeks to be at the research frontier in the interdisciplinary field of directed protein evolution by developing novel methods for generating diversity at the gene level, analyzing consequence of mutational biases on the protein level and developing novel high-throughput screening systems that will ultimately lead to tailored-biocatalysts for significant applications in industry. They train students in the cutting edge technologies of laboratory evolution, biocatalyst engineering and high throughput screening methodologies. The Schwaneberg Group believes in integrating fundamental principles of protein design with environmental awareness in their research and seeks to promote international scientific collaborations. Read more about Prof. Schwaneberg and his work on the [http://www.biotec.rwth-aachen.de/ Schwaneberg Group's website].<br />
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<br />
This project would not have been possible without the generous help and advice from many great people and organizations. We thank all the partners listed below for their essential contributions and financial support that covered registration fees, travel costs, the organization of the meetup in September, laboratory materials and expenses for services and materials.<br />
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=Partners=<br />
<span class="anchor" id="partners"></span><br />
<div align="center"><br />
{|cellpadding="25"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|159px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|318px|Niersverband]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Genscript_Logo.png|240px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|193px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|256px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="35"<br />
|[[File:Aachen_bmbf.jpg|326px|BMBF]]<br />
|[[File:Aachen_idt_.png|217px|IDT]]<br />
|}<br />
<br />
{|cellpadding="25"<br />
|[[File:M2p_labs_logo.jpg|103px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|109px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|121px|pro RWTH]]<br />
|}<br />
{|cellpadding="25"<br />
|[[File:Aachen_Logo_iAMB.png|229px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|229px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|246px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|}<br />
{|cellpadding="35"<br />
|[[File:Aachen_Logo_ABBt.png|209px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|239px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|209px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|150px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
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=Attribution of Scientific and General Support=<br />
<span class="anchor" id="support"></span><br />
Great projects do not only depend on solid funding, but even more on the invaluable support by great people. We found great people not only in our 'home institute' the iAMB, but across many partner institutions.<br />
<br />
<br />
* '''RWTH Institute of Molecular Biotechnology''' (Biology VII)<br />
** Dr. Ulrich Commandeur ''for giving us access to essential resources of the bio7''<br />
** Christina Dickmeis M.Sc. ''who answered lots of questions''<br />
* '''RWTH Institute of Biotechnology''' (Biology VI)<br />
** David Schönauer and Alan Mertens M.Sc. ''who helped us to purify proteins''<br />
* '''Helmholtz Institute for Biomedical Engineering'''<br />
** Prof. Dr. Lothar Elling and Sophia Böcker, M.Sc. ''for giving us access to their gal-3 expression plasmid''<br />
* '''RWTH Institute of Applied Microbiology''' (iAMB/Biology IV)<br />
** Prof. Dr. Miriam Agler-Rosenbaum ''for scientific information on quorum sensing''<br />
** Dr. Martin Zimmermann ''who counseled us on balancing iGEM with our studies''<br />
** Dr. Andrea Germer ''for teaching us Gibson cloning''<br />
** Erick Bosire Maosa M.Sc. ''who advised us on cultivation of Pseudomonas''<br />
** Gisela Beissel, Annette Schreer and Kalle Hüser ''for their great patience with our entropy generation''<br />
* '''Forschungszentrum Jülich'''<br />
** Marianne Heß ''who was and is essential for travel organization''<br />
** Dr. Hanno Scharr ''for advice on image analysis''<br />
* '''Fab Lab Aachen'''<br />
** René Bohne, Jan Zimmermann and Jan Thar ''who generously gave us access to the lasercutter and 3D printer''<br />
* '''Others'''<br />
** Dr. Helen Rosenkranz, ABBt, ''for helping us with hundreds of administrative paperwork''<br />
** Dr. Heinz-Albert Becker, NEAnderLab, ''for his help with the organization of the school project''<br />
** Ulrike Eisel, Gymnasium am Neandertal, ''for her help with the organization of the school project''<br />
** Fachschaft Biowissenschaften ''for food supplies and access to their rooms''<br />
** Dr. Joachim Fröhlingsdorf, MakeLight, ''who inspired us to expand our OD/F project''<br />
** Univ.-Prof. Dr. Wolfgang Dott, Uniklinik RWTH Aachen, ''for helpful feedback regarding fields of application for our biosensor''<br />
<br />
Finally, we want to thank '''Simon&nbsp;Unthan''', '''Michael&nbsp;Limberg''', '''Henrik&nbsp;Cordes''', '''Sven&nbsp;Jager''' and '''Team&nbsp;Bielefeld''' for their advice guiding us through our first iGEM participation! <br />
<br />
Special thanks to '''Dr.-Ing. Suresh Sudarsan''' for a final check for typos on our wiki!<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/AttributionsTeam:Aachen/Attributions2015-09-09T13:45:55Z<p>R.hanke: /* Members */</p>
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# General Support<br />
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# Lab support<br />
# Difficult technique support<br />
# Project advisor support<br />
# Wiki support<br />
# Presentation coaching<br />
# Policy & Practices support<br />
# Thanks and acknowledgements for all other people involved in helping make a successful iGEM team.<br />
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=Members=<br />
<span class="anchor" id="members"></span><br />
<br />
A core concept of iGEM is the collaboration within an interdisciplinary student team. Accordingly, students of different age, gender and field of study came together to found our team in Aachen, in order to realize our project with joint forces and enthusiasm for the overall goal. Working closely together, we therefore not only have the chance to learn from each other, but also to excel ourselves. Using our collective creativity and common responsibility, we will create something special in order to make our contribution to synthetic biology.<br />
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<a href="https://2014.igem.org/User:Mosthege" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Michael Osthege </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Man for Everything<br />
<br/><br/><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Aachen_team_member_Michael_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<a href="https://2014.igem.org/User:Fgohr" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Florian Gohr </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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King Gibson<br />
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<a href="https://2014.igem.org/User:AZimmermann" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Arne Zimmermann </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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The Patience himself<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/88/Aachen_team_member_Arne_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Nbailly" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Nina Bailly </b><br />
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<i> Molecular and Applied Biotechnology </i><br />
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Flask Prep Princess<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/48/Aachen_team_member_Nina_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:VeraA" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Vera Alexandrova </b><br />
<br/><br/><br />
<i> Biology </i><br />
<br/><br/><br />
Goddess of Plasmid Prep<br />
<br/><br/><br />
<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/81/Aachen_team_member_Vera_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Pdemling" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Philipp Demling </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
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Prince of Bad Puns<br />
<br/><br/><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/7/77/Aachen_team_member_Philipp_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:R.hanke" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> René Hanke </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
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Chief of Communication<br />
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<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_team_member_Rene_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:PatrickO" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Patrick Opdensteinen </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
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Graphics God<br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/1a/Aachen_team_member_Patrick_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Bpeeters" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Björn Peeters </b><br />
<br/><br/><br />
<i> Computational Engineering Science </i><br />
<br/><br/><br />
Hardware Master<br />
<br/><br/><br />
<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/8d/Aachen_team_member_Bjoern_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Eshani.sood" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Eshani Sood </b><br />
<br/><br/><br />
<i> Biomedical Engineering </i><br />
<br/><br/><br />
Sunshine<br />
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<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/52/Aachen_team_member_Eshani_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Mjoppich" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Markus Joppich </b><br />
<br/><br/><br />
<i> Computer Science </i><br />
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Software Expert & Travel Assistant<br />
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<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/83/Aachen_team_member_Markus_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Ansgar" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Ansgar Niemöller </b><br />
<br/><br/><br />
<i> Computational Engineering Science </i><br />
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GUI Master<br />
<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/4e/Aachen_team_member_Ansgar_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:J.plum" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Julia Plum </b><br />
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<i> Biology and Business Administration </i><br />
<br/><br/><br />
Fundraising & Balancing<br />
<br/><br/><br />
<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c9/Aachen_team_member_Julia_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:StefanReinhold" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
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<b> Stefan Reinhold </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
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Treasurer<br />
<br/><br/><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0c/Aachen_team_member_Stefan_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Aschechtel" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Anna Schechtel </b><br />
<br/><br/><br />
<i> Biology </i><br />
<br/><br/><br />
Chip Queen<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/a/a4/Aachen_team_member_Anna_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
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= Advisors =<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/5/57/Aachen_team_member_Suresh_01.jpg" width="200px" /></html><br />
<br />
'''Dr.-Ing. Suresh Sudarsan'''<br />
<br />
I'm working as a post-doc with Prof. Blank at RWTH Aachen University. In my Ph.D. I worked under the guidance of Prof. Andreas Schmid (2008-2012) at TU Dortmund, and Prof. Matthias Reuss (2009-2011) at the University of Stuttgart, with a focus on elucidating the link between the central and aromatic metabolism of ''P. putida'' using a systems biology approach.<br />
<br />
I'm fascinated about understanding the collective behavior of microorganisms and their metabolic potential in different niches. In my research, I use tools in ''metabolic engineering & systems biology'' such as metabolomics, fast sampling, kinetic/dynamic modeling and metabolic flux analysis. <br />
<br />
In iGEM, I enjoy working with a group of young scientists from Aachen to achieve our common goal of detecting ''Pseudomonas aeruginosa'' on hard surfaces. Besides science, I try to get myself involved in adventurous sports...but honestly... I just like to relax my day with a delicious meal and a good sci-fi movie!<br />
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<br />
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<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/c/c8/Aachen_team_member_Ljubica.jpg" width="200px" /></html><br />
<br />
'''Dr. rer. nat. Ljubica Vojcic'''<br />
<br />
I am working as a Subgroup Leader in Prof. Schwaneberg research group at the Institute of Biotechnology, RWTH Aachen. The research area of the Schwaneberg group focuses on directed protein evolution by developing novel methods for generating diversity at the gene level, analyzing consequences of mutational biases on the protein level and developing novel high-throughput screening systems that will lead to improved biocatalysts for prominent applications in industry. In particular, my core expertise is development of high throughput screening systems for different enzyme classes in order to redefine the screening step no longer as bottleneck in directed evolution. <br />
<br />
In iGEM, I enjoyed very much to work with highly motivated and ambitious young scientists from RWTH Aachen University. I truly believe that our collaboration has just started and that we will enjoy jointly solving the scientific challenges in the near future. <br />
<br />
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=Instructors=<br />
<span class="anchor" id="instructors"></span><br />
== Prof. Dr.-Ing. Lars M. Blank ==<br />
==== RWTH Institute for Applied Microbiology (iAMB) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/4/42/Aachen_LarsBlank.jpg" width="150px" /></html> <br />
Prof. Blank focuses his research on fundamental and applied aspects of microbial metabolism. Of specific interest is the interaction between the metabolic network and the introduced genetic and environmental perturbations. The research on in silico/in vivo metabolic network operations is aimed at a deeper understanding of cell function, with the ultimate goal of rational cell engineering.<br />
<br />
In his teaching, Prof. Blank focuses on the integration of biological concepts with the tools from bioinformatics and engineering. He believes that a sound knowledge base in life sciences is the key for creative and thus successful work in the areas of Metabolic Engineering and Synthetic Biology. Read more about Prof. Blank's work on the [http://www.iamb.rwth-aachen.de/html/members.php?s=det&id=3 iAMB's website].<br />
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<br />
== Prof. Dr. Wolfgang Wiechert ==<br />
==== Forschungszentrum Jülich, Institute of Bio- and Geosciences (IGB-1) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/8/88/Aachen_WolfgangWiechert.jpg" width="150px" /></html> <br />
Prof. Wiechert's main area of work lies within the field of applied systems bio(techno)logy of microorganisms with a special focus on methodological developments for quantitative biology. Characteristics of his research work are a close integration of experimental and theoretical work within multi disciplinary projects. As the head of the Systems Biotechnology research division at Forschungszentrum Jülich, he is developing methods for quantitative metabolomics, fluxomics and proteomics including model based mathematical methods for experimental design, parameter estimation, and process optimization in biotechnological systems. Future work will also incorporate micro fluidic methods for single cell analysis. In general, all research results are used to drive forward the process of gaining knowledge in the course of an iterative improvement of industrial production systems. This proceeds in close cooperation of all working groups at the IBG-1. Together with industrial partners also diverse examples from industry are investigated and further developed. Read more about Prof. Wiechert's work on the [http://www.fz-juelich.de/SharedDocs/Personen/IBG/IBG-1/EN/Research_groups/general/wiechert.html/ IBG-1 website].<br />
<html><br><br><br></p></html><br />
<br />
== Prof. Dr. Ulrich Schwaneberg ==<br />
==== RWTH Institute for Biotechnology, Leibniz Institute for Interactive Materials (DWI) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/f/fe/Aachen_UlrichSchwaneberg.jpg" width="150px" /></html> <br />
The Schwaneberg Group seeks to be at the research frontier in the interdisciplinary field of directed protein evolution by developing novel methods for generating diversity at the gene level, analyzing consequence of mutational biases on the protein level and developing novel high-throughput screening systems that will ultimately lead to tailored-biocatalysts for significant applications in industry. They train students in the cutting edge technologies of laboratory evolution, biocatalyst engineering and high throughput screening methodologies. The Schwaneberg Group believes in integrating fundamental principles of protein design with environmental awareness in their research and seeks to promote international scientific collaborations. Read more about Prof. Schwaneberg and his work on the [http://www.biotec.rwth-aachen.de/ Schwaneberg Group's website].<br />
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<br />
This project would not have been possible without the generous help and advice from many great people and organizations. We thank all the partners listed below for their essential contributions and financial support that covered registration fees, travel costs, the organization of the meetup in September, laboratory materials and expenses for services and materials.<br />
<br />
=Partners=<br />
<span class="anchor" id="partners"></span><br />
<div align="center"><br />
{|cellpadding="25"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|159px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|318px|Niersverband]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Genscript_Logo.png|240px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|193px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|256px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="35"<br />
|[[File:Aachen_bmbf.jpg|326px|BMBF]]<br />
|[[File:Aachen_idt_.png|217px|IDT]]<br />
|}<br />
<br />
{|cellpadding="25"<br />
|[[File:M2p_labs_logo.jpg|103px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|109px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|121px|pro RWTH]]<br />
|}<br />
{|cellpadding="25"<br />
|[[File:Aachen_Logo_iAMB.png|229px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|229px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|246px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|}<br />
{|cellpadding="35"<br />
|[[File:Aachen_Logo_ABBt.png|209px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|239px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|209px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|150px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
=Attribution of Scientific and General Support=<br />
<span class="anchor" id="support"></span><br />
Great projects do not only depend on solid funding, but even more on the invaluable support by great people. We found great people not only in our 'home institute' the iAMB, but across many partner institutions.<br />
<br />
<br />
* '''RWTH Institute of Molecular Biotechnology''' (Biology VII)<br />
** Dr. Ulrich Commandeur ''for giving us access to essential resources of the bio7''<br />
** Christina Dickmeis M.Sc. ''who answered lots of questions''<br />
* '''RWTH Institute of Biotechnology''' (Biology VI)<br />
** David Schönauer and Alan Mertens M.Sc. ''who helped us to purify proteins''<br />
* '''Helmholtz Institute for Biomedical Engineering'''<br />
** Prof. Dr. Lothar Elling and Sophia Böcker, M.Sc. ''for giving us access to their gal-3 expression plasmid''<br />
* '''RWTH Institute of Applied Microbiology''' (iAMB/Biology IV)<br />
** Prof. Dr. Miriam Agler-Rosenbaum ''for scientific information on quorum sensing''<br />
** Dr. Martin Zimmermann ''who counseled us on balancing iGEM with our studies''<br />
** Dr. Andrea Germer ''for teaching us Gibson cloning''<br />
** Erick Bosire Maosa M.Sc. ''who advised us on cultivation of Pseudomonas''<br />
** Gisela Beissel, Annette Schreer and Kalle Hüser ''for their great patience with our entropy generation''<br />
* '''Forschungszentrum Jülich'''<br />
** Marianne Heß ''who was and is essential for travel organization''<br />
** Dr. Hanno Scharr ''for advice on image analysis''<br />
* '''Fab Lab Aachen'''<br />
** René Bohne, Jan Zimmermann and Jan Thar ''who generously gave us access to the lasercutter and 3D printer''<br />
* '''Others'''<br />
** Dr. Helen Rosenkranz, ABBt, ''for helping us with hundreds of administrative paperwork''<br />
** Dr. Heinz-Albert Becker, NEAnderLab, ''for his help with the organization of the school project''<br />
** Ulrike Eisel, Gymnasium am Neandertal, ''for her help with the organization of the school project''<br />
** Fachschaft Biowissenschaften ''for food supplies and access to their rooms''<br />
** Dr. Joachim Fröhlingsdorf, MakeLight, ''who inspired us to expand our OD/F project''<br />
** Univ.-Prof. Dr. Wolfgang Dott, Uniklinik RWTH Aachen, ''for helpful feedback regarding fields of application for our biosensor''<br />
<br />
Finally, we want to thank '''Simon&nbsp;Unthan''', '''Michael&nbsp;Limberg''', '''Henrik&nbsp;Cordes''', '''Sven&nbsp;Jager''' and '''Team&nbsp;Bielefeld''' for their advice guiding us through our first iGEM participation! <br />
<br />
Special thanks to '''Dr.-Ing. Suresh Sudarsan''' for a final check for typos on our wiki!<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T14:01:29Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> To watch our <b>final presentation</b> just click <a href="https://www.youtube.com/watch?v=-pKLyq3BD0k" target="_blank"> here </a>.</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
</table><br />
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<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<a href="https://2014.igem.org/Team:Aachen/Collaborations" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/81/Aachen_14-10-15_Collaborating_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
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<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
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</html><br />
</center><br />
<br />
{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T14:00:21Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> To watch our final presentation just click <a href="https://www.youtube.com/watch?v=-pKLyq3BD0k" target="_blank"> here </a>.</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
</table><br />
<br />
<br />
<br />
<!-- NAVIGATION BUTTONS --><br />
<ul class="team-grid" style="width:530px;margin-left:20px;float:left"><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Project</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_14-10-16_Project_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
<div class="menukachel">Policy & Practices</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Team</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/cf/Aachen_main_Team.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
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{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:58:02Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> To watch our final presentation just click <a href="https://www.youtube.com/watch?v=-pKLyq3BD0k"> here </a>.</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
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{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:57:03Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> You watch the final presentation of our project just click <a href="https://www.youtube.com/watch?v=-pKLyq3BD0k"> here </a>.</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
</table><br />
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<br />
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<!-- NAVIGATION BUTTONS --><br />
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<br />
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<a href="https://2014.igem.org/Team:Aachen/Project" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Project</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_14-10-16_Project_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
<div class="menukachel">Policy & Practices</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
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<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
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</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/cf/Aachen_main_Team.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<br />
{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:55:27Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> You watch the final presentation of our project just click [link=https://www.youtube.com/watch?v=-pKLyq3BD0k|here]].</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
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</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:54:46Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> You watch the final presentation of our project just click [File:Aachen_Logo_iAMB.png|115px|link=https://www.youtube.com/watch?v=-pKLyq3BD0k|here]].</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Project</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
<div class="menukachel">Policy & Practices</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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</div><br />
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<br />
{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:53:11Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> You watch the final presentation of our project just click [https://www.youtube.com/watch?v=-pKLyq3BD0k|here].</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
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</table><br />
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<!-- NAVIGATION BUTTONS --><br />
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<a href="https://2014.igem.org/Team:Aachen/Project" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Project</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_14-10-16_Project_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/PolicyPractices" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
<div class="menukachel">Policy & Practices</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Interlab_Study" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/81/Aachen_14-10-15_Collaborating_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Attributions" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Team</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/cf/Aachen_main_Team.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
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</html><br />
</center><br />
<br />
{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:51:56Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> You watch the final presentation of our project just click [[https://www.youtube.com/watch?v=-pKLyq3BD0k here]].</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
</table><br />
<br />
<br />
<br />
<!-- NAVIGATION BUTTONS --><br />
<ul class="team-grid" style="width:530px;margin-left:20px;float:left"><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Project" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Project</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_14-10-16_Project_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/PolicyPractices" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
<div class="menukachel">Policy & Practices</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
</ul><br />
</html><br />
<br />
<html><br />
<ul class="team-grid" style="width:1060px;margin-left:20px;margin-right:20px;float:right"><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Interlab_Study" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/81/Aachen_14-10-15_Collaborating_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Attributions" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Team</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/cf/Aachen_main_Team.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
</ul><br />
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<a href="https://2014.igem.org/Team:Aachen/Team"><img src="https://static.igem.org/mediawiki/2014/d/d2/Aachen_Team_Aachen_Teamfoto_small.jpg" width="1012px" style="border: 3px solid #0069B3; border-radius: 20px; "></a><br />
</html><br />
</center><br />
<br />
{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:50:49Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;"> You watch the final presentation of our project just click [https://www.youtube.com/watch?v=-pKLyq3BD0k here].</p></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
</table><br />
<br />
<br />
<br />
<!-- NAVIGATION BUTTONS --><br />
<ul class="team-grid" style="width:530px;margin-left:20px;float:left"><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Project" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Project</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_14-10-16_Project_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/PolicyPractices" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;line-height: 2em;" ><br />
<div class="menukachel">Policy & Practices</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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</ul><br />
</html><br />
<br />
<html><br />
<ul class="team-grid" style="width:1060px;margin-left:20px;margin-right:20px;float:right"><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Interlab_Study" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Collaborations" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/81/Aachen_14-10-15_Collaborating_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
</li><br />
<br />
<li style="width:225px;margin-left: 20px;margin-right: 20px;margin-bottom: 30px;margin-top: 10px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Attributions" style="color:black"><br />
<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Team</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/cf/Aachen_main_Team.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
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{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:Aachen/AttributionsTeam:Aachen/Attributions2015-05-05T13:45:55Z<p>R.hanke: </p>
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<div>__NOTOC__<br />
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# General Support<br />
# Fundraising help and advice<br />
# Partners<br />
# Project support and advice<br />
# Lab support<br />
# Difficult technique support<br />
# Project advisor support<br />
# Wiki support<br />
# Presentation coaching<br />
# Policy & Practices support<br />
# Thanks and acknowledgements for all other people involved in helping make a successful iGEM team.<br />
--><br />
=Members=<br />
<span class="anchor" id="members"></span><br />
<br />
A core concept of iGEM is the collaboration within an interdisciplinary student team. Accordingly, students of different age, gender and field of study came together to found our team in Aachen, in order to realize our project with joint forces and enthusiasm for the overall goal. Working closely together, we therefore not only have the chance to learn from each other, but also to excel ourselves. Using our collective creativity and common responsibility, we will create something special in order to make our contribution to synthetic biology.<br />
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<center><br />
<html><ul class="team-grid" style="width:1040px"><br />
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<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Mosthege" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Michael Osthege </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Man for Everything<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/35/Aachen_team_member_Michael_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Fgohr" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Florian Gohr </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
King Gibson<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/ca/Aachen_team_member_Florian_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%;height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:AZimmermann" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Arne Zimmermann </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
The Patience himself<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/88/Aachen_team_member_Arne_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Nbailly" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Nina Bailly </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Flask Prep Princess<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/48/Aachen_team_member_Nina_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:VeraA" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Vera Alexandrova </b><br />
<br/><br/><br />
<i> Biology </i><br />
<br/><br/><br />
Goddess of Plasmid Prep<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/81/Aachen_team_member_Vera_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Pdemling" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Philipp Demling </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Prince of Bad Puns<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/7/77/Aachen_team_member_Philipp_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:R.hanke" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> René Hanke </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Creative Mind & Cook<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_team_member_Rene_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:PatrickO" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br />
<b> Patrick Opdensteinen </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Graphics God<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/1a/Aachen_team_member_Patrick_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Bpeeters" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Björn Peeters </b><br />
<br/><br/><br />
<i> Computational Engineering Science </i><br />
<br/><br/><br />
Hardware Master<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/8d/Aachen_team_member_Bjoern_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Eshani.sood" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Eshani Sood </b><br />
<br/><br/><br />
<i> Biomedical Engineering </i><br />
<br/><br/><br />
Sunshine<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/52/Aachen_team_member_Eshani_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Mjoppich" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Markus Joppich </b><br />
<br/><br/><br />
<i> Computer Science </i><br />
<br/><br/><br />
Software Expert & Travel Assistant<br />
<br/><br/><br />
<!-- click for more information --><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/8/83/Aachen_team_member_Markus_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Ansgar" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Ansgar Niemöller </b><br />
<br/><br/><br />
<i> Computational Engineering Science </i><br />
<br/><br/><br />
GUI Master<br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/4e/Aachen_team_member_Ansgar_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:J.plum" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Julia Plum </b><br />
<br/><br/><br />
<i> Biology and Business Administration </i><br />
<br/><br/><br />
Fundraising & Balancing<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/c9/Aachen_team_member_Julia_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:StefanReinhold" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Stefan Reinhold </b><br />
<br/><br/><br />
<i> Molecular and Applied Biotechnology </i><br />
<br/><br/><br />
Treasurer<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0c/Aachen_team_member_Stefan_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
<br />
<li style="width:186px;margin-left: 11px;margin-right: 11px;margin-bottom: 11px;margin-top: 11px;"><br />
<a href="https://2014.igem.org/User:Aschechtel" style="color:black"><br />
<div class="team-item team-info" style="height: 180px; width: 180px;"><br />
<br/><br/><br />
<b> Anna Schechtel </b><br />
<br/><br/><br />
<i> Biology </i><br />
<br/><br/><br />
Chip Queen<br />
<br/><br/><br />
<!-- click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/a/a4/Aachen_team_member_Anna_01.jpg); norepeat scroll 0% 0% transparent; background-size:100%; height: 180px; width: 180px;"> </div></a><br />
</li><br />
</ul><br />
</html><br />
</center><br />
<br />
= Advisors =<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/5/57/Aachen_team_member_Suresh_01.jpg" width="200px" /></html><br />
<br />
'''Dr.-Ing. Suresh Sudarsan'''<br />
<br />
I'm working as a post-doc with Prof. Blank at RWTH Aachen University. In my Ph.D. I worked under the guidance of Prof. Andreas Schmid (2008-2012) at TU Dortmund, and Prof. Matthias Reuss (2009-2011) at the University of Stuttgart, with a focus on elucidating the link between the central and aromatic metabolism of ''P. putida'' using a systems biology approach.<br />
<br />
I'm fascinated about understanding the collective behavior of microorganisms and their metabolic potential in different niches. In my research, I use tools in ''metabolic engineering & systems biology'' such as metabolomics, fast sampling, kinetic/dynamic modeling and metabolic flux analysis. <br />
<br />
In iGEM, I enjoy working with a group of young scientists from Aachen to achieve our common goal of detecting ''Pseudomonas aeruginosa'' on hard surfaces. Besides science, I try to get myself involved in adventurous sports...but honestly... I just like to relax my day with a delicious meal and a good sci-fi movie!<br />
<br />
<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/c/c8/Aachen_team_member_Ljubica.jpg" width="200px" /></html><br />
<br />
'''Dr. rer. nat. Ljubica Vojcic'''<br />
<br />
I am working as a Subgroup Leader in Prof. Schwaneberg research group at the Institute of Biotechnology, RWTH Aachen. The research area of the Schwaneberg group focuses on directed protein evolution by developing novel methods for generating diversity at the gene level, analyzing consequences of mutational biases on the protein level and developing novel high-throughput screening systems that will lead to improved biocatalysts for prominent applications in industry. In particular, my core expertise is development of high throughput screening systems for different enzyme classes in order to redefine the screening step no longer as bottleneck in directed evolution. <br />
<br />
In iGEM, I enjoyed very much to work with highly motivated and ambitious young scientists from RWTH Aachen University. I truly believe that our collaboration has just started and that we will enjoy jointly solving the scientific challenges in the near future. <br />
<br />
<br />
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=Instructors=<br />
<span class="anchor" id="instructors"></span><br />
== Prof. Dr.-Ing. Lars M. Blank ==<br />
==== RWTH Institute for Applied Microbiology (iAMB) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/4/42/Aachen_LarsBlank.jpg" width="150px" /></html> <br />
Prof. Blank focuses his research on fundamental and applied aspects of microbial metabolism. Of specific interest is the interaction between the metabolic network and the introduced genetic and environmental perturbations. The research on in silico/in vivo metabolic network operations is aimed at a deeper understanding of cell function, with the ultimate goal of rational cell engineering.<br />
<br />
In his teaching, Prof. Blank focuses on the integration of biological concepts with the tools from bioinformatics and engineering. He believes that a sound knowledge base in life sciences is the key for creative and thus successful work in the areas of Metabolic Engineering and Synthetic Biology. Read more about Prof. Blank's work on the [http://www.iamb.rwth-aachen.de/html/members.php?s=det&id=3 iAMB's website].<br />
<html><br><br><br></p></html><br />
<br />
== Prof. Dr. Wolfgang Wiechert ==<br />
==== Forschungszentrum Jülich, Institute of Bio- and Geosciences (IGB-1) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/8/88/Aachen_WolfgangWiechert.jpg" width="150px" /></html> <br />
Prof. Wiechert's main area of work lies within the field of applied systems bio(techno)logy of microorganisms with a special focus on methodological developments for quantitative biology. Characteristics of his research work are a close integration of experimental and theoretical work within multi disciplinary projects. As the head of the Systems Biotechnology research division at Forschungszentrum Jülich, he is developing methods for quantitative metabolomics, fluxomics and proteomics including model based mathematical methods for experimental design, parameter estimation, and process optimization in biotechnological systems. Future work will also incorporate micro fluidic methods for single cell analysis. In general, all research results are used to drive forward the process of gaining knowledge in the course of an iterative improvement of industrial production systems. This proceeds in close cooperation of all working groups at the IBG-1. Together with industrial partners also diverse examples from industry are investigated and further developed. Read more about Prof. Wiechert's work on the [http://www.fz-juelich.de/SharedDocs/Personen/IBG/IBG-1/EN/Research_groups/general/wiechert.html/ IBG-1 website].<br />
<html><br><br><br></p></html><br />
<br />
== Prof. Dr. Ulrich Schwaneberg ==<br />
==== RWTH Institute for Biotechnology, Leibniz Institute for Interactive Materials (DWI) ====<br />
<html><p><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/f/fe/Aachen_UlrichSchwaneberg.jpg" width="150px" /></html> <br />
The Schwaneberg Group seeks to be at the research frontier in the interdisciplinary field of directed protein evolution by developing novel methods for generating diversity at the gene level, analyzing consequence of mutational biases on the protein level and developing novel high-throughput screening systems that will ultimately lead to tailored-biocatalysts for significant applications in industry. They train students in the cutting edge technologies of laboratory evolution, biocatalyst engineering and high throughput screening methodologies. The Schwaneberg Group believes in integrating fundamental principles of protein design with environmental awareness in their research and seeks to promote international scientific collaborations. Read more about Prof. Schwaneberg and his work on the [http://www.biotec.rwth-aachen.de/ Schwaneberg Group's website].<br />
<html><br><br><br></p><span id="team"></span></html><br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
This project would not have been possible without the generous help and advice from many great people and organizations. We thank all the partners listed below for their essential contributions and financial support that covered registration fees, travel costs, the organization of the meetup in September, laboratory materials and expenses for services and materials.<br />
<br />
=Partners=<br />
<span class="anchor" id="partners"></span><br />
<div align="center"><br />
{|cellpadding="25"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|159px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|318px|Niersverband]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Genscript_Logo.png|240px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|193px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|256px|Labomedic]]<br />
|}<br />
<br />
{|cellpadding="35"<br />
|[[File:Aachen_bmbf.jpg|326px|BMBF]]<br />
|[[File:Aachen_idt_.png|217px|IDT]]<br />
|}<br />
<br />
{|cellpadding="25"<br />
|[[File:M2p_labs_logo.jpg|103px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|109px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|121px|pro RWTH]]<br />
|}<br />
{|cellpadding="25"<br />
|[[File:Aachen_Logo_iAMB.png|229px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|229px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|246px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|}<br />
{|cellpadding="35"<br />
|[[File:Aachen_Logo_ABBt.png|209px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|239px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|209px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|150px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
=Attribution of Scientific and General Support=<br />
<span class="anchor" id="support"></span><br />
Great projects do not only depend on solid funding, but even more on the invaluable support by great people. We found great people not only in our 'home institute' the iAMB, but across many partner institutions.<br />
<br />
<br />
* '''RWTH Institute of Molecular Biotechnology''' (Biology VII)<br />
** Dr. Ulrich Commandeur ''for giving us access to essential resources of the bio7''<br />
** Christina Dickmeis M.Sc. ''who answered lots of questions''<br />
* '''RWTH Institute of Biotechnology''' (Biology VI)<br />
** David Schönauer and Alan Mertens M.Sc. ''who helped us to purify proteins''<br />
* '''Helmholtz Institute for Biomedical Engineering'''<br />
** Prof. Dr. Lothar Elling and Sophia Böcker, M.Sc. ''for giving us access to their gal-3 expression plasmid''<br />
* '''RWTH Institute of Applied Microbiology''' (iAMB/Biology IV)<br />
** Prof. Dr. Miriam Agler-Rosenbaum ''for scientific information on quorum sensing''<br />
** Dr. Martin Zimmermann ''who counseled us on balancing iGEM with our studies''<br />
** Dr. Andrea Germer ''for teaching us Gibson cloning''<br />
** Erick Bosire Maosa M.Sc. ''who advised us on cultivation of Pseudomonas''<br />
** Gisela Beissel, Annette Schreer and Kalle Hüser ''for their great patience with our entropy generation''<br />
* '''Forschungszentrum Jülich'''<br />
** Marianne Heß ''who was and is essential for travel organization''<br />
** Dr. Hanno Scharr ''for advice on image analysis''<br />
* '''Fab Lab Aachen'''<br />
** René Bohne, Jan Zimmermann and Jan Thar ''who generously gave us access to the lasercutter and 3D printer''<br />
* '''Others'''<br />
** Dr. Helen Rosenkranz, ABBt, ''for helping us with hundreds of administrative paperwork''<br />
** Dr. Heinz-Albert Becker, NEAnderLab, ''for his help with the organization of the school project''<br />
** Ulrike Eisel, Gymnasium am Neandertal, ''for her help with the organization of the school project''<br />
** Fachschaft Biowissenschaften ''for food supplies and access to their rooms''<br />
** Dr. Joachim Fröhlingsdorf, MakeLight, ''who inspired us to expand our OD/F project''<br />
** Univ.-Prof. Dr. Wolfgang Dott, Uniklinik RWTH Aachen, ''for helpful feedback regarding fields of application for our biosensor''<br />
<br />
Finally, we want to thank '''Simon&nbsp;Unthan''', '''Michael&nbsp;Limberg''', '''Henrik&nbsp;Cordes''', '''Sven&nbsp;Jager''' and '''Team&nbsp;Bielefeld''' for their advice guiding us through our first iGEM participation! <br />
<br />
Special thanks to '''Dr.-Ing. Suresh Sudarsan''' for a final check for typos on our wiki!<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:42:15Z<p>R.hanke: </p>
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<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
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<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
</tr><br />
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<div class="menukachel">Policy & Practices</div><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/b/b7/Aachen_14-10-16_PolicyPractices_main_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Collaborations</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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{|cellpadding="12"<br />
|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
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{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/Team:AachenTeam:Aachen2015-05-05T13:40:49Z<p>R.hanke: </p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/HeaderFront}}<br />
<br />
<!-- [[File:Aachen_Cellock_rand.png|left|250px]] --><br />
<br/><br />
<html><br />
<br />
<div style="font-size:300%;color:#0069b8;margin-left:40px;">Cellock Holmes - A Case of Identity</div ><br/><br />
<br />
<div style="width:490px;margin-left:40px;margin-right:20px;float:left"><br />
<div style="font-size:175%;margin-top:12px;">Welcome to the iGEM Aachen 2014 Wiki!</div ><br />
<p style="margin-left:0px;margin-right:0px;">Until now, an ideal method to detect pathogenic bacteria is still elusive. The existing techniques require expensive equipment, trained personnel or labourious routines. </p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">We, the iGEM team Aachen, have developed a '''novel biosensor system''' called ''Cellock Holmes'' that '''detects bacteria on solid surfaces''' using a low-cost, rapid and portable technique.</p><br />
<br />
<p style="margin-left:0px;margin-right:0px;">In this project, we demonstrate a unique way of combining '''Open Source biology, software and hardware'''.</p><br />
</div><br />
<br />
<br />
<!-- ACHIEVEMENTS --><br />
<table style="width:490px;margin-left:20px;margin-right:40px;float:right"><br />
<tr><td><div style="font-size:175%;margin-top:12px;">Achievements</div></td></tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">The whole project was awarded <b>Best Measurement Project</b> and won the track.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/igem.org/0/0a/Icons_measurement.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our image analysis software <i>Measurarty</i> was awarded <b>Best Supporting Software</b> in the overgrad section.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/1/18/Aachen_SupportingSoftware.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">Our work on biosafety was rewarded with the <b>Safety Commendation</b> special award.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/8/86/Aachen_Icon_Safety.png" width="80px" align="right" /></td><br />
</tr><br />
<br />
<tr><br />
<td><p style="margin-left:0px;margin-right:20px;overflow:auto;">We fulfilled all Bronze and Silver criteria and won a <b>Gold Medal</b>.</p></td><br />
<td><img style="margin-bottom:25px;" src="https://static.igem.org/mediawiki/2014/5/5d/Aachen_Goldmedal_header.png" width="80px" align="right" /></td><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Interlab Study</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/3/39/Aachen_Interlab_Cellocks.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="menukachel" style="top:44%;">Collaborations</div><br />
</div><br />
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<div class="team-item team-info" style="width:219px;height:219px;" ><br />
<div class="menukachel" style="top:44%;">Notebook</div><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/4/42/Aachen_14-10-14_NotebookiFG.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/c/cf/Aachen_main_Team.png); norepeat scroll 0% 0% transparent; background-size:100%;width:219px;height:219px;"> </div></a><br />
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|[[File:Logo_Buergerstiftung-Aachen_hoch.jpg|80px|center|link=http://www.buergerstiftung-aachen.de|Bürgerstiftung Aachen]]<br />
|[[File:Aachen_Niersverband_Firmenlogo.jpg|159px|Niersverband]]<br />
|[[File:Aachen_Genscript_Logo.png|120px|Genscript]]<br />
|[[File:Aachen_Eurofinsgenomics.png|97px|Eurofins Genomics]]<br />
|[[File:Aachen_Labomedic_Logo.jpg|128px|Labomedic]]<br />
|}<br />
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{|cellpadding="18"<br />
|[[File:Aachen_bmbf.jpg|163px|BMBF]]<br />
|[[File:Aachen_idt_.png|109px|IDT]]<br />
|[[File:M2p_labs_logo.jpg|52px|m2p labs]]<br />
|[[File:Aachen_Roth_Logo.png|55px|Carl Roth]]<br />
|[[File:Aachen_ProRWTH_logo.png|62px|link=http://www.prorwth.de/|pro RWTH]]<br />
|}<br />
{|cellpadding="13"<br />
|[[File:Aachen_Logo_iAMB.png|115px|link=http://www.iamb.rwth-aachen.de|Institute of Applied Microbiology - iAMB]]<br />
|[[File:Aachen_Logo_bio7.png|115px|link=http://www.molbiotech.rwth-aachen.de|Institute for Molecular Biotechnology]]<br />
|[[File:Aachen_Logo_HISynBio.png|123px|link=http://www.helmholtz.de/en/about_us/initiating_and_networking/assuring_excellence/synthetic_biology|Helmholtz Association - Initiative on Synthetic Biology]]<br />
|[[File:Aachen_Logo_ABBt.png|105px|link=http://www.biologie.rwth-aachen.de|Aachen Biology and Biotechnology - ABBt]]<br />
|[[File:Aachen_juelich.png|120px|link=http://www.fz-juelich.de/|Forschungszentrum Jülich]]<br />
|[[File:Aachen_FabLabAachenLogo.jpg|105px|link=http://hci.rwth-aachen.de/fablab|Fab Lab Aachen]]<br />
|[[File:Aachen_Schwaneberg_Group.png|75px|link=http://www.biotec.rwth-aachen.de|Schwaneberg Group]]<br />
|}<br />
<div><br />
{{Team:Aachen/FooterFront}}</div>R.hankehttp://2014.igem.org/User:R.hankeUser:R.hanke2014-12-02T14:10:52Z<p>R.hanke: /* */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<center><br />
{{Team:Aachen/TeamMembersBanner}}<br />
</center><br />
== ==<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/b/b7/Aachen_team_member_Rene_01.jpg" width="200px" /></html><br />
<br />
'''René Hanke - Lab Division & Public Relations'''<br />
<br />
''Molecular and Applied Biotechnology (B.Sc. student)''<br />
<br />
What facinates me about the iGEM is the chance of designing and realising such an enormous project, autonomously. As Co-founder of our team, I am really glad that we have established such a diverse team, together exploring synthetic biology as a promising, novel field of research.<br />
In my opinion, the iGEM-competition bears a unique potential not only to learn new biotechnological techniques and methods, but to gain experience in a lot of other areas such as engineering, public relations and fundraising.<br />
Moreover, the prospect to face and solve the challenges of participating in an international competition tempts me. I particularly await visiting Boston and taking part in the final Jamboree!!<br />
<br />
If there is some time apart from working for the iGEM I love to go dancing or enjoy reading some thrilling books.<br />
<br />
'''Mainly involved in...'''<br />
* [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] school project<br />
* presenting our devices at the [https://2014.igem.org/Team:Aachen/Collaborations/MakerFaire MakerFaire]<br />
* organisation, lab work, fundraising, presentation, embellishing our wiki<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/NotebookTeam:Aachen/Notebook2014-10-18T03:55:55Z<p>R.hanke: /* Notebook */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-14_NotebookiFG.png|300px|right]]<br />
= Notebook =<br />
<br />
During the summer, we kept record of our work in the lab and on the engineering side of our project in a notebook on this wiki. This way, members of our team can retrace what others have worked on. Moreover, you can follow the development of our project in detail.<br />
<br />
Experiments and developments in the wetlab are documented in the [https://2014.igem.org/Team:Aachen/Notebook/Wetlab "Wetlab"] notebook. Here, you can find all data on our experiments concerning the biological side of our project. This notebook is organized chronologically, with one entry per day.<br />
<br />
<br />
Under [https://2014.igem.org/Team:Aachen/Notebook/Protocols "Protocols"], you can find preparation methods of things frequently used in our experiments, such as various cultivation media, and details of procedures we regularly use, for example, transformations.<br />
<br />
<br />
In the [https://2014.igem.org/Team:Aachen/Notebook/Engineering "Engineering"] section of our notebook, our team recorded construction and circuit plans for the devices we built on our own for the project.<br />
<br />
<br />
The [https://2014.igem.org/Team:Aachen/Notebook/Software Software] section catalogues all the software we have developed in order to lead our project to a success. <br />
<br />
<br />
Under [https://2014.igem.org/Team:Aachen/Notebook/LabEquipment Equipment] you can find detailed lists of all the hardware we used in our experiments.<br />
<br />
<br />
In the [https://2014.igem.org/Team:Aachen/Notebook/Index Abbreveations] subpage there is a lists of all the commonly used abbreveations on this wiki you might not be familiar with.<br />
<br />
<html><br />
<center><br />
<ul class="menusmall-grid"><br />
<!-- Overview --><br />
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<li style="width: 156px;margin-left: 20px;margin-right: 20px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Wetlab" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:40%;">Wetlab</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0b/Aachen_14-10-13_GFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 20px;margin-right: 20px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Protocols" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:40%;">Protocols</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/54/Aachen_14-10-13_FRET_Arrows_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 20px;margin-right: 20px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Engineering" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:40%;">Engineering</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 20px;margin-right: 20px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Software" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:40%;">Software</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<li style="width: 156px;margin-left: 20px;margin-right: 20px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/LabEquipment" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:25%; line-height:1.5em;">Lab Equipment</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
<br />
<!--<br />
<li style="width: 156px;margin-left: 20px;margin-right: 20px;"><br />
<a class="menulink" href="https://2014.igem.org/Team:Aachen/Notebook/Index" style="color:black"><br />
<div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:32%;">Index</div></div><br />
<div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/02/Aachen_14-10-13_Fusion_Protein_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"><br />
</div><br />
</a><br />
</li><br />
--><br />
<br />
</ul><br />
</center><br />
</html><br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SafetyTeam:Aachen/Safety2014-10-18T03:51:40Z<p>R.hanke: /* Safety */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
= Safety =<br />
Our iGEM team is committed to consider all aspects of the entire project, especially biosafety. For this project, two biosafety aspects have to be covered. On the one hand, we are using ''E. coli'' as '''genetically modified organism''', and on the other hand, we are detecting ''Pseudomonas aeruginosa'', an '''opportunistic human pathogen'''. It infects people suffering from cystic fibrosis or immunodeficiency as well as severe burns or open wounds. When sampling ''P. aeruginosa'', we should prevent proliferation and spread of the bacterium. For ''E. coli'', we have to take care of biological containment of a genetically modified organism. <br />
<br />
In general, we developed and designed the measurement device as '''closed system''' for a better safety handling. This way, neither the sampled pathogens nor the genetically modified sensor cells can escape our biosensor unit. For the detection, we are using one-time usage sampling and sensor chips which can be disposed of after '''autoclaving or irradation''' with strong UV light. Moreover, the electronic components are in a separate compartment and inaccessible for the user, preventing electric shock or other injuries.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Security_WatsOn.png|title=Biosafety level for ''WatsOn''|subtitle=Don't forget to use ''WatsOn'' only in laboratoris with the biosafty standard 1|width=500px}}<br />
</center><br />
<br />
To detect ''P. aeruginosa'', a sampling agar chip is slightly pressed against the solid surface to be tested. This sampling chip is put on the sensor chip and both are placed in a petri dish which is closed thoroughly. Thereby, the cells have no contact with the device during or after the measurement. However, the sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. Afterwards, both chips can be autoclaved and disposed. The whole lining of the measurement device is built from plastic so that it can be disinfected easily.<br />
<!-- Afterwards, the sampling chip is immediately introduced into our measurement device and will not be removed until the detection is finished and the chips have been disinfected. The sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. However, once introduced into the measurement device, the sensor chips, too, will not be removed before disinfection. The living cells inside the measurement device are effectively killed after a measurement by '''using desinfectants''' such as Bacillol. For this procedure, the drawer of the measurement device is opened and Bacillol is poured over the sampling and sensor chips. --> <br />
<br />
To '''simulate the worst case scenario''', we did replica plating of some exemplary sensor chips. In three experiments, we got an arithmetic mean of five colonies which were picked up. From that we concluded that the '''risk of infection is really low''' even if the measurement device and chips are not handled properly.<br />
<br />
For further analysis of our project from a safety perspective, please view our [https://igem.org/Safety/Safety_Form?team_id=1319 safety form].<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SafetyTeam:Aachen/Safety2014-10-18T03:44:29Z<p>R.hanke: /* Safety */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
= Safety =<br />
Our iGEM team is committed to consider all aspects of the entire project, especially biosafety. For this project, two biosafety aspects have to be covered. On the one hand, we are using ''E. coli'' as '''genetically modified organism''', and on the other hand, we are detecting ''Pseudomonas aeruginosa'', an '''opportunistic human pathogen'''. It infects people suffering from cystic fibrosis or immunodeficiency as well as severe burns or open wounds. When sampling ''P. aeruginosa'', we should prevent proliferation and spread of the bacterium. For ''E. coli'', we have to take care of biological containment of a genetically modified organism. <br />
<br />
In general, we developed and designed the measurement device as '''closed system''' for a better safety handling. This way, neither the sampled pathogens nor the genetically modified sensor cells can escape our biosensor unit. For the detection, we are using one-time usage sampling and sensor chips which can be disposed of after '''autoclaving or irradation''' with strong UV light. Moreover, the electronic components are in a separate compartment and inaccessible for the user, preventing electric shock or other injuries.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Security_WatsOn.png|title=Biosafety level for ''WatsOn''|subtitle=Don't forget to use ''WatsOn'' only in laboratoris with the biosafty standard 1|width=500px}}<br />
</center><br />
<br />
To detect ''P. aeruginosa'', a sampling agar chip is slightly pressed against the solid surface to be tested. The sampling chip is placed on the sensor chip in a petri dish which will be closed and not open at all. The cells have no contact with the device during and after the measurement, but the sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. Afterwards, both chips can be autoclaved and disposed. The whole lining of the measurement device is built from plastic so that it can be disinfected easily.<br />
<!-- Afterwards, the sampling chip is immediately introduced into our measurement device and will not be removed until the detection is finished and the chips have been disinfected. The sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. However, once introduced into the measurement device, the sensor chips, too, will not be removed before disinfection. The living cells inside the measurement device are effectively killed after a measurement by '''using desinfectants''' such as Bacillol. For this procedure, the drawer of the measurement device is opened and Bacillol is poured over the sampling and sensor chips. --> <br />
<br />
To '''simulate the worst case scenario''', we did replica plating of some exemplary sensor chips. In three experiments, we got an arithmetic mean of five colonies which were picked up. From that we concluded that the '''risk of infection is really low''' even if the measurement device and chips are not handled properly.<br />
<br />
For further analysis of our project from a safety perspective, please view our [https://igem.org/Safety/Safety_Form?team_id=1319 safety form].<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SafetyTeam:Aachen/Safety2014-10-18T03:44:01Z<p>R.hanke: /* Safety */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
= Safety =<br />
Our iGEM team is committed to consider all aspects of the entire project, especially biosafety. For this project, two biosafety aspects have to be covered. On the one hand, we are using ''E. coli'' as '''genetically modified organism''', and on the other hand, we are detecting ''Pseudomonas aeruginosa'', an '''opportunistic human pathogen'''. It infects people suffering from cystic fibrosis or immunodeficiency as well as severe burns and open wounds. When sampling ''P. aeruginosa'', we should prevent proliferation and spread of the bacterium. For ''E. coli'', we have to take care of biological containment of a genetically modified organism. <br />
<br />
In general, we developed and designed the measurement device as '''closed system''' for a better safety handling. This way, neither the sampled pathogens nor the genetically modified sensor cells can escape our biosensor unit. For the detection, we are using one-time usage sampling and sensor chips which can be disposed of after '''autoclaving or irradation''' with strong UV light. Moreover, the electronic components are in a separate compartment and inaccessible for the user, preventing electric shock or other injuries.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Security_WatsOn.png|title=Biosafety level for ''WatsOn''|subtitle=Don't forget to use ''WatsOn'' only in laboratoris with the biosafty standard 1|width=500px}}<br />
</center><br />
<br />
To detect ''P. aeruginosa'', a sampling agar chip is slightly pressed against the solid surface to be tested. The sampling chip is placed on the sensor chip in a petri dish which will be closed and not open at all. The cells have no contact with the device during and after the measurement, but the sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. Afterwards, both chips can be autoclaved and disposed. The whole lining of the measurement device is built from plastic so that it can be disinfected easily.<br />
<!-- Afterwards, the sampling chip is immediately introduced into our measurement device and will not be removed until the detection is finished and the chips have been disinfected. The sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. However, once introduced into the measurement device, the sensor chips, too, will not be removed before disinfection. The living cells inside the measurement device are effectively killed after a measurement by '''using desinfectants''' such as Bacillol. For this procedure, the drawer of the measurement device is opened and Bacillol is poured over the sampling and sensor chips. --> <br />
<br />
To '''simulate the worst case scenario''', we did replica plating of some exemplary sensor chips. In three experiments, we got an arithmetic mean of five colonies which were picked up. From that we concluded that the '''risk of infection is really low''' even if the measurement device and chips are not handled properly.<br />
<br />
For further analysis of our project from a safety perspective, please view our [https://igem.org/Safety/Safety_Form?team_id=1319 safety form].<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SafetyTeam:Aachen/Safety2014-10-18T03:43:47Z<p>R.hanke: /* Safety */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
= Safety =<br />
Our iGEM team is committed to consider all aspects of the entire project, especially biosafety. For this project, two biosafety aspects have to be dealt with. On the one hand, we are using ''E. coli'' as '''genetically modified organism''', and on the other hand, we are detecting ''Pseudomonas aeruginosa'', an '''opportunistic human pathogen'''. It infects people suffering from cystic fibrosis or immunodeficiency as well as severe burns and open wounds. When sampling ''P. aeruginosa'', we should prevent proliferation and spread of the bacterium. For ''E. coli'', we have to take care of biological containment of a genetically modified organism. <br />
<br />
In general, we developed and designed the measurement device as '''closed system''' for a better safety handling. This way, neither the sampled pathogens nor the genetically modified sensor cells can escape our biosensor unit. For the detection, we are using one-time usage sampling and sensor chips which can be disposed of after '''autoclaving or irradation''' with strong UV light. Moreover, the electronic components are in a separate compartment and inaccessible for the user, preventing electric shock or other injuries.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Security_WatsOn.png|title=Biosafety level for ''WatsOn''|subtitle=Don't forget to use ''WatsOn'' only in laboratoris with the biosafty standard 1|width=500px}}<br />
</center><br />
<br />
To detect ''P. aeruginosa'', a sampling agar chip is slightly pressed against the solid surface to be tested. The sampling chip is placed on the sensor chip in a petri dish which will be closed and not open at all. The cells have no contact with the device during and after the measurement, but the sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. Afterwards, both chips can be autoclaved and disposed. The whole lining of the measurement device is built from plastic so that it can be disinfected easily.<br />
<!-- Afterwards, the sampling chip is immediately introduced into our measurement device and will not be removed until the detection is finished and the chips have been disinfected. The sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. However, once introduced into the measurement device, the sensor chips, too, will not be removed before disinfection. The living cells inside the measurement device are effectively killed after a measurement by '''using desinfectants''' such as Bacillol. For this procedure, the drawer of the measurement device is opened and Bacillol is poured over the sampling and sensor chips. --> <br />
<br />
To '''simulate the worst case scenario''', we did replica plating of some exemplary sensor chips. In three experiments, we got an arithmetic mean of five colonies which were picked up. From that we concluded that the '''risk of infection is really low''' even if the measurement device and chips are not handled properly.<br />
<br />
For further analysis of our project from a safety perspective, please view our [https://igem.org/Safety/Safety_Form?team_id=1319 safety form].<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SafetyTeam:Aachen/Safety2014-10-18T03:43:14Z<p>R.hanke: /* Safety */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
= Safety =<br />
Our iGEM team is committed to consider all aspects of the entire project, especially biosafety. For this project, two biosafety aspects have to be considered. On the one hand, we are using ''E. coli'' as '''genetically modified organism''', and on the other hand, we are detecting ''Pseudomonas aeruginosa'', an '''opportunistic human pathogen'''. It infects people suffering from cystic fibrosis or immunodeficient as well as severe burns and open wounds. When sampling ''P. aeruginosa'', we should prevent proliferation and spread of the bacterium. For ''E. coli'', we have to take care of biological containment of a genetically modified organism. <br />
<br />
In general, we developed and designed the measurement device as '''closed system''' for a better safety handling. This way, neither the sampled pathogens nor the genetically modified sensor cells can escape our biosensor unit. For the detection, we are using one-time usage sampling and sensor chips which can be disposed of after '''autoclaving or irradation''' with strong UV light. Moreover, the electronic components are in a separate compartment and inaccessible for the user, preventing electric shock or other injuries.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Security_WatsOn.png|title=Biosafety level for ''WatsOn''|subtitle=Don't forget to use ''WatsOn'' only in laboratoris with the biosafty standard 1|width=500px}}<br />
</center><br />
<br />
To detect ''P. aeruginosa'', a sampling agar chip is slightly pressed against the solid surface to be tested. The sampling chip is placed on the sensor chip in a petri dish which will be closed and not open at all. The cells have no contact with the device during and after the measurement, but the sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. Afterwards, both chips can be autoclaved and disposed. The whole lining of the measurement device is built from plastic so that it can be disinfected easily.<br />
<!-- Afterwards, the sampling chip is immediately introduced into our measurement device and will not be removed until the detection is finished and the chips have been disinfected. The sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. However, once introduced into the measurement device, the sensor chips, too, will not be removed before disinfection. The living cells inside the measurement device are effectively killed after a measurement by '''using desinfectants''' such as Bacillol. For this procedure, the drawer of the measurement device is opened and Bacillol is poured over the sampling and sensor chips. --> <br />
<br />
To '''simulate the worst case scenario''', we did replica plating of some exemplary sensor chips. In three experiments, we got an arithmetic mean of five colonies which were picked up. From that we concluded that the '''risk of infection is really low''' even if the measurement device and chips are not handled properly.<br />
<br />
For further analysis of our project from a safety perspective, please view our [https://igem.org/Safety/Safety_Form?team_id=1319 safety form].<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SafetyTeam:Aachen/Safety2014-10-18T03:42:06Z<p>R.hanke: /* Safety */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<br />
[[File:Aachen_14-10-13_Pathogen_Cell_iNB.png|right|150px]]<br />
<br />
= Safety =<br />
<br />
Our iGEM team is committed to consider all aspects of the entire project, especially biosafety. For this project, two biosafety aspects have to be considered. On the one hand, we are using ''E. coli'' as '''genetically modified organism''', and on the other hand, we are detecting ''Pseudomonas aeruginosa'', an '''opportunistic human pathogen'''. It infects immunodeficient people as well as severe burns and open wounds. When sampling ''P. aeruginosa'', we should prevent proliferation and spread of the bacterium. For ''E. coli'', we have to take care of biological containment of a genetically modified organism. <br />
<br />
In general, we developed and designed the measurement device as '''closed system''' for a better safety handling. This way, neither the sampled pathogens nor the genetically modified sensor cells can escape our biosensor unit. For the detection, we are using one-time usage sampling and sensor chips which can be disposed of after '''autoclaving or irradation''' with strong UV light. Moreover, the electronic components are in a separate compartment and inaccessible for the user, preventing electric shock or other injuries.<br />
<br />
<center><br />
{{Team:Aachen/Figure|Aachen_Security_WatsOn.png|title=Biosafety level for ''WatsOn''|subtitle=Don't forget to use ''WatsOn'' only in laboratoris with the biosafty standard 1|width=500px}}<br />
</center><br />
<br />
To detect ''P. aeruginosa'', a sampling agar chip is slightly pressed against the solid surface to be tested. The sampling chip is placed on the sensor chip in a petri dish which will be closed and not open at all. The cells have no contact with the device during and after the measurement, but the sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. Afterwards, both chips can be autoclaved and disposed. The whole lining of the measurement device is built from plastic so that it can be disinfected easily.<br />
<!-- Afterwards, the sampling chip is immediately introduced into our measurement device and will not be removed until the detection is finished and the chips have been disinfected. The sensor chips must be handled in '''S1 environments only''' since they contain genetically modified ''E. coli''. However, once introduced into the measurement device, the sensor chips, too, will not be removed before disinfection. The living cells inside the measurement device are effectively killed after a measurement by '''using desinfectants''' such as Bacillol. For this procedure, the drawer of the measurement device is opened and Bacillol is poured over the sampling and sensor chips. --> <br />
<br />
To '''simulate the worst case scenario''', we did replica plating of some exemplary sensor chips. In three experiments, we got an arithmetic mean of five colonies which were picked up. From that we concluded that the '''risk of infection is really low''' even if the measurement device and chips are not handled properly.<br />
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For further analysis of our project from a safety perspective, please view our [https://igem.org/Safety/Safety_Form?team_id=1319 safety form].<br />
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{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/Project/2D_BiosensorTeam:Aachen/Project/2D Biosensor2014-10-18T03:40:27Z<p>R.hanke: /* Achievements */</p>
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= 2D Biosensor =<br />
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With our 2D biosensor technology we are able to detect the pathogen ''Pseudomonas aeruginosa'' on solid surfaces. The sensor system is comprised of '''two distinct but inseparable modules''', a biological and a technical part:<br />
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* Sensor chips containing '''''Cellocks''''', our '''engineered detective cells''' that fluoresce in the presence of the pathogen, make up the biological part of ''Cellock Holmes''.<br />
* Our '''measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn'']''' and the complementary '''software [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty'']''' complete our sensing technology on the technical side. <br />
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== Principle of Operation ==<br />
<span class="anchor" id="biosensorpoo"></span><br />
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''Cellock Holmes'' is designed upon a SynBio approach comprising a '''two-dimensional biosensor and a measurement unit'''. The two-dimensional biosensor is devised to recognize quorum sensing molecules secreted by the pathogen cells and to generate a distinct fluorescence signal; while the measurement device recognizes and analyzes the produced signal. On the molecular side, we use the '''[https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct]''' to transform regular ''E. coli'' cells into ''Cellocks''.<br />
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{{Team:Aachen/Figure|Aachen 17-10-14 The basics of quorum sensing ipo.png||title=The principle of quorum sensing|subtitle=Microorganisms can sense the presence of their own kind based on quorum sensing which is a form of chemical communication. Depending on their cell density, quorum sensing allows these cells to activate or deactivate certain gene expression cascades (Waters and Bassler, 2005) for a specific function.|width=900px}}<br />
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Our '''sensor cells, ''Cellocks'', are immobilized in agar chips'''. To make the chips, we mix the ''Cellocks'' with liquid LB agar. <br />
In the course of our project, we designed a casting mold specifically for the production of our agar chips. When the agar has cooled down, the chips are cut out of the mold and are ready to use. Storage of the readily usable sensor chips is possible for up to two days at 4°C when using LB medium or up to five days if TB medium is used. A detailed description of the sensor chip manufacturing can be found in our [https://2014.igem.org/Team:Aachen/Notebook/Protocols/detection Protocols] section.<br />
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{{Team:Aachen/Figure|Aachen 14-10-14 Flowsheet OD-device part1 ipo.png|title=Assay to detect ''P.&nbsp;aeruginosa'' using ''Cellock Holmes''|subtitle=This flow sheet shows the procedure to sample and detect ''P.&nbsp;aeruginosa'': A sampling chip is briefly put onto the potentially contaminated surface, added onto one of our sensor chips and inserted into ''WatsOn''.|width=900px}}<br />
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Using ''Cellock Holmes'', we developed a simple assay to detect ''P.&nbsp;aeruginosa''. Initially, a so called sampling chip is placed on a solid surface that is potentially contaminated with the pathogen. Subsequently, the sampling chip is removed from the surface and put onto one of our sensor chips. Theorectically, the sensor chips could be directly used for sampling, however, this was avoided in our project to '''match [https://2014.igem.org/Team:Aachen/Safety biosafety regulations]''' and to prevent the spread of genetically modified organisms (GMOs) into the environment. The two layered chip-stack is then put into a petri dish which is inserted into our measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for evalutation.<br />
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{{Team:Aachen/Figure|Aachen 14-10-14 Flowsheet OD-device part2 ipo.png|title=Mode of action inside ''WatsOn''|subtitle=Chips are incubated at 37°C to stimulate cell growth and then illuminated with blue light to excite fluorescence. A picture is taken and analyzed for fluorescence signals using the software ''Measurarty''.|width=900px}}<br />
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Inside ''WatsOn'', the chips are incubated at 37°C and the sampled populations of microorganisms attached on the sampling chip start to grow and multiply. During incubation the chips can be '''illuminated with blue light''' at any time, and a '''photo of the chips''' is taken. The '''software ''Measurarty''''' then analyzes any fluorescent signal. ''P.&nbsp;aeruginosa'' secrets an increasing number of quorum sensing molecules that are recognized by ''Cellocks'', thereby producing a fluorescence signal. For detection of ''P.&nbsp;aeruginosa'', we focused on a quorum sensing molecule called N-3-oxo-dodecanoyl-L-homoserine lactone (for short: 3-oxo-C<sub>12</sub>-HSL), which is involved in virulence regulation of ''P.&nbsp;aeruginosa'' (Jimenez, Koch, Thompson et al., 2012). The incorporation of the 3-oxo-C<sub>12</sub>-HSL detection system into the ''Cellocks'' is explained in detail in the [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh Construct] section.<br />
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<!-- ==A Novel Molecular Approach==<br />
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For our biosensor, our team genetically modified ''E. coli'' cells to be able to elecit a '''fluorescent response to autoinducers''' produced by the pathogen ''Pseudomonas aeruginosa'' during quorum sensing. In the case of ''P.&nbsp;aeruginosa'', these autoinducers are N-3-oxo-dodecanoyl-L-homoserine lactone, or 3-oxo-C-12-HSL for short. The quorum sensing system of this pathogen contains the '''LasR activator''' which binds 3-oxo-C-12-HSL, and the '''LasI promoter''', which is activated by the LasR-HSL complex. Both LasR activator and LasI promoter are available as BioBricks [http://parts.igem.org/Part:BBa_C0179 C0179] and [http://parts.igem.org/Part:BBa_J64010 J64010].<br />
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As a reporter gene, we use '''GFP'''. However, expression of GFP is not simply controlled through the LasI promoter activity in our approach. Instead, our sensor cells contain genes for a constitutively expressed fusion protein consisting of GFP and a dark quencher, and an '''HSL-inducible protease'''. We use the REACh protein as dark quencher for GFP and the TEV protease to cleave the complex; [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter here] you can read more about the REACh construct and the TEV protease. <br />
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{{Team:Aachen/Figure|align=center|Aachen_REACh_approach.png|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=500px}}<br />
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When ''P.&nbsp;aeruginosa cells'' are stuck on our agar chip and come close to our sensor cells, the latter take up the HSL molecules secreted by the pathogens. Inside the sensor cells, the autoinducer binds to the LasR gene product and activate the expression of the TEV protease. The protease then cleaves the GFP-REACh construct. When '''illuminated with light of 480&nbsp;nm''', the excitation wavelenght of GFP, our sensor cells in the vicinity of ''P.&nbsp;aeruginosa'' give a '''fluorescence signal'''. On the other hand, sensor cells that were not anywhere close to the pathogens do not express the protease. Therefore, the GFP will still be attached to the dark quencher in these cells, and no fluorescence is produced.<br />
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== Development & Optimization ==<br />
<span class="anchor" id="biosensordevelopment"></span><br />
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{{Team:Aachen/FigureFloat|Aachen_ILOV_GFP_HM_1,5h.png|title=iLOV and GFP in the Gel Doc<sup>TM</sup>|subtitle=Sensor cells producing iLOV (A) and GFP (B) 1.5&nbsp;h after induction.|left|width=500px}}<br />
=== Equipment and medium selection ===<br />
Our first approach (before developing our own device) was to use the Molecular Imager&reg; Gel Doc™ XR+ from BIO-RAD in our lab to detect fluorescence. This device uses UV and white light illuminators. However, only two different filters were available for the excitation light wavelength, which resulted in very limited possibilities for the excitation of fluorescent molecules. For example, it was possible to detect the expression of iLOV in our sensor chips, but not the expression of GFP. Hence, the '''Gel Doc™ was not suitable for our project'''.<br />
{{Team:Aachen/FigureFloat|Aachen_Chip_medium_geldoc.png|title=Differend medium in the Gel Doc™|subtitle=complex media exhibited high background fluorescence while less back- ground fluorescence was observed with the minimal media (HM, M9, NA).|right|width=500px}}<br />
{{Team:Aachen/FigureFloat|Aachen_5days_K131026_neb_tb_1,5h.jpg |title=Testing our chips' shelf-life|subtitle= Chips of [http://parts.igem.org/Part:BBa_K131026 K131026] in NEB were stored five days at 4°C. The right chip was induced with 0.2&nbsp;µL of 500&nbsp;µg/mL HSL and an image was taken after 1.5&nbsp;h.|left|width=500px}}<br />
We tested different media (LB, TB, M9, NA and HM) for the preparation of our sensor chips. The medium compositions can be found in the [https://2014.igem.org/Team:Aachen/Notebook/Protocols Protocols] section. We screened for an optimized medium composition to minimize background fluorescence and to enhance cell growth. The results of the analysis are presented in the table below. Due to the low background fluorescence in ''WatsOn'' and the excellent cell growth, we '''chose LB&nbsp;medium''' over the other tested media for sensor chip manufacturing.<br />
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{| class="wikitable"<br />
! !! LB !! TB !! NA !! M9 !! HM <br />
|-<br />
| Growth of ''Cellock'' || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
|-<br />
| Background fluorescence in GelDoc || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
|-<br />
| Background fluorescence in ''WatsOn'' || <div style="text-align: center;">-</div> || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
|}<br />
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Another set of experiments were conducted to test the '''long-time storage''' of the sensor chips. We varied the glycerol content of the chips as well as the storage temperature. Storage at -20°C resulted in the loss of our sensor cells. Adding 5-10% (v/v) glycerol ensured survival of the sensor cells, but resulted in the loss of fluorescence ability. Hence, we concluded that long-time storage of the sensor chips at -20°C is not possible under the tested conditions. However, the 'ready-to-use' sensor chips can be kept at at 4°C for two days when using LB medium, and storage at this temperature for 5 days is possible with chips made from TB medium.<br />
<!--Regarding the medium used for our sensor chips, LB medium showed a high background fluorescence when exposed to UV light in the Gel Doc. Surprisingly, the background fluorescence resulting from the LB medium was too high to detect a signal emitted by our sensor cells. Hence, minimal media (NA, M9, Hartman (HM)) was used to minimize background fluorescence, but this approach resulted in less to no growth of our sensor cells. In our device ''WatsOn'', optimized wavelengths of 450&nbsp;nm and 480&nbsp;nm were used for excitation of iLOV and GFP, respectively. When exposed to either excitation wavelength TB medium, which is basically an improved LB medium and highly supports cell growth, showed strong background fluorescence in our own device. High background fluorescence was also observed for TB medum when using the Gel Doc. In contrast to the Gel Doc LB medium showed minimal fluorescence in our device ''WatsOn'' and no difficulties in cultivation of our ''Cellocks'' were observed. Because of the reduced fluorescence compared to TB medium when using ''Watson'' for sensor chip evaluation and because of sufficient cultivation conditions for our 'Cellocks'' LB medium was chosen over TB mediium for sensor chip manufacturing. --><br />
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{{Team:Aachen/FigureFloat|Aachen_2_chipform.jpg|title=Sensor chip manufacturing using the closed mold|subtitle=When injecting the liquid agar into a closed mold we encounter problems due to frequent bubble formation.|left|width=500px}}<br />
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=== Optimal Agarose Concentration for Sensor Chip Manufacturing ===<br />
For the sensor chip manufacturing, agarose was preferred over agar because of the uniform linkage between molecules that results in a better chip homogeneity. In addition, agarose reduced diffusion of the inducer molecules through the chip. A reduction in diffusion is essential for the formation of distinct fluorescent spots on the sensor chips.<br />
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{{Team:Aachen/FigureFloat|Aachen_Final_chipform.jpg|title=The finalized chip mold|subtitle=An open casting mold was found to be optimal for sensor chip manufacturing, because this approach was fast, easy to handle and generated a reproducible chip quality.|left|width=500px}}<br />
=== Optimal Chip Configuration ===<br />
Several approaches were tested for the production of agarose-based sensor chips with reproducible quality. The first approach was to cast every sensor chip individually. To achieve a plain chip surface, a requirement for high quality images, we casted the sensor chips between two microscope slides. However, this approach was not adequate because the agar was too liquid and leaked from the microscope slides. In a second approach, we designed a closed mold into which liquid agar is injected using a pipette, but we encountered a high number of bubbles in the resulting chips. Bubbles in the sensor chips interfered with fluorescence evaluation. Finally, we tried an open casting mold. Once solidified, we cut the agar along precast indentations in the casting mold to form the chips. An advantage of the open mold is the ability to simultaneously produce nine sensor chips while the surface tension of the liquid agar ensures a plane chip surface.<br />
=== Induction of the Sensor Chips ===<br />
To test our molecular constructs, we simulated the presence of ''P.&nbsp;aeruginosa'' by using IPTG or 3-oxo-C<sub>12</sub>-HSL. Initial experiments showed that diffusion of the inducers hinder the formation of distinct fluorescent spots. Through this set of experiments we determined that the best compromise between diffusion and spot intensity is an induction volume of 2.0&nbsp;µL for IPTG and 0.2&nbsp;µL for HSL. Furthermore, detection of growing ''P.&nbsp;aeruginosa'' based on secreted HSLs was possible using the [http://parts.igem.org/Part:BBa_K131026 K131026] construct. The experiments for optimizing the induction of our sensor chips are described in more detail in the [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensorachievements Achievements] section.<br />
=== Negative Control ===<br />
To ensure that the fluorescence signal resulted from the sensor construct and not from the medium or ''E. coli'' cells themselves, [http://parts.igem.org/Part:BBa_B0015 B0015] in NEB10β cells was used as negative control during sensor chip induction with IPTG, HSL and ''P.&nbsp;aeruginosa''.<br />
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{{Team:Aachen/Figure|Aachen_B0015_IPTG_HSL_Pseudomonas.png|title=B0015 in NEB10β was used as a negativ control|subtitle=Induction with A) 0.2&nbsp;µL of 100&nbsp;mM IPTG, image taken after 2.5&nbsp;h; B) 0.2&nbsp;µL of 500&nbsp;µg/mL 3-oxo-C<sub>12</sub>-HSL, image after 2.5&nbsp;h; C) with five spots of ''Pseudomonas&nbsp;aeruginosa'' liquid culture on the left and one big spot on the right, image taken after 2&nbsp;h.|width=900px}}<br />
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==Achievements==<br />
<span class="anchor" id="biosensorachievements"></span><br />
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We developed and optimized a 2D biosensor, which is able to detect IPTG, 3-oxo-C{{sub|12}}-HSL and living ''Pseudomonas&nbsp;aeruginosa'' cells. <br />
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{{Team:Aachen/FigureFloat|Aachen_K1319042_Platereader.gif|title=Testing K1319042 in our sensor chips|subtitle=Sensor chips based on [http://parts.igem.org/Part:BBa_K1319042 K1319042] were investigated for fluorescence using a plate reader. Blue color indicates the absence of fluorescence, while red color indicates fluorescence. The upper chip was not induced, while the lower chip was induced with IPTG (2.0&nbsp;µL, 100mM).|width=260px}}<br />
=== Testing our Sensor Chips in a Plate Reader ===<br />
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To establish a prove-of-principle for our sensor chip design, we used our construct [http://parts.igem.org/Part:BBa_K1319042 K1319042], an IPTG inducible iLOV. ''E. coli'' cells carrying the this construct were introduced into sensor chips and fluorescence was measured every 15&nbsp;minutes after induction with 2&nbsp;µL of 100&nbsp;mM IPTG. The results are displayed on the left.<br />
We observed a distinct difference in fluorescence between the non-induced chip (top) and the induced chip (bottom). The middle of the bottom chip started to exhibit a clear and visible fluorescence that increased over time and spread outwards. The top chip, however, also showed an increase in the measured fluorescence over time which was primarily due to the leaky promoter and background fluorescence.<br />
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{{Team:Aachen/FigureFloatRight|Aachen_K131026_Platereader.gif|title=Testing K131026 in our sensor chips|subtitle=Sensor chips based on [http://parts.igem.org/Part:BBa_K131026 K131026] were investigated for fluorescence using a plate reader. Blue color indicates the absence of fluorescence, while red color indicates fluorescence. The lower chip was induced with with 3-oxo-C{{sub|12}}-HSL (0.2&nbsp;µL, 500 µg/mL).|width=360px}}<br />
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=== Detecting 3-oxo-C{{sub|12}}-HSL with Sensor Chips ===<br />
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In an initial attempt to detect 3-oxo-C{{sub|12}}-HSL, we incorporated the [http://parts.igem.org/Part:BBa_K131026 K131026] construct generated by the 2008 iGEM Team Calgary in our sensor chips. This construct generates a fluorescent signal based on GFP in presence of 3-oxo-C{{sub|12}}-HSL molecules produced by ''P.&nbsp;aeruginosa'' during quorum sensing (Jimenez, Koch, Thompson et al., 2012). First, we tested the construct by direct induction with 3-oxo-C{{sub|12}}-HSL (0.2&nbsp;µL, 500&nbsp;µg/mL). The fluorescence measurement was taken every 15&nbsp;minutes with an excitation wavelength of 496&nbsp;nm and an emission wavelength of 516&nbsp;nm. The results of this test are shown on the right.<br />
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A distinct fluorescence signal was observed on the induced chip (bottom) compared to the non-induced chip (top). <br />
Fluorescence started in the middle of the chip, the point of induction, and then extended outwards while growing in intesnity. The basal level of fluorescence was attributed to leakiness of the promoter and general background fluorescence of growing ''E. coli'' cells. In the induced chip (bottom), the background fluorescence was lower than in the non-induced chip (top) because the signal masked the noise. The difference between the induced and non-induced chips indicates a clear response to the HSL and proofed the ability of our 2D sensor chip design to detect HSLs produced by ''Pseudomonas&nbsp;aeruginosa''.<br />
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{{Team:Aachen/FigureFloat|Aachen_I746909_slower_reduced.gif|title=IPTG-inducible superfolder GFP (I746909) in sensor chips|subtitle=Expression of superfolder GFP ([http://parts.igem.org/Part:BBa_I746909 I746909]) was induced by the addition of IPTG (2&nbsp;µL,&nbsp;100mM) on the right chip. The left chip was not induced.|width=480px}}<br />
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=== Detecting IPTG with Sensor Chips ===<br />
The clip displayed on the left side shows the construct [http://parts.igem.org/Part:BBa_I746909 I746909] from the 2007 iGEM Team Cambridge which expresses super folder GFP under the control of a T7 promoter in combination with our 2D sensor chip technology. The [http://parts.igem.org/Part:BBa_I746909 I746909] construct was introduced into BL21(DE3) cells to make the expression IPTG-inducible since the genome of BL21(De3) contains the T7 RNA Polymerase under the control of a lacI promoter.<br />
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While the left chip does not show visible fluorescence, the right chip exhibits a strong fluorescence signal. This proves the ability of our sensor chip technology to detect IPTG. The fluorescence response is also high enough to be detected and analyzed by our measurement device ''WatsOn''.<br />
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{{Team:Aachen/FigureFloatRight|Aachen_K131026_HSLdetection_slow.gif|title=Detection of 3-oxo-C{{sub|12}}-HSL with K131026|subtitle=0.2&nbsp;µL of 3-oxo-C{{sub|12}}-HSL was placed in the middle of a sensor chip based on [http://parts.igem.org/Part:BBa_K131026 K131026] followed by incubation at 37°C in ''WatsOn''.|width=480px}}<br />
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===Detecting the 3-oxo-C{{sub|12}}-HSL with K131026 in our Sensor Chips using ''WatsOn''===<br />
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The next step towards the final goal of detecting living cells of ''Pseudomonas&nbsp;aeruginosa'' was to reproduce the detection of 3-oxo-C{{sub|12}}-HSL, already established in the plate reader, in our own [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] device. Therefore, we again used ''E. coli'' BL21(DE3) cells carrying [http://parts.igem.org/Part:BBa_K131026 K131026] and induced with 0.2&nbsp;µL 3-oxo-C{{sub|12}}-HSL of a concentration of 500&nbsp;µg/mL. In the clip displayed on the left, the right chip was induced and - as a negative control - the left chip was not induced. Pictures were taken every four&nbsp;minutes.<br />
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The result was a clear replication of the success of the plate reader experiment. The induced chip showed a clear fluorescence response eminating from the center, where the induction with HSL took place. This demonstrated the ability of not only our sensor chip technology but also our measurement device ''WatsOn to successfully'' detect 3-oxo-C{{sub|12}}-HSL.<br />
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{{Team:Aachen/FigureFloat|Aachen_K131026_Pseudomonas_aeruginosa_detection.gif|title=Detection of ''Pseudomonas&nbsp;aeruginosa'' with K131026|subtitle=Direct detection of ''Pseudomonas&nbsp;aeruginosa'' on sensor chips based on [http://parts.igem.org/Part:BBa_K131026 K131026].|width=480px}}<br />
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===Detecting ''Pseudomonas&nbsp;aeruginosa'' with K131026 in our Sensor Chip with ''WatsOn''===<br />
<br />
After establishing the successful detection of 3-oxo-C{{sub|12}}-HSLs with our sensor chips the next step was to detect living cells of ''Pseudomonas aeruginosa'' with our measurement device ''WatsOn''. Therefore sensor chips based on [http://parts.igem.org/Part:BBa_K131026 K131026] were prepared and the right chip was induced with 0.2&nbsp;µL of a ''Pseudomonas aeruginosa'' culture while the left chip was not induced (Detection of 3-oxo-C12 HSL with K131026, displayed below). On the induced chip, a clear fluorescence signal was visible in response to ''P. aeruginosa''. The fluorescence signal emerged outward from the induction point and showed a significant difference to the non-induced chip. The results clearly demonstrate the ability of our sensor chip technology and our measurement device ''WatsOn'' to detect ''P. aeruginosa''!<br />
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== Outlook ==<br />
<span class="anchor" id="biosensoroutlook"></span><br />
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We are '''committed to improve''' our sensor chip platform. The current technique of using a simple agarose chip is not sufficient to collect all microorganisms from the sampled surface. Therefore, the aim is to improve the sampling chip by using a different, more adhesive material. <br />
<br />
Furthermore, diffusion in the sensor chips will be reduced to '''limit the spread of the fluorescence signal'''. Currently, the fluorescence spot grows beyond the point of induction and makes it difficult to differentitate between multiple points of induction. By introducing diffusion barriers into our chips, the growth of the fluorescence spots might be reduced, thus enabling the detection of multiple sources of fluorescence lying close together. <br />
<br />
Additionally, the application of our sensor chips in combination with our ''WatsOn'' device is currently being evaluated for the detection of signals other than fluorescence. '''Detecting bio- and chemiluminescence''' has been identified and will be investigated as an area of potential future application. <br />
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==References==<br />
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* Waters, C. M., & Bassler, B. L. (2005). QUORUM SENSING: Cell-to-Cell Communication In Bacteria. Annual Review of Cell and Developmental Biology, 21(1), 319-346. Available online at http://www.annualreviews.org/doi/full/10.1146/annurev.cellbio.21.012704.131001.<br />
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* Jimenez, P. N., Koch, G., Thompson, J. A., Xavier, K. B., Cool, R. H., & Quax, W. J. (2012). The Multiple Signaling Systems Regulating Virulence in ''Pseudomonas aeruginosa''. Microbiology and Molecular Biology Reviews, 76(1), 46-65. Available online at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294424/#B63.<br />
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{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/Project/2D_BiosensorTeam:Aachen/Project/2D Biosensor2014-10-18T03:40:09Z<p>R.hanke: /* Achievements */</p>
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= 2D Biosensor =<br />
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With our 2D biosensor technology we are able to detect the pathogen ''Pseudomonas aeruginosa'' on solid surfaces. The sensor system is comprised of '''two distinct but inseparable modules''', a biological and a technical part:<br />
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* Sensor chips containing '''''Cellocks''''', our '''engineered detective cells''' that fluoresce in the presence of the pathogen, make up the biological part of ''Cellock Holmes''.<br />
* Our '''measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn'']''' and the complementary '''software [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty'']''' complete our sensing technology on the technical side. <br />
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== Principle of Operation ==<br />
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''Cellock Holmes'' is designed upon a SynBio approach comprising a '''two-dimensional biosensor and a measurement unit'''. The two-dimensional biosensor is devised to recognize quorum sensing molecules secreted by the pathogen cells and to generate a distinct fluorescence signal; while the measurement device recognizes and analyzes the produced signal. On the molecular side, we use the '''[https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct]''' to transform regular ''E. coli'' cells into ''Cellocks''.<br />
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{{Team:Aachen/Figure|Aachen 17-10-14 The basics of quorum sensing ipo.png||title=The principle of quorum sensing|subtitle=Microorganisms can sense the presence of their own kind based on quorum sensing which is a form of chemical communication. Depending on their cell density, quorum sensing allows these cells to activate or deactivate certain gene expression cascades (Waters and Bassler, 2005) for a specific function.|width=900px}}<br />
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Our '''sensor cells, ''Cellocks'', are immobilized in agar chips'''. To make the chips, we mix the ''Cellocks'' with liquid LB agar. <br />
In the course of our project, we designed a casting mold specifically for the production of our agar chips. When the agar has cooled down, the chips are cut out of the mold and are ready to use. Storage of the readily usable sensor chips is possible for up to two days at 4°C when using LB medium or up to five days if TB medium is used. A detailed description of the sensor chip manufacturing can be found in our [https://2014.igem.org/Team:Aachen/Notebook/Protocols/detection Protocols] section.<br />
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{{Team:Aachen/Figure|Aachen 14-10-14 Flowsheet OD-device part1 ipo.png|title=Assay to detect ''P.&nbsp;aeruginosa'' using ''Cellock Holmes''|subtitle=This flow sheet shows the procedure to sample and detect ''P.&nbsp;aeruginosa'': A sampling chip is briefly put onto the potentially contaminated surface, added onto one of our sensor chips and inserted into ''WatsOn''.|width=900px}}<br />
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Using ''Cellock Holmes'', we developed a simple assay to detect ''P.&nbsp;aeruginosa''. Initially, a so called sampling chip is placed on a solid surface that is potentially contaminated with the pathogen. Subsequently, the sampling chip is removed from the surface and put onto one of our sensor chips. Theorectically, the sensor chips could be directly used for sampling, however, this was avoided in our project to '''match [https://2014.igem.org/Team:Aachen/Safety biosafety regulations]''' and to prevent the spread of genetically modified organisms (GMOs) into the environment. The two layered chip-stack is then put into a petri dish which is inserted into our measurement device [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] for evalutation.<br />
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{{Team:Aachen/Figure|Aachen 14-10-14 Flowsheet OD-device part2 ipo.png|title=Mode of action inside ''WatsOn''|subtitle=Chips are incubated at 37°C to stimulate cell growth and then illuminated with blue light to excite fluorescence. A picture is taken and analyzed for fluorescence signals using the software ''Measurarty''.|width=900px}}<br />
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Inside ''WatsOn'', the chips are incubated at 37°C and the sampled populations of microorganisms attached on the sampling chip start to grow and multiply. During incubation the chips can be '''illuminated with blue light''' at any time, and a '''photo of the chips''' is taken. The '''software ''Measurarty''''' then analyzes any fluorescent signal. ''P.&nbsp;aeruginosa'' secrets an increasing number of quorum sensing molecules that are recognized by ''Cellocks'', thereby producing a fluorescence signal. For detection of ''P.&nbsp;aeruginosa'', we focused on a quorum sensing molecule called N-3-oxo-dodecanoyl-L-homoserine lactone (for short: 3-oxo-C<sub>12</sub>-HSL), which is involved in virulence regulation of ''P.&nbsp;aeruginosa'' (Jimenez, Koch, Thompson et al., 2012). The incorporation of the 3-oxo-C<sub>12</sub>-HSL detection system into the ''Cellocks'' is explained in detail in the [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh Construct] section.<br />
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For our biosensor, our team genetically modified ''E. coli'' cells to be able to elecit a '''fluorescent response to autoinducers''' produced by the pathogen ''Pseudomonas aeruginosa'' during quorum sensing. In the case of ''P.&nbsp;aeruginosa'', these autoinducers are N-3-oxo-dodecanoyl-L-homoserine lactone, or 3-oxo-C-12-HSL for short. The quorum sensing system of this pathogen contains the '''LasR activator''' which binds 3-oxo-C-12-HSL, and the '''LasI promoter''', which is activated by the LasR-HSL complex. Both LasR activator and LasI promoter are available as BioBricks [http://parts.igem.org/Part:BBa_C0179 C0179] and [http://parts.igem.org/Part:BBa_J64010 J64010].<br />
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As a reporter gene, we use '''GFP'''. However, expression of GFP is not simply controlled through the LasI promoter activity in our approach. Instead, our sensor cells contain genes for a constitutively expressed fusion protein consisting of GFP and a dark quencher, and an '''HSL-inducible protease'''. We use the REACh protein as dark quencher for GFP and the TEV protease to cleave the complex; [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter here] you can read more about the REACh construct and the TEV protease. <br />
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{{Team:Aachen/Figure|align=center|Aachen_REACh_approach.png|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=500px}}<br />
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When ''P.&nbsp;aeruginosa cells'' are stuck on our agar chip and come close to our sensor cells, the latter take up the HSL molecules secreted by the pathogens. Inside the sensor cells, the autoinducer binds to the LasR gene product and activate the expression of the TEV protease. The protease then cleaves the GFP-REACh construct. When '''illuminated with light of 480&nbsp;nm''', the excitation wavelenght of GFP, our sensor cells in the vicinity of ''P.&nbsp;aeruginosa'' give a '''fluorescence signal'''. On the other hand, sensor cells that were not anywhere close to the pathogens do not express the protease. Therefore, the GFP will still be attached to the dark quencher in these cells, and no fluorescence is produced.<br />
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== Development & Optimization ==<br />
<span class="anchor" id="biosensordevelopment"></span><br />
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{{Team:Aachen/FigureFloat|Aachen_ILOV_GFP_HM_1,5h.png|title=iLOV and GFP in the Gel Doc<sup>TM</sup>|subtitle=Sensor cells producing iLOV (A) and GFP (B) 1.5&nbsp;h after induction.|left|width=500px}}<br />
=== Equipment and medium selection ===<br />
Our first approach (before developing our own device) was to use the Molecular Imager&reg; Gel Doc™ XR+ from BIO-RAD in our lab to detect fluorescence. This device uses UV and white light illuminators. However, only two different filters were available for the excitation light wavelength, which resulted in very limited possibilities for the excitation of fluorescent molecules. For example, it was possible to detect the expression of iLOV in our sensor chips, but not the expression of GFP. Hence, the '''Gel Doc™ was not suitable for our project'''.<br />
{{Team:Aachen/FigureFloat|Aachen_Chip_medium_geldoc.png|title=Differend medium in the Gel Doc™|subtitle=complex media exhibited high background fluorescence while less back- ground fluorescence was observed with the minimal media (HM, M9, NA).|right|width=500px}}<br />
{{Team:Aachen/FigureFloat|Aachen_5days_K131026_neb_tb_1,5h.jpg |title=Testing our chips' shelf-life|subtitle= Chips of [http://parts.igem.org/Part:BBa_K131026 K131026] in NEB were stored five days at 4°C. The right chip was induced with 0.2&nbsp;µL of 500&nbsp;µg/mL HSL and an image was taken after 1.5&nbsp;h.|left|width=500px}}<br />
We tested different media (LB, TB, M9, NA and HM) for the preparation of our sensor chips. The medium compositions can be found in the [https://2014.igem.org/Team:Aachen/Notebook/Protocols Protocols] section. We screened for an optimized medium composition to minimize background fluorescence and to enhance cell growth. The results of the analysis are presented in the table below. Due to the low background fluorescence in ''WatsOn'' and the excellent cell growth, we '''chose LB&nbsp;medium''' over the other tested media for sensor chip manufacturing.<br />
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{| class="wikitable"<br />
! !! LB !! TB !! NA !! M9 !! HM <br />
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| Growth of ''Cellock'' || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
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| Background fluorescence in GelDoc || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
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| Background fluorescence in ''WatsOn'' || <div style="text-align: center;">-</div> || <div style="text-align: center;">'''+'''</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div> || <div style="text-align: center;">-</div><br />
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Another set of experiments were conducted to test the '''long-time storage''' of the sensor chips. We varied the glycerol content of the chips as well as the storage temperature. Storage at -20°C resulted in the loss of our sensor cells. Adding 5-10% (v/v) glycerol ensured survival of the sensor cells, but resulted in the loss of fluorescence ability. Hence, we concluded that long-time storage of the sensor chips at -20°C is not possible under the tested conditions. However, the 'ready-to-use' sensor chips can be kept at at 4°C for two days when using LB medium, and storage at this temperature for 5 days is possible with chips made from TB medium.<br />
<!--Regarding the medium used for our sensor chips, LB medium showed a high background fluorescence when exposed to UV light in the Gel Doc. Surprisingly, the background fluorescence resulting from the LB medium was too high to detect a signal emitted by our sensor cells. Hence, minimal media (NA, M9, Hartman (HM)) was used to minimize background fluorescence, but this approach resulted in less to no growth of our sensor cells. In our device ''WatsOn'', optimized wavelengths of 450&nbsp;nm and 480&nbsp;nm were used for excitation of iLOV and GFP, respectively. When exposed to either excitation wavelength TB medium, which is basically an improved LB medium and highly supports cell growth, showed strong background fluorescence in our own device. High background fluorescence was also observed for TB medum when using the Gel Doc. In contrast to the Gel Doc LB medium showed minimal fluorescence in our device ''WatsOn'' and no difficulties in cultivation of our ''Cellocks'' were observed. Because of the reduced fluorescence compared to TB medium when using ''Watson'' for sensor chip evaluation and because of sufficient cultivation conditions for our 'Cellocks'' LB medium was chosen over TB mediium for sensor chip manufacturing. --><br />
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{{Team:Aachen/FigureFloat|Aachen_2_chipform.jpg|title=Sensor chip manufacturing using the closed mold|subtitle=When injecting the liquid agar into a closed mold we encounter problems due to frequent bubble formation.|left|width=500px}}<br />
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=== Optimal Agarose Concentration for Sensor Chip Manufacturing ===<br />
For the sensor chip manufacturing, agarose was preferred over agar because of the uniform linkage between molecules that results in a better chip homogeneity. In addition, agarose reduced diffusion of the inducer molecules through the chip. A reduction in diffusion is essential for the formation of distinct fluorescent spots on the sensor chips.<br />
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{{Team:Aachen/FigureFloat|Aachen_Final_chipform.jpg|title=The finalized chip mold|subtitle=An open casting mold was found to be optimal for sensor chip manufacturing, because this approach was fast, easy to handle and generated a reproducible chip quality.|left|width=500px}}<br />
=== Optimal Chip Configuration ===<br />
Several approaches were tested for the production of agarose-based sensor chips with reproducible quality. The first approach was to cast every sensor chip individually. To achieve a plain chip surface, a requirement for high quality images, we casted the sensor chips between two microscope slides. However, this approach was not adequate because the agar was too liquid and leaked from the microscope slides. In a second approach, we designed a closed mold into which liquid agar is injected using a pipette, but we encountered a high number of bubbles in the resulting chips. Bubbles in the sensor chips interfered with fluorescence evaluation. Finally, we tried an open casting mold. Once solidified, we cut the agar along precast indentations in the casting mold to form the chips. An advantage of the open mold is the ability to simultaneously produce nine sensor chips while the surface tension of the liquid agar ensures a plane chip surface.<br />
=== Induction of the Sensor Chips ===<br />
To test our molecular constructs, we simulated the presence of ''P.&nbsp;aeruginosa'' by using IPTG or 3-oxo-C<sub>12</sub>-HSL. Initial experiments showed that diffusion of the inducers hinder the formation of distinct fluorescent spots. Through this set of experiments we determined that the best compromise between diffusion and spot intensity is an induction volume of 2.0&nbsp;µL for IPTG and 0.2&nbsp;µL for HSL. Furthermore, detection of growing ''P.&nbsp;aeruginosa'' based on secreted HSLs was possible using the [http://parts.igem.org/Part:BBa_K131026 K131026] construct. The experiments for optimizing the induction of our sensor chips are described in more detail in the [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor#biosensorachievements Achievements] section.<br />
=== Negative Control ===<br />
To ensure that the fluorescence signal resulted from the sensor construct and not from the medium or ''E. coli'' cells themselves, [http://parts.igem.org/Part:BBa_B0015 B0015] in NEB10β cells was used as negative control during sensor chip induction with IPTG, HSL and ''P.&nbsp;aeruginosa''.<br />
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{{Team:Aachen/Figure|Aachen_B0015_IPTG_HSL_Pseudomonas.png|title=B0015 in NEB10β was used as a negativ control|subtitle=Induction with A) 0.2&nbsp;µL of 100&nbsp;mM IPTG, image taken after 2.5&nbsp;h; B) 0.2&nbsp;µL of 500&nbsp;µg/mL 3-oxo-C<sub>12</sub>-HSL, image after 2.5&nbsp;h; C) with five spots of ''Pseudomonas&nbsp;aeruginosa'' liquid culture on the left and one big spot on the right, image taken after 2&nbsp;h.|width=900px}}<br />
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==Achievements==<br />
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We developed and optimized a 2D biosensor, which is able to detect IPTG, 3-oxo-C{{sub|12}}-HSL and living ''Pseudomonas&nbsp;aeruginosa'' cells. <br />
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{{Team:Aachen/FigureFloat|Aachen_K1319042_Platereader.gif|title=Testing K1319042 in our sensor chips|subtitle=Sensor chips based on [http://parts.igem.org/Part:BBa_K1319042 K1319042] were investigated for fluorescence using a plate reader. Blue color indicates the absence of fluorescence, while red color indicates fluorescence. The upper chip was not induced, while the lower chip was induced with IPTG (2.0&nbsp;µL, 100mM).|width=260px}}<br />
=== Testing our Sensor Chips in a Plate Reader ===<br />
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To establish a prove-of-principle for our sensor chip design, we used our construct [http://parts.igem.org/Part:BBa_K1319042 K1319042], an IPTG inducible iLOV. ''E. coli'' cells carrying the this construct were introduced into sensor chips and fluorescence was measured every 15&nbsp;minutes after induction with 2&nbsp;µL of 100&nbsp;mM IPTG. The results are displayed on the left.<br />
We observed a distinct difference in fluorescence between the non-induced chip (top) and the induced chip (bottom). The middle of the bottom chip started to exhibit a clear and visible fluorescence that increased over time and spread outwards. The top chip, however, also showed an increase in the measured fluorescence over time which was primarily due to the leaky promoter and background fluorescence.<br />
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{{Team:Aachen/FigureFloatRight|Aachen_K131026_Platereader.gif|title=Testing K131026 in our sensor chips|subtitle=Sensor chips based on [http://parts.igem.org/Part:BBa_K131026 K131026] were investigated for fluorescence using a plate reader. Blue color indicates the absence of fluorescence, while red color indicates fluorescence. The lower chip was induced with with 3-oxo-C{{sub|12}}-HSL (0.2&nbsp;µL, 500 µg/mL).|width=360px}}<br />
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=== Detecting 3-oxo-C{{sub|12}}-HSL with Sensor Chips ===<br />
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In an initial attempt to detect 3-oxo-C{{sub|12}}-HSL, we incorporated the [http://parts.igem.org/Part:BBa_K131026 K131026] construct generated by the 2008 iGEM Team Calgary in our sensor chips. This construct generates a fluorescent signal based on GFP in presence of 3-oxo-C{{sub|12}}-HSL molecules produced by ''P.&nbsp;aeruginosa'' during quorum sensing (Jimenez, Koch, Thompson et al., 2012). First, we tested the construct by direct induction with 3-oxo-C{{sub|12}}-HSL (0.2&nbsp;µL, 500&nbsp;µg/mL). The fluorescence measurement was taken every 15&nbsp;minutes with an excitation wavelength of 496&nbsp;nm and an emission wavelength of 516&nbsp;nm. The results of this test are shown on the right.<br />
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A distinct fluorescence signal was observed on the induced chip (bottom) compared to the non-induced chip (top). <br />
Fluorescence started in the middle of the chip, the point of induction, and then extended outwards while growing in intesnity. The basal level of fluorescence was attributed to leakiness of the promoter and general background fluorescence of growing ''E. coli'' cells. In the induced chip (bottom), the background fluorescence was lower than in the non-induced chip (top) because the signal masked the noise. The difference between the induced and non-induced chips indicates a clear response to the HSL and proofed the ability of our 2D sensor chip design to detect HSLs produced by ''Pseudomonas&nbsp;aeruginosa''.<br />
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{{Team:Aachen/FigureFloat|Aachen_I746909_slower_reduced.gif|title=IPTG-inducible superfolder GFP (I746909) in sensor chips|subtitle=Expression of superfolder GFP ([http://parts.igem.org/Part:BBa_I746909 I746909]) was induced by the addition of IPTG (2&nbsp;µL,&nbsp;100mM) on the right chip. The left chip was not induced.|width=480px}}<br />
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=== Detecting IPTG with Sensor Chips ===<br />
The clip displayed on the left side shows the construct [http://parts.igem.org/Part:BBa_I746909 I746909] from the 2007 iGEM Team Cambridge which expresses super folder GFP under the control of a T7 promoter in combination with our 2D sensor chip technology. The [http://parts.igem.org/Part:BBa_I746909 I746909] construct was introduced into BL21(DE3) cells to make the expression IPTG-inducible since the genome of BL21(De3) contains the T7 RNA Polymerase under the control of a lacI promoter.<br />
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While the left chip does not show visible fluorescence, the right chip exhibits a strong fluorescence signal. This proves the ability of our sensor chip technology to detect IPTG. The fluorescence response is also high enough to be detected and analyzed by our measurement device ''WatsOn''.<br />
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{{Team:Aachen/FigureFloatRight|Aachen_K131026_HSLdetection_slow.gif|title=Detection of 3-oxo-C{{sub|12}}-HSL with K131026|subtitle=0.2&nbsp;µL of 3-oxo-C{{sub|12}}-HSL was placed in the middle of a sensor chip based on [http://parts.igem.org/Part:BBa_K131026 K131026] followed by incubation at 37°C in ''WatsOn''.|width=480px}}<br />
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===Detecting the 3-oxo-C{{sub|12}}-HSL with K131026 in our Sensor Chips using ''WatsOn''===<br />
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The next step towards the final goal of detecting living cells of ''Pseudomonas&nbsp;aeruginosa'' was to reproduce the detection of 3-oxo-C{{sub|12}}-HSL, already established in the plate reader, in our own [https://2014.igem.org/Team:Aachen/Project/Measurement_Device ''WatsOn''] device. Therefore, we again used ''E. coli'' BL21(DE3) cells carrying [http://parts.igem.org/Part:BBa_K131026 K131026] and induced with 0.2&nbsp;µL 3-oxo-C{{sub|12}}-HSL of a concentration of 500&nbsp;µg/mL. In the clip displayed on the left, the right chip was induced and - as a negative control - the left chip was not induced. Pictures were taken every four&nbsp;minutes.<br />
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The result was a clear replication of the success of the plate reader experiment. The induced chip showed a clear fluorescence response eminating from the center, where the induction with HSL took place. This demonstrated the ability of not only our sensor chip technology but also our measurement device ''WatsOn to successfully'' detect 3-oxo-C{{sub|12}}-HSL.<br />
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{{Team:Aachen/FigureFloat|Aachen_K131026_Pseudomonas_aeruginosa_detection.gif|title=Detection of ''Pseudomonas&nbsp;aeruginosa'' with K131026|subtitle=Direct detection of ''Pseudomonas&nbsp;aeruginosa'' on sensor chips based on [http://parts.igem.org/Part:BBa_K131026 K131026].|width=480px}}<br />
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===Detecting ''Pseudomonas&nbsp;aeruginosa'' with K131026 in our Sensor Chip with ''WatsOn''===<br />
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After establishing the successful detection of 3-oxo-C{{sub|12}}-HSLs with our sensor chips the next step was to detect living cells of ''Pseudomonas aeruginosa'' with our measurement device ''WatsOn''. Therefore sensor chips based on [http://parts.igem.org/Part:BBa_K131026 K131026] were prepared and the right chip was induced with 0.2&nbsp;µL of a ''Pseudomonas aeruginosa'' culture while the left chip was not induced (Detection of 3-oxo-C12 HSL with K131026, displayed below). On the induced chip, a clear fluorescence signal was visible in response to ''P. aeruginosa''. The fluorescence signal emerged outward from the induction point and showed a significant difference to the non-induced chip. The results clearly demonstrate the ability of our sensor chip technology and our measurement device ''WatsOn'' to detect ''P. aeruginosa''!<br />
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[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]<br />
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== Outlook ==<br />
<span class="anchor" id="biosensoroutlook"></span><br />
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We are '''committed to improve''' our sensor chip platform. The current technique of using a simple agarose chip is not sufficient to collect all microorganisms from the sampled surface. Therefore, the aim is to improve the sampling chip by using a different, more adhesive material. <br />
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Furthermore, diffusion in the sensor chips will be reduced to '''limit the spread of the fluorescence signal'''. Currently, the fluorescence spot grows beyond the point of induction and makes it difficult to differentitate between multiple points of induction. By introducing diffusion barriers into our chips, the growth of the fluorescence spots might be reduced, thus enabling the detection of multiple sources of fluorescence lying close together. <br />
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Additionally, the application of our sensor chips in combination with our ''WatsOn'' device is currently being evaluated for the detection of signals other than fluorescence. '''Detecting bio- and chemiluminescence''' has been identified and will be investigated as an area of potential future application. <br />
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==References==<br />
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* Waters, C. M., & Bassler, B. L. (2005). QUORUM SENSING: Cell-to-Cell Communication In Bacteria. Annual Review of Cell and Developmental Biology, 21(1), 319-346. Available online at http://www.annualreviews.org/doi/full/10.1146/annurev.cellbio.21.012704.131001.<br />
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* Jimenez, P. N., Koch, G., Thompson, J. A., Xavier, K. B., Cool, R. H., & Quax, W. J. (2012). The Multiple Signaling Systems Regulating Virulence in ''Pseudomonas aeruginosa''. Microbiology and Molecular Biology Reviews, 76(1), 46-65. Available online at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294424/#B63.<br />
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{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:37:10Z<p>R.hanke: /* Blog #1 - The opening */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|left|width=500px}}<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
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The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
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On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
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The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
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To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
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The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|10404745_641111075966352_965198584_o.jpg|right|width=200px}}<br />
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Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
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So stay tuned!<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Kaiser-Karls-Gymnasium.jpg|right|width=200px}}<br />
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Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
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The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
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So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
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we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
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In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
<br />
<html><br />
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$('.box_skitter_large_blog_2').css({width: 780, height: 580}).skitter({animation: 'fade', label: false, numbers: true, numbers_align: 'right', auto_play: true, controls: true, controls_position: 'rightBottom' , navigation: false , interval: 2500, theme: 'clean'});<br />
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<div class="border_box"><br />
<div class="box_skitter box_skitter_large_blog_2"><br />
<ul><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/4/4a/Aachen_arduino_Inhalt_Box.jpg/780px-Aachen_arduino_Inhalt_Box.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
</ul><br />
</div><br />
</div><br />
</div><br />
</div><br />
</html><br />
<br />
Guess what we are building?<br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Opening_Arduino_Box.jpg|width=250px}}<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:36:43Z<p>R.hanke: /* Blog #1 - The opening */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|left|width=500px}}<br />
<br />
Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
<br />
For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
<br />
Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
<br />
[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
<br />
By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
<br />
This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
<br />
The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
<br />
Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
<br />
Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
<br />
The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|10404745_641111075966352_965198584_o.jpg|right|width=200px}}<br />
<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Kaiser-Karls-Gymnasium.jpg|right|width=200px}}<br />
<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
<br />
[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
<br />
Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/5/5c/Aachen_prepping_school_project_1.jpg/450px-Aachen_prepping_school_project_1.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
<br />
Can you guess what we are assembling?<br />
<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/8/80/Aachen_device_building_1_4.JPG/780px-Aachen_device_building_1_4.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
<br />
{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
<br />
[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
<br />
Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Opening_Arduino_Box.jpg|title=Group Picture|width=250px}}<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:35:37Z<p>R.hanke: /* Blog #8 - iGEM team members back 2 school */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|left|width=500px}}<br />
<br />
Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
<br />
For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
<br />
Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
<br />
By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
<br />
The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
<br />
The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|10404745_641111075966352_965198584_o.jpg|right|width=200px}}<br />
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Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Kaiser-Karls-Gymnasium.jpg|right|width=200px}}<br />
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Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
<br />
Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
<br />
[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
<br />
Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:35:07Z<p>R.hanke: /* Blog #10 - Microorganisms on the rise */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|left|width=500px}}<br />
<br />
Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
<br />
For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
<br />
The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
<br />
The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|10404745_641111075966352_965198584_o.jpg|right|width=200px}}<br />
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Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
<br />
[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
<br />
Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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<br />
Guess what we are building?<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
<br />
[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:34:20Z<p>R.hanke: /* Blog #21 - iGEM Meetup Last Weekend - A Great Success! */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|left|width=500px}}<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
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The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
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On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
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The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
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To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
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The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
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So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
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The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
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So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
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In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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Guess what we are building?<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:33:03Z<p>R.hanke: /* Blog #12 - Glowing vanilla pudding */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
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On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
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The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
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The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
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So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
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<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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<br />
Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:32:47Z<p>R.hanke: /* Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
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The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_mrsa.jpg|width=200px|left|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
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The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
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The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/5/5c/Aachen_prepping_school_project_1.jpg/450px-Aachen_prepping_school_project_1.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/8/80/Aachen_device_building_1_4.JPG/780px-Aachen_device_building_1_4.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
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In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:32:16Z<p>R.hanke: /* Blog #12 - Glowing vanilla pudding */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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<center><br />
{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_mrsa.jpg|width=200px|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
<br />
The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
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Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen KKG (15).jpg|left|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
<br />
The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/8/80/Aachen_device_building_1_4.JPG/780px-Aachen_device_building_1_4.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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<br />
Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:31:56Z<p>R.hanke: /* Blog #14 - Students Explore Careers in Synthetic Biology */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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<center><br />
{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_mrsa.jpg|width=200px|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
<br />
The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Cellock_liegend.png|left|width=300px}}<br />
<br />
Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
<br />
Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen KKG (15).jpg|right|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
<br />
The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
<br />
[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/5/5c/Aachen_prepping_school_project_1.jpg/450px-Aachen_prepping_school_project_1.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/8/80/Aachen_device_building_1_4.JPG/780px-Aachen_device_building_1_4.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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<br />
Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
<br />
[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:30:56Z<p>R.hanke: /* Blog #7 - The Biobricks have arrived */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
<br />
The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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<center><br />
{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
<br />
Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
<br />
On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
<br />
By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
<br />
{{Team:Aachen/Figure|Aachen_mrsa.jpg|width=200px|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
<br />
The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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[[File:Cellock_liegend.png|left|300px|frameless]]<br />
Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen KKG (15).jpg|right|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
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The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
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So stay tuned!<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_Biobricks_arrival_2014.jpg|left|width=300px}}<br />
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Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
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<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/5/5c/Aachen_prepping_school_project_1.jpg/450px-Aachen_prepping_school_project_1.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
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In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
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This year Aachen is rocking iGEM!<br />
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{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:29:30Z<p>R.hanke: Undo revision 397492 by R.hanke (talk)</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
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The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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<center><br />
{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
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On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_mrsa.jpg|width=200px|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
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The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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[[File:Cellock_liegend.png|left|300px|frameless]]<br />
Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
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Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen KKG (15).jpg|right|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
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The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
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[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
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So stay tuned!<br />
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= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
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[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
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= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
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[[File:Aachen_Biobricks_arrival_2014.jpg|left|400px]]<br />
Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
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The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
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So stay tuned!<br />
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= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
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= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
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Can you guess what we are assembling?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
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[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
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= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
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Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
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In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
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= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
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Hello iGEM enthusiasts,<br />
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interested to see what is inside the box from the previous post?<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
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Guess what we are building?<br />
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= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
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[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
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This year Aachen is rocking iGEM!<br />
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{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/BlogTeam:Aachen/Blog2014-10-18T03:29:15Z<p>R.hanke: /* Blog #7 - The Biobricks have arrived */</p>
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= Blog #21 - iGEM Meetup Last Weekend - A Great Success! =<br />
by [[User:Nbailly|Nina]] 09:27, 16 September 2014 (CDT)<br />
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Last weekend, six iGEM teams from all over Germany – namely Braunschweig, Darmstadt, Bielefeld, Tübingen, Freiburg and Munich – met with our team in Aachen.<br />
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The weekend started with a welcome ceremony for all iGEM teams in the Couven hall on our RWTH campus. After our Jeopardy battle, the teams from Bielefeld, Darmstand, Braunschweig, Tübingen, Munich and Aachen presented their project ideas in 15-minute talks to the public audience. [https://2014.igem.org/Team:Aachen/Blog/14-09-16-01 Read more...]<br />
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For a German version of this blog entry, please click [https://2014.igem.org/Team:Aachen/Blog/14-09-16-02 here].<br />
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<center><br />
{{Team:Aachen/Figure|Aachen_IGEM_Aachen_Meetup_Gruppenbild_3.jpg|title=Group Picture|subtitle=A final group picture taken by Carsten Ludwig from team Braunschweig.|width=500px}} <br />
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= Blog #20 - Won a gene synthesis from Eurofins =<br />
by [[User:Mosthege|Michael]] 03:25, 18 July 2014 (CDT)<br />
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Two weeks ago we had an email in our inbox that made us very happy: We had won a gene synthesis from [http://eurofinsgenomics.eu/en/eurofins-genomics/corporate-information/deals-promotions/igem-sponsorship.aspx Eurofins Genomics]!<br />
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On Wednesday, we were then visited by Ms. Blumstein who handed us the voucher. Then we took this beautiful photo:<br />
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[[Image:Aachen_14-07-16_GruppenbildEurofins.jpg|center|300px]]<br />
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= Blog #19 - Noneffective Antibiotics (Part III): Have the Pharma Giants Lost The Race?=<br />
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By [[User:NBailly|NBailly]] 15:39, July 15 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_David-Goliath-S1-300x261.jpg|left|width=300px|title=David and Goliath|subtitle=Small Companies have taken leading position in antibiotics research. Picture by LegalIT Lawyers.}}<br />
<html>It is not the big pharma companies that will develop the desperately needed new generation of antibiotics that can even cope with multi-resistant bacteria such as MRSA. Instead, some smaller companies who never gave up researching this field are now future market leaders. As the German business news magazine <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Wirtschaftswoche</a> reported this June, it is companies like the British-Swedish Astra Zeneca or Hoffmann-La Roche spin off Basilea that are now in a leading position.</html><br />
[https://2014.igem.org/Team:Aachen/Blog/14-07-15-01 Read more...]<br />
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= Blog #18 - Noneffective Antibiotics (Part II): Hospitals as Receptacles for Multi-Resistant Pathogens =<br />
By [[User:NBailly|NBailly]] 17:21, July 14 2014 (CDT)<br />
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{{Team:Aachen/Figure|Aachen_mrsa.jpg|width=200px|title=SEM of a human immune cell ingesting MRSA|subtitle=Picture by NIAID.}}<br />
<html>In their article <a href="http://www.wiwo.de/technologie/forschung/wirkungslose-antibiotika-krankenhaeuser-als-sammelbecken-von-multiresistenten-keimen/10076108-2.html">Noneffective Antibiotics</a> published in June, the German business news magazine Wirtschaftswoche explains it as follows: Antibiotics are the natural weapon of molds or soil microbes against competing bacterial growth. These bacteria under siege in turn counterattack with resistances: attack and defense – the natural course of evolution. Thus it was only natural, too, that since the first human use of penicillin and co., pathogens have developed strategies in order to escape the antibiotics’ effect albeit these drugs are quite insidious weapons.</html> [https://2014.igem.org/Team:Aachen/Blog/14-07-14-01 Read more...]<br />
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= Blog #17 - Open Hardware at the Maker Faire Hannover =<br />
[[User:Mosthege|Michael]] 03:55, 6 July 2014 (CDT)<br />
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This weekend [[User:fgohr|Florian]], [[User:R.hanke|René]] and [[User:mosthege|Michael]] joined [[User:Ansgar|Ansgar]] on a trip to the [http://makerfairehannover.com/ Maker Faire Hannover 2014].<br />
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The Maker Faire is an exhibition with things that people built on their own using readily available tools. Dozens of 3D printers and microcontrollers can be examined and there are a lot of devices visitors can interact with.<br />
Apart from the fire-spitting dragon, our OD and fluorescence measurement devices attracted a lot of attention. We spoke with hundreds of visitors and had a lot of interesting conversations. [https://2014.igem.org/Team:Aachen/Blog/14-07-06-01 Read more...]<br />
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= Blog #16 - iGEM team at RWTH Open House =<br />
By [[User:NBailly|NBailly]] 15:22, June 29 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_14-06-28_Erstinfotag_(2).JPG|left|width=300px|title=Our iGEM stand|subtitle=[[User:NBailly|Nina]] and [[User:fgohr|Florian]] showed students how they can get involved in research outside of the programs..}}<br />
<html>Yesterday, RWTH organized an <a href="http://www.rwth-aachen.de/cms/root/Studium/Vor_dem_Studium/Liste/~tfg/ErstInfoTag-Entdecke-die-Welt-des-Studi/">open house</a> for students from ages 14 to 16. Different departments, institutes and student councils presented exhibits, latest research projects, and the many programs they offer. Students could actively try out science and research in prepared experiments at each stand. Various groups of student representatives also offered first hand advice to students with respect to what to study and when and where to collect information. In presentations about the different fields of studies, students gained first insights into the world of academic professions and other career perspectives.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-29-01 Read more...]<br />
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= Blog #15 - Noneffective Antibiotics (Part I): Dangerous Battle against Killer Germs =<br />
By [[User:NBailly|NBailly]] 17:06, June 23 2014 (CDT)<br />
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{{Team:Aachen/FigureFloat|Aachen_SEM_of_Pseudomonas_aeruginosa.jpg|width=400px|title= SEM of ''Pseudomonas aeruginosa''|subtitle=Picture by Janice Haney Carr.}}<br />
<html>Are we soon going to be dying of pneumonia again? It is almost unimaginable, but the danger that our antibiotics will soon fail against plagues thought to be conquered a long time ago, is eminent. In fact, the situation has grown very acute. The all-purpose weapon antibiotic is on the verge of losing its vigor since many pathogens, such as the pneumonia causing bacterium <i>Pseudomonas aeruginosa</i> , have become resistant. Experts of the World Health Organization (WHO) have already raised a loud alarm: In their recently published first <a href="http://www.who.int/drugresistance/documents/surveillancereport/en/" title="WHO Antimicrobial resistance: global report on surveillance 2014" target="_blank">global resistance report</a>, they are drawing a rather apocalyptic picture. If nothing is done, doctors soon might not be able to do anything but stand helplessly next to their patients while they are dying from nowadays easily curable diseases or even smallest wound infections.</html> [https://2014.igem.org/Team:Aachen/Blog/14-06-23-01 Read more...]<br />
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= Blog #14 - Students Explore Careers in Synthetic Biology =<br />
By [[User:NBailly|NBailly]] 21:11, June 12 2014 (CDT)<br />
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[[File:Cellock_liegend.png|left|300px|frameless]]<br />
Our "Synthetic Biology" teaching module has come to an end. Today was our last day at Kaiser-Karl-Gymnasium in Aachen, where we have worked together with a grade 9 biology-chemistry class for past 1 1/2 months. <!--more-->The students have learned about the iGEM and synthetic biology in general. We presented our project to the class, and explained various aspects for our endeavour in more detail.<br />
<br />
To give interested students some overview of how they can get involved in synthetic biology, Vera, Florian, Ansgar and Björn gave short presentations about each university program at RWTH represented in our team. [https://2014.igem.org/Team:Aachen/Blog/14-06-12-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #13 - Teaching Module Wrap-Up =<br />
By [[User:NBailly|NBailly]] 16:32, June 05 2014 (CDT)<br />
<br />
Today [[User:NBailly|Nina]] and [[User:AZimmermann|Arne]] discussed last class's experiment. Arne explained to the students the meaning behind the values measured, and how the students can use the value to determine the concentration of riboflavin in their vanilla pudding samples. [https://2014.igem.org/Team:Aachen/Blog/14-06-05-01 Read more...]<br />
<br />
[[File:Cellock_stehend.png|center|300px|frameless]]<br />
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= Blog #12 - Glowing vanilla pudding =<br />
By [[User:NBailly|NBailly]] 16:16, June 02 2014 (CDT)<br />
<br />
{{Team:Aachen/Figure|Aachen KKG (15).jpg|right|width=300px|title=Our iGEM stand|subtitle=Things needed for a cool experiment.}}<br />
The topics of today's double lesson was quorum sensing as well as measurement of fluorescence. At the beginning of class, the students form 6 groups and start an experiment dealing with fluorescence: Each group weighs and dissolves 4g of vanilla pudding powder in 50mL of water. While conducting the experiment, each group is supervised by a member of our iGEM team. [https://2014.igem.org/Team:Aachen/Blog/14-06-02-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #11 - No time for high politics =<br />
By [[User:NBailly|NBailly]] 15:42, May 31 2014 (CDT)<br />
<br />
{{Team:Aachen/FigureFloat|Aachen HuClimateUN.jpg|width=300px|title=UN Climate Change Conference|subtitle=Summits like the UN Climate Change Conference are the wrong approach to problems such as antibiotic resistances, says Lars Fischer. Picture from the Intern Blog of American University.}}<br />
International collaborations against antibiotic resistances are all well and good, but the UN Climate Change conference of all collaborations shows why coordination at the government level is the wrong approach, says Lars Fischer, editorial journalist at "Spektrum Der Wissenschaft".<br />
Not even a century ago, the discovery of antibiotics caused a decisive turn for the better in the millennia-long battle against infectious diseases. But while many already saw pathogenic agents eradicated and a golden age of medicine seemed within reach, we have now however reached an abyss: a dramatic relapse into a world looms ahead, where microorganisms are again rulers over life and death. <br />
<br />
The threat emanating from the increasing antibiotic resistances is existential—for every one of us, as well as the countries and society itself. That the world community unites in a supranational board in order to face the latter, suggests itself. However, as alluring as the vision of an intergovernmental panel on antimicrobial resistance may be, as evoked by Mark Woolhouse and Jeremy Farrar (authors of the Nature article "Policy: An intergovernmental panel on antimicrobial resistance", published May 2014), this thought is gravely mistaken. [https://2014.igem.org/Team:Aachen/Blog/14-05-31-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #10 - Microorganisms on the rise =<br />
By [[User:NBailly|NBailly]] 16:05, May 26 2014 (CDT)<br />
<br />
[[File:10404745_641111075966352_965198584_o.jpg|right|200px]]<br />
Last lesson students at Kaiser-Karl-Gymnasium took environmental samples using a variety of different contact agar plates. On the weekend, René examined the plates under the microscope and took photos. Today [[User:R.hanke|René]] and [[User:NBailly|Nina]] present the students the results of the experiment.<!--more--> But first, we showed the students an excerpt from the TV show "Planetopia" that broaches the issue "Hygiene in every-day life". [https://2014.igem.org/Team:Aachen/Blog/14-05-26-01 Read more...]<br />
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{{Team:Aachen/BlockSeparator}}<br />
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= Blog #9 - Going to Munich =<br />
By [[User:AZimmermann|AZimmermann]] 15:02, May 23 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
on the coming weekend 3 of our team ([[User:Mjoppich|Markus]], [[User:Mosthege|Michael]] and [[User:AZimmermann|Arne]]) are going to travel to Munich for the iGEM meetup iGEM meets CAS. We are very excited for this and can’t wait to meet all the other teams who will be attending. Stay tuned to this blog to see the first pictures when we come back!<br />
<br />
So stay tuned!<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #8 - iGEM team members back 2 school =<br />
By [[User:NBailly|NBailly]] 16:00, May 22 2014 (CDT)<br />
<br />
[[File:Aachen_Kaiser-Karls-Gymnasium.jpg|right|200px]]<br />
Hello iGEM enthusiasts,<br />
Since our last visit, the student of the biology-chemistry course at Kaiser-Karl-Gymnasium in Aachen have been busy studying the basics of protein biosynthesis and the "lock and key" model. Now the 9th graders are prepared to have a closer look at synthetic biology and our project.<br />
<br />
[https://2014.igem.org/Team:Aachen/Blog/14-05-22-01 Read more...]<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #7 - The Biobricks have arrived =<br />
By [[User:AZimmermann|AZimmermann]] 16:02, May 12 2014 (CDT)<br />
<br />
[[FigureFloat:Aachen_Biobricks_arrival_2014.jpg|left|400px]]<br />
Hello iGEM enthusiasts,<br />
we have finally gotten the iGEM 2014 biobricks!<br />
Now we can really start working on the molecular side of our project.<br />
<br />
<br />
The reveal of our project, coupled with the launch of our new website will be done by the end of next week.<br />
<br />
So stay tuned!<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #6 - Preparing Cool Experiments =<br />
By [[User:AZimmermann|AZimmermann]] 12:12, May 7 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
We are currently working together with the Kaiser-Karl-Gymnasium in Aachen. Together we are teaching the students about synthetic biology, iGEM and our project in particular. As a part of this, we are designing cool experiments for the students to do themselves. Here a some nice pictures of us preparing them:<br />
<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/27/Aachen_prepping_school_project_2.jpg/450px-Aachen_prepping_school_project_2.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/1/1b/Aachen_prepping_scholl_project_3.jpg/450px-Aachen_prepping_scholl_project_3.jpg"/></a><div class="label_text"><p></p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/65/Aachen_prepping_school_project_4.jpg/450px-Aachen_prepping_school_project_4.jpg"/></a><div class="label_text"><p>We got a fluorescence readout!</p></div></li><br />
</ul><br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #5 - Assembly in progress =<br />
By [[User:AZimmermann|AZimmermann]] 12:56, May 5 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
if you are like us and can't wait for our wiki page to go fully online (see last post for more information) and the project to be fully revealed, here are some pictures to tide you over until then:<br />
<br />
Can you guess what we are assembling?<br />
<br />
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<ul><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/2/2b/Aachen_Device_Building_1_1.JPG/780px-Aachen_Device_Building_1_1.JPG"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e8/Aachen_device_building_1_2.JPG/780px-Aachen_device_building_1_2.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/6/60/Aachen_device_building_1_3.JPG/780px-Aachen_device_building_1_3.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/8/80/Aachen_device_building_1_4.JPG/780px-Aachen_device_building_1_4.JPG"></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
</ul><br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #4 - We are approved! =<br />
By [[User:AZimmermann|AZimmermann]] 11:00, May 4 2014 (CDT)<br />
<br />
{{Team:Aachen/Figure|Aachen_NEB_Kit_Arrival.jpg|width=400px|title= Also in this blog...|subtitle=NEB is awesome!}}<br />
Hello iGEM enthusiasts,<br />
<br />
we are more than happy to finally be able to announce that our application has been finally approved by the iGEM headquarters. Now nothing will stand between us and our journey towards the giant Jamboree at the end of October! <br />
<br />
[https://2014.igem.org/Team:Aachen/Blog/14-05-04-01 Read more...]<br />
<br />
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{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #3 - School Project Kick-Off =<br />
By [[User:NBailly|NBailly]] 20:48, April 28 2014 (CDT)<br />
<br />
Today was the kick-off for the cooperation between our iGEM team and the Kaiser-Karl-Gymnasium, a secondary school in Aachen.<br />
In the upcoming weeks, exciting school lessons with members of our iGEM team await the students of the 9th grade biology-chemistry class. Different aspects of our project will be highlighted and explained to the students. Demonstrative experiments will explain the practical relevance.<br />
<br />
In today's lesson, our members [[User:NBailly|Nina]] and [[User:R.hanke|René]] offered the students a short impression of what to expect in the course of this teaching module. We also explained synthetic biology and the goal of our project.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #2 - The box is opened =<br />
By [[User:AZimmermann|AZimmermann]] 9:46, April 28 2014 (CDT)<br />
<br />
Hello iGEM enthusiasts,<br />
<br />
interested to see what is inside the box from the previous post?<br />
<br />
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<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/e/e1/Aachen_Peltier_Temperatursensor.jpg/780px-Aachen_Peltier_Temperatursensor.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
<li><a><img src="https://static.igem.org/mediawiki/2014/thumb/c/c4/Aachen_Widerstaende_LEDs.jpg/780px-Aachen_Widerstaende_LEDs.jpg"/></a><div class="label_text"><p>Hier Text möglich</p></div></li><br />
</ul><br />
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<br />
Guess what we are building?<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Blog #1 - The opening =<br />
By [[User:AZimmermann|AZimmermann]] 10:31, April 24 2014 (CDT)<br />
<br />
[[File:Aachen_Opening_Arduino_Box.jpg|left|250px]]<br />
Hello everyone,<br />
the iGEM competition has officially started and we are taking part!<br />
If you are as excited as we are stay tuned as we will unveil everything about our project in the upcoming weeks. This blog will function as a behind the scenes look of the project and the team. So stay tuned for everything iGEM Aachen!<br />
<br />
In the meantime you can check us out on [http://www.facebook.com/iGEMAachen Facebook] or [http://twitter.com/igemaachen Twitter]<br />
for more updates.<br />
<br />
This year Aachen is rocking iGEM!<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:26:19Z<p>R.hanke: /* iGEM Team Aachen BioBricks */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<center><br />
{| class="wikitable"<br />
! BioBrick !! Describtion<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319000 K1319000]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319001 K1319001]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319002 K1319002]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319003 K1319003]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319004 K1319004]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319008 K1319008]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319009 K1319009]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319010 K1319010]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319011 K1319011]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319012 K1319012]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319013 K1319013]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319014 K1319014]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319015 K1319015]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319016 K1319016]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319017 K1319017]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319020 K1319020]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042]<br />
|} </center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
<br />
Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319009 K1319009]==<br />
<br />
===mRFP-gal3-his fusion protein CDS===<br />
<span class="anchor" id="partsK1319009"></span><br />
<br />
This is a fusion protein created from E1010, K1319003 and K1319007.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319000 K1319000] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
<br />
===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (GFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
===Usage and Biology===<br />
<br />
A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
<br />
===Usage and Biology===<br />
<br />
For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:25:57Z<p>R.hanke: /* iGEM Team Aachen BioBricks */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<center><br />
{| class="wikitable"<br />
! BioBrick !! function<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319000 K1319000]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319001 K1319001]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319002 K1319002]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319003 K1319003]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319004 K1319004]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319008 K1319008]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319009 K1319009]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319010 K1319010]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319011 K1319011]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319012 K1319012]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319013 K1319013]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319014 K1319014]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319015 K1319015]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319016 K1319016]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319017 K1319017]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319020 K1319020]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042]<br />
|} </center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
<br />
Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319009 K1319009]==<br />
<br />
===mRFP-gal3-his fusion protein CDS===<br />
<span class="anchor" id="partsK1319009"></span><br />
<br />
This is a fusion protein created from E1010, K1319003 and K1319007.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319000 K1319000] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
<br />
===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (GFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
===Usage and Biology===<br />
<br />
A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
<br />
===Usage and Biology===<br />
<br />
For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:25:38Z<p>R.hanke: /* iGEM Team Aachen BioBricks */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<center><br />
{| class="wikitable"<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319000 K1319000]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319001 K1319001]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319002 K1319002]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319003 K1319003]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319004 K1319004]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319008 K1319008]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319009 K1319009]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319010 K1319010]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319011 K1319011]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319012 K1319012]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319013 K1319013]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319014 K1319014]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319015 K1319015]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319016 K1319016]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319017 K1319017]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319020 K1319020]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042]<br />
|} </center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
<br />
Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319009 K1319009]==<br />
<br />
===mRFP-gal3-his fusion protein CDS===<br />
<span class="anchor" id="partsK1319009"></span><br />
<br />
This is a fusion protein created from E1010, K1319003 and K1319007.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319000 K1319000] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
<br />
===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (GFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
===Usage and Biology===<br />
<br />
A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
<br />
===Usage and Biology===<br />
<br />
For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:24:04Z<p>R.hanke: /* iGEM Team Aachen BioBricks */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<center><br />
{| class="wikitable"<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319000 K1319000]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319001 K1319001]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319002 K1319002]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319003 K1319003]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319004 K1319004]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319008 K1319008]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319009 K1319009]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319010 K1319010]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319011 K1319011]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319012 K1319012]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319013 K1319013]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319014 K1319014]<br />
|-<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319015 K1319015]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319016 K1319016]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319017 K1319017]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319020 K1319020]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042]<br />
||<br />
|} </center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
<br />
Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319009 K1319009]==<br />
<br />
===mRFP-gal3-his fusion protein CDS===<br />
<span class="anchor" id="partsK1319009"></span><br />
<br />
This is a fusion protein created from E1010, K1319003 and K1319007.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319000 K1319000] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
<br />
===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (GFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
===Usage and Biology===<br />
<br />
A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
<br />
===Usage and Biology===<br />
<br />
For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:23:12Z<p>R.hanke: /* iGEM Team Aachen BioBricks */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<center><br />
{| class="wikitable"<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319000 K1319000]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319001 K1319001]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319002 K1319002]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319003 K1319003]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319004 K1319004]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319008 K1319008]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319009 K1319009]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319010 K1319010]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319011 K1319011]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319012 K1319012]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319013 K1319013]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319014 K1319014]<br />
|-<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319015 K1319015]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319016 K1319016]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319017 K1319017]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319020 K1319020]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042]<br />
|-<br />
|} </center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
<br />
Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319009 K1319009]==<br />
<br />
===mRFP-gal3-his fusion protein CDS===<br />
<span class="anchor" id="partsK1319009"></span><br />
<br />
This is a fusion protein created from E1010, K1319003 and K1319007.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319000 K1319000] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
<br />
===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (GFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
===Usage and Biology===<br />
<br />
A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
<br />
===Usage and Biology===<br />
<br />
For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:22:46Z<p>R.hanke: /* iGEM Team Aachen BioBricks */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<center><br />
{| class="wikitable"<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319000 K1319000]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319001 K1319001]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319002 K1319002]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319003 K1319003]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319004 K1319004]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319008 K1319008]<br />
|-<br />
| [https://2014.igem.org/Team:Aachen/Parts#partsK1319009 K1319009]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319010 K1319010]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319011 K1319011]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319012 K1319012]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319013 K1319013]<br />
||[https://2014.igem.org/Team:Aachen/Parts#partsK1319014 K1319014]<br />
|-<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319015 K1319015]<br />
|| [https://2014.igem.org/Team:Aachen/Parts#partsK1319016 K1319016]<br />
||[https://2014.igem.org/Team:Aachen/Parts#partsK1319017 K1319017]<br />
||[https://2014.igem.org/Team:Aachen/Parts#partsK1319020 K1319020]<br />
||[https://2014.igem.org/Team:Aachen/Parts#partsK1319042 K1319042]<br />
|} </center><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
<br />
Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
<br />
=== IPTG-induced and T7-driven expression of TEV protease ===<br />
<br />
This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319009 K1319009]==<br />
<br />
===mRFP-gal3-his fusion protein CDS===<br />
<span class="anchor" id="partsK1319009"></span><br />
<br />
This is a fusion protein created from E1010, K1319003 and K1319007.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
<br />
=== Constitutive expression of K1319000 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319000 K1319000] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
<br />
=== Constitutive expression of K1319001 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
<br />
=== Constitutive expression of K1319002 ===<br />
<br />
This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
<br />
=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
<br />
===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
<br />
===Constitutive expression of GFP-REACh2 fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
<br />
===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
<br />
===Constitutive expression of GFP-EYFP fusion protein===<br />
<br />
This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (EGFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
<br />
===TEV protease cleavage site===<br />
<br />
This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
===Usage and Biology===<br />
<br />
A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
<br />
=== LasI induced iLOV ===<br />
<br />
This device produces iLOV (K660004) in response to a quorum sensing input.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
<br />
===Translational unit of mRFP-galectin3-His===<br />
<br />
This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
<br />
===Usage and Biology===<br />
<br />
For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
<br />
===IPTG inducible iLOV===<br />
<br />
This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
===iGEM Team Aachen Biobrick overview===<br />
<br />
<groupparts>iGEM14 Aachen</groupparts><br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-18T03:18:28Z<p>R.hanke: /* WatsOn */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li style="margin-right:20px;margin-left:20px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
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<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li style="margin-right:20px;margin-left:20px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li style="margin-right:20px;margin-left:20px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Interaction of electronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The [http://www.raspberrypi.org/ Raspberry Pi] is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The [http://www.arduino.cc/ Arduino] board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': A 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide an user interface and manage the connection to the hardware.<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
The scheme below shows the different components of the software:<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
Features of the GUI include:<br />
* Change settings [1]:<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
* Take image/s [2]: <br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image [3]. Previous images can be selected with the arrow buttons.<br />
* Analyze image [4]:<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
''Download the GUI sourcecode:'' [https://static.igem.org/mediawiki/2014/9/90/Aachen_WatsOn_GUI.zip Download]<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Subsequently, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://static.igem.org/mediawiki/2014/7/77/Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/c/cd/Aachen_WatsOn_arduino.zip Download] <br />
<br />
===Measurarty===<br />
We have developed our own image analysis pipeline ''Measurarty''. Please go to the [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] project page for further information.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
''Download the laser cutting plan here: [https://static.igem.org/mediawiki/2014/f/fd/Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1|| black spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information about ''WatsOn'' and the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. For security reasons it has been placed into an aluminium casing. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup Raspberry Pi - Setup].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<span class="anchor" id="fn1"></span><br />
<sup>1</sup>By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* To check if the camera works, enter "raspistill -t 5000 -o camera_test.jpg" in the terminal. An overlay shows a 5 second preview from the camera on the screen, then an image is taken and saved as "camera_test.jpg" in the current directory.<br />
* An issue concerning the Raspberry Pi camera is that it supports just a fixed-focus which is per default set to infinity. This can be solved by removing the glue dots fixing the lense und unscrewing it until the required distance is focused.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Raspberry Pi Camera Module<br />
** http://elinux.org/Rpi_Camera_Module<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
* General<br />
** [http://elinux.org/R-Pi_Troubleshooting Raspberry Pi Troubleshooting]<br />
** [http://raspberrywebserver.com/linux-basics/ Linux basics]<br />
** [http://www.raspberrypi.org/ Raspberry Pi Foundation]<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-18T03:18:03Z<p>R.hanke: Undo revision 395451 by R.hanke (talk)</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li style="margin-right:40px;"><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li style="margin-right:40px;"><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Interaction of electronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The [http://www.raspberrypi.org/ Raspberry Pi] is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The [http://www.arduino.cc/ Arduino] board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': A 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide an user interface and manage the connection to the hardware.<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
The scheme below shows the different components of the software:<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
Features of the GUI include:<br />
* Change settings [1]:<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
* Take image/s [2]: <br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image [3]. Previous images can be selected with the arrow buttons.<br />
* Analyze image [4]:<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
''Download the GUI sourcecode:'' [https://static.igem.org/mediawiki/2014/9/90/Aachen_WatsOn_GUI.zip Download]<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Subsequently, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://static.igem.org/mediawiki/2014/7/77/Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/c/cd/Aachen_WatsOn_arduino.zip Download] <br />
<br />
===Measurarty===<br />
We have developed our own image analysis pipeline ''Measurarty''. Please go to the [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] project page for further information.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
''Download the laser cutting plan here: [https://static.igem.org/mediawiki/2014/f/fd/Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1|| black spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information about ''WatsOn'' and the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. For security reasons it has been placed into an aluminium casing. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup Raspberry Pi - Setup].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<span class="anchor" id="fn1"></span><br />
<sup>1</sup>By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* To check if the camera works, enter "raspistill -t 5000 -o camera_test.jpg" in the terminal. An overlay shows a 5 second preview from the camera on the screen, then an image is taken and saved as "camera_test.jpg" in the current directory.<br />
* An issue concerning the Raspberry Pi camera is that it supports just a fixed-focus which is per default set to infinity. This can be solved by removing the glue dots fixing the lense und unscrewing it until the required distance is focused.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Raspberry Pi Camera Module<br />
** http://elinux.org/Rpi_Camera_Module<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
* General<br />
** [http://elinux.org/R-Pi_Troubleshooting Raspberry Pi Troubleshooting]<br />
** [http://raspberrywebserver.com/linux-basics/ Linux basics]<br />
** [http://www.raspberrypi.org/ Raspberry Pi Foundation]<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-18T03:17:32Z<p>R.hanke: /* WatsOn */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li style="margin-right:20px;margin-left:20px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li style="margin-right:20px;margin-left:20px;"><br />
<a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><li style="margin-right:20px;margin-left:20px;"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Interaction of electronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The [http://www.raspberrypi.org/ Raspberry Pi] is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The [http://www.arduino.cc/ Arduino] board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': A 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide an user interface and manage the connection to the hardware.<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
The scheme below shows the different components of the software:<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
Features of the GUI include:<br />
* Change settings [1]:<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
* Take image/s [2]: <br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image [3]. Previous images can be selected with the arrow buttons.<br />
* Analyze image [4]:<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
''Download the GUI sourcecode:'' [https://static.igem.org/mediawiki/2014/9/90/Aachen_WatsOn_GUI.zip Download]<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Subsequently, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://static.igem.org/mediawiki/2014/7/77/Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/c/cd/Aachen_WatsOn_arduino.zip Download] <br />
<br />
===Measurarty===<br />
We have developed our own image analysis pipeline ''Measurarty''. Please go to the [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] project page for further information.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
''Download the laser cutting plan here: [https://static.igem.org/mediawiki/2014/f/fd/Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1|| black spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information about ''WatsOn'' and the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. For security reasons it has been placed into an aluminium casing. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup Raspberry Pi - Setup].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<span class="anchor" id="fn1"></span><br />
<sup>1</sup>By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* To check if the camera works, enter "raspistill -t 5000 -o camera_test.jpg" in the terminal. An overlay shows a 5 second preview from the camera on the screen, then an image is taken and saved as "camera_test.jpg" in the current directory.<br />
* An issue concerning the Raspberry Pi camera is that it supports just a fixed-focus which is per default set to infinity. This can be solved by removing the glue dots fixing the lense und unscrewing it until the required distance is focused.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Raspberry Pi Camera Module<br />
** http://elinux.org/Rpi_Camera_Module<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
* General<br />
** [http://elinux.org/R-Pi_Troubleshooting Raspberry Pi Troubleshooting]<br />
** [http://raspberrywebserver.com/linux-basics/ Linux basics]<br />
** [http://www.raspberrypi.org/ Raspberry Pi Foundation]<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOnTeam:Aachen/Notebook/Engineering/WatsOn2014-10-18T03:16:46Z<p>R.hanke: /* WatsOn */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<br />
= ''WatsOn'' =<br />
<br />
This page contains technical details and construction manuals for our measurement device ''WatsOn'' as well as information on the software controlling the hardware. For more details, please click on the respective tile. For the image analysis software, please visit our [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] page.<br />
<br />
<html><br />
<center><br />
<ul class="team-grid" style="width:inherit;"><br />
<!-- Overview --><br />
<br />
<li style="margin-right:40px;"><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonhardware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Hardware</div><br />
<!-- <br />
<br/><br/><br />
<b>Hardware</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/5/59/Aachen_14-10-16_Hardware_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<br />
<li style="margin-right:40px;"><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">Software</div><br />
<!-- <br/><br><br />
<b>Software</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/1/13/Aachen_14-10-16_Software_button_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
<li><a href="https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy" style="color:black"><br />
<div class="team-item team-info" ><br />
<div class="menukachel">DIY</div><br />
<!-- <br/><br/><br />
<b>DIY</b><br />
<br/><br/><br />
click for more information --><br />
</div><br />
<div class="team-item team-img" style="background: url(https://static.igem.org/mediawiki/2014/9/9e/Aachen_14-10-15_DIY_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%"> </div></a><br />
</li><br />
<br />
</ul><br />
</center><br />
</html><br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Hardware =<br />
<span class="anchor" id="watsonhardware"></span><br />
<br />
{{Team:Aachen/FigureFloat|Aachen_Device_11.jpg|title=''WatsOn''|subtitle= |width=200px}}<br />
<br />
Our hardware consists of the casing and the electronical components. The casing which can be seen on the left was built from laser cut acrylic glass. A detailed description of the assembly is described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsondiy Build your own ''WatsOn].<br />
<br />
The connection between the different electronical elements is visualized below.<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Hardware_Graphics.png|title=Interaction of electronical components||width=750px}}<br />
<br />
* '''Raspberry Pi''' : The [http://www.raspberrypi.org/ Raspberry Pi] is a small single-board computer which runs a Linux operating system from an inserted SD card. The steps which are required to set up a fully working system are described in the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup DIY section] of this page. The main purpose of the Raspberry Pi is to run the software described above, to control the attached camera and to show the GUI on the display. The big advantage of this board is that it is very powerful, cheap and therefore perfectly fit for our needs.<br />
<br />
* '''Raspberry Pi camera''': The camera is directly connected to the Raspberry Pi board and takes the images of the chips.<br />
<br />
* '''Arduino''': The [http://www.arduino.cc/ Arduino] board is also a single-board computer with less computing power than the Raspberry Pi but with a greater focus on controlling electronical components. Therefore, it is used to control the LEDs and the Peltier heater.<br />
<br />
* '''Relay''': The 2-channel relay works like two light switches which are either turned on or off. They control the 450&nbsp;nm and 480&nbsp;nm LEDs. The channels are connected and turned on and off by the Arduino board.<br />
<br />
* '''Peltier element''': A Peltier component transforms an applied power into a temperature gradient which leads to a hot surface on one side of the element and a cooler one on the other side. The Peltier element connected to the aluminum block heats up the interior of the device to incubate the sensing cells at 37°C.<br />
<br />
* '''USB WiFi stick''': The USB WiFi stick connects the Raspberry Pi to a local network.<br />
<br />
* '''Display''': A 8-digit display is connected to the Arduino board and shows the current interior temperature<br />
<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_010.png|title=010|subtitle=|width=70px}}<br />
{{Team:Aachen/FigureFloatRight|Aachen_Filter_505.png|title=505|subtitle=|width=70px}}<br />
<br />
* '''Filter slides''': To block the undesired wavelenghts emitted from the LEDs a filter slide is placed in front of the camera. This step is taken to get a clear fluorescence signal from the chips. The characteristic of the filter slide is selected depending on the frequency of the LEDs which are either 450&nbsp;nm or 480&nbsp;nm ones. We used '505 Sally Green' for the 450&nbsp;nm and '010 Medium Yellow' for the 480&nbsp;nm LEDs. The filters are shown on the right.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
= Software =<br />
<span class="anchor" id="watsonsoftware"></span><br />
<br />
The software consists of several parts which provide an user interface and manage the connection to the hardware.<br />
<br />
===GUI (Graphical User Interface)===<br />
On the graphical interface, the user can take images and time lapses of the chips inside the device. The software is written in C++. It makes use of the [http://qt-project.org/ Qt-Library] to provide a clear interface and a comfortable way to manage various software aspects such as handling images and establishing network connections. An advantage resulting from the utilization of Qt-Library is the multi-platform support for Windows, MacOS and Linux. Additionally, Qt is available with an Open Source license which can be used for free. The software can be used locally on the Raspberry Pi or remotely from a device in the same network.<br />
<br />
The scheme below shows the different components of the software:<br />
<br />
[[File:Aachen_Device_GUI.png|center|800px]]<br />
<br />
Features of the GUI include:<br />
* Change settings [1]:<br />
** The user can specify the iso-value and the shutter speed of the camera.<br />
** Custom settings can be labeled and saved for future reference.<br />
** Existing settings can be updated or deleted unless they are default configurations.<br />
* Take image/s [2]: <br />
** The excitation wavelength of GFP (480&nbsp;nm) and iLOV (450&nbsp;nm) can be selected.<br />
** The GUI offers two possibilities to take images:<br />
*** Take a single image with the active camera settings.<br />
*** Take time lapse shootings with the active camera settings and the specified interval. When activated, the images are saved automatically to a user defined directory with ascending filenames.<br />
** The last image which was taken by the camera is shown in the GUI, information containing the time stamp and used camera settings are displayed next to the image [3]. Previous images can be selected with the arrow buttons.<br />
* Analyze image [4]:<br />
** The image is analyzed by an image segmentation algorithm and shows whether the pathogen ''Pseudomonas&nbsp;aeruginosa'' is present on the chip or not<br />
<br />
''Download the GUI sourcecode:'' [https://static.igem.org/mediawiki/2014/9/90/Aachen_WatsOn_GUI.zip Download]<br />
<br />
===Backend===<br />
The backend is a software that runs on the Raspberry Pi and is responsible for the connection between the GUI and the hardware. If the user interface is executed on another device, e.g. a notebook, it has to be in the same network as the Raspberry Pi. The backend works like a web server that receives commands and acts according to the submitted parameters. It can take images and returns them to the GUI.<br />
<br />
Before an image is taken, the backend turns on the specified LEDs by sending a command to the connected Arduino board. Subsequently, the LEDs are turned off using the same mechanism. These steps are repeated in the given interval for a time lapse shooting.<br />
<br />
''Download the backend sourcecode:'' [https://static.igem.org/mediawiki/2014/7/77/Aachen_Device_Backend.zip Download]<br />
<html><br></html><br />
<br />
{{Team:Aachen/Figure|Aachen_Device_SoftwareBackend.png|title=Sample connection between GUI and backend for taking an image|subtitle= |width=900px}}<br />
<br />
===Arduino===<br />
The software on the Arduino board sets the power and thus controls the temperature of the Peltier heater. The power is set by evaluating the received values from the temperature sensors for the interior of the device and the aluminum block. Additionally, the Arduino receives commands from the Raspberry Pi to turn the LEDs on and off.<br />
<br />
''Download the Arduino sourcecode:'' [https://static.igem.org/mediawiki/2014/c/cd/Aachen_WatsOn_arduino.zip Download] <br />
<br />
===Measurarty===<br />
We have developed our own image analysis pipeline ''Measurarty''. Please go to the [https://2014.igem.org/Team:Aachen/Notebook/Software/Measurarty ''Measurarty''] project page for further information.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
[[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]]<br />
<br />
= DIY: How To Build Your Own ''WatsOn'' =<br />
<span class="anchor" id="watsondiy"></span><br />
<br />
==Technical Components==<br />
If you want to create your own ''WatsOn'' first take a look at the following list of necessary components. All parts except the laser cut acrylic glass can be readily purchased and do not require further adjustments.<br />
<br />
''Download the laser cutting plan here: [https://static.igem.org/mediawiki/2014/f/fd/Aachen_WatsOn_laser_cut.svg.zip Download] (for acrylic glass with a height of 6&nbsp;mm)<br />
<br />
'''All needed components, their quantities and prices for creating your own ''WatsOn'''''<br />
{| class="wikitable sortable"<br />
! align="center" |'''''WatsOn'''''<br />
!! align="center" | <br />
!! align="center" |''' 1€='''<br />
!! align="center" |''' $1.27'''<br />
!! align="center" |''' on 14/10/2014'''<br />
!! align="center" | <br />
|- class="unsortable"<br />
!Quantity !! Component !! Costs [€]!! Costs [$]!! Final [€]!! Final [$]<br />
|-<br />
| 1|| [http://www.prolighting.de/Zubehoer/Farbfilter/Lee-Filter_HT/Lee-Filters_Musterheft_Designer_Edition_i174_3965_0.htm filter slides] (medium yellow 010, sally green 505)||1.57||2.00||1.57||2.00<br />
|-<br />
| 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600 Arduino UNO R3]||9.17||11.65||9.17||11.65<br />
|-<br />
| 1|| [http://www.dx.com/p/arduino-2-channel-relay-shield-module-red-144140 2-channel relay shield]||2.72||3.46||2.72||3.46<br />
|-<br />
| 40||jumper-wire cable||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191 40er male header (10-Piece Pack)]||2.14||2.72||2.14||2.72<br />
|-<br />
| 1|| [http://www.dx.com/p/jtron-2-54mm-40-pin-single-row-seat-single-row-female-header-black-10-pcs-278953 40er female header (10-Piece Pack)]||2.05||2.60||2.05||2.60<br />
|-<br />
| 1|| [http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-brown-5-piece-pack-130926 circuit board]||2.35||2.99||2.35||2.99<br />
|-<br />
| 1|| [http://www.newark.com/pro-signal/rp006/audio-video-cable-hdmi-1m-black/dp/96T7446 HDMI cable]||1.47||1.87||1.47||1.87<br />
|-<br />
| 1|| [http://www.dx.com/p/hd-053-high-speed-usb-2-0-7-port-hub-black-174817 7 port USB hub]||5.28||6.71||5.28||6.71<br />
|-<br />
| 1||[http://www.dx.com/p/dx-original-ultra-mini-usb-2-0-802-11n-b-g-150mbps-wi-fi-wlan-wireless-network-adapter-black-252716 USB WiFi stick]||4.21||5.35||4.21||5.35<br />
|-<br />
| 1||USB mouse and keyboard||9.84||12.50||9.84||12.50<br />
|-<br />
| 1|| [http://corporate.evonik.com/en/products/pages/default.aspx case acrylic glass XT 6mm~0.5<sup>2</sup>]||39.88||50.65||39.88||50.65<br />
|-<br />
| 1|| black spray paint for acrylic glass||5.15||6.54||5.15||6.54<br />
|-<br />
| 1|| [http://www.newark.com/raspberry-pi/raspberry-modb-512m/raspberry-pi-model-b-board/dp/68X0155 Raspberry Pi model B board]||27.56||35.00||27.56||35.00<br />
|-<br />
| 1||[http://www.newark.com/raspberry-pi/rpi-camera-board/add-on-brd-camera-module-raspberry/dp/69W0689 Raspberry Pi camera module]||19.69||25.00||19.69||25.00<br />
|-<br />
| 1||[http://www.pollin.de/shop/dt/NzUwOTc4OTk-/ 7” display]||39.35||49.97||39.35||49.97<br />
|-<br />
| 1||[http://www.dx.com/p/diy8-x-seven-segment-displays-module-for-arduino-595-driver-250813 8-segment display]||3.04||3.86||3.04||3.86<br />
|-11.81<br />
| 2|| [http://www.dx.com/p/arduino-dht11-digital-temperature-humidity-sensor-138531 digital temperature sensor DHT-22]||5.91||7.50||11.82||15.00<br />
|-<br />
| 1 ||aluminum block 100x100x15 mm||11.20||14.23||11.20||14.23<br />
|-<br />
| 1|| [http://www.dx.com/p/tec1-12706-semiconductor-thermoelectric-cooler-peltier-white-157283 Peltier heater 12V 60W]||3.54||4.49||3.54||4.49<br />
|-<br />
| 1||power supply||25.90||32.89||25.90||32.89<br />
|-<br />
| 6|| [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html superflux LED 480nm]||0.99||1.26||5.94||7.54<br />
|-<br />
| 16||LED 450nm||0.37||0.47||5.94||7.54<br />
|-<br />
| 2|| Resistor 40 Ohm||0.12||0.15||0.24||0.30<br />
|-<br />
| 4|| Resistor 100 Ohm||0.12||0.15||0.48||0.60<br />
|-<br />
| 1||cupboard button||0.98||1.24||0.98||1.24<br />
|- class="sortbottom" style="background:#cfe2f4; border-top:2px #808080 solid; font-weight:bold"<br />
| -||Total||-||-||243.88||309.70<br />
|}<br />
<br />
You can find more economical information about ''WatsOn'' and the project on our [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page.<br />
<br />
<br />
For building our '''''WatsOn''''' we used some tools that are not included in the list of necessary components because we assume that they are already available. We used a soldering iron to solder the resistors to the LEDs and fix the headers on the mount of the LEDs. For building electrical circuits our multimeter was very helpful. Furthermore, we applied special glue for plastic to hold the acrylic glass in place. All other components were fixed with tape or hot glue which is versatile and can be removed quickly during alignment of components.<br />
<br />
==Breadboard==<br />
<br />
{{Team:Aachen/Figure|Aachen_Device_Fritzing.png|align=center|title=Wiring of our device||width=900px}}<br />
<br />
==Construction Manual==<br />
<br />
{| class="wikitable centered"<br />
|-<br />
| [[File:Aachen_Device_1.jpg|300px]] || Start building your own ''WatsOn'' by assembling the base plate, the sides and the interior wall.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_2_3.jpg|350px] [File:Aachen_Device_.3jpg|300px]] || Fix the Peltier heater on the back of the aluminum block and place it in the hole of the interior wall.<html><br/></html>Arrange the 4x4 450&nbsp;nm LEDs and the 2x3 480&nbsp;nm LEDs<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_7.jpg|350px]] || Assemble the camera holder with the camera and the corresponding filter slide on the lower part. Above the camera, you can place the temperature sensor for measuring the indoor temperature. Finally, put the fan on the back of the camera holder. <br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_8.jpg|350px]] || Connect the electronic components on the outside and the inside according to the wiring diagramm.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_4.jpg|350px]] || Put together the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_9.jpg|350px]] || Position the front panel and insert the drawer.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_10.jpg|350px]] || Place the temperature sensor measuring the aluminum block temperature directly on the block and put the back panel in front of it.<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_6.jpg|350px]] || Setup the power supply<sup>[https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#fn1 1]</sup> and connect all devices to either 5&nbsp;V or 12&nbsp;V. For security reasons it has been placed into an aluminium casing. Plug the USB hub connector into the Raspberry. If you use the GUI locally on the device a mouse and a keyboard need to be attached to the USB hub to navigate on the user interface. Follow the steps described in the section [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pisetup Raspberry Pi - Setup].<br />
|-style="border-top: 2px #808080 solid;"<br />
| [[File:Aachen_Device_11.jpg|350px]] || Mount the device on top of the power supply casing. Add the display and apply some stickers to enjoy your custom-made ''WatsOn''.<br />
|}<br />
<br />
<span class="anchor" id="fn1"></span><br />
<sup>1</sup>By German law only certified electricians may work on 230&nbsp;V electronics. Therefore, the electrical workshop at our institute created the power supply specifically for our design.<br />
<br />
== Raspberry Pi - Setup ==<br />
<span class="anchor" id="pisetup"></span><br />
<br />
In order to get a running linux system on the Raspberry Pi which includes all required components and configurations the following steps have to be considered:<br />
<br />
* The Raspberry Pi needs an SD card on which the operating system will be installed. Go to the [http://www.raspberrypi.org/downloads/ download page of the Raspberry Pi Foundation] and select an operating system of your choice - we used Raspbian - or just download the NOOBS package which offers all different operating systems during setup. <br />
* Follow the specific image installation guidelines to install the downloaded system onto your SD card.<br />
* Once finished, insert the SD card in the slot on the Raspberry Pi board, connect a monitor over HDMI, plug in a USB mouse and keyboard and start the Raspberry Pi by connecting it to the micro USB power supply. Follow the installation instructions; these should be straightforward. After the installation you will be shown the desktop of your new system.<br />
* To be able to use the Raspberry Pi camera you need activate it over a terminal. Search for a desktop icon labeled "LxTerminal", double click it and a terminal will appear where you can enter commands which will be executed after you press Return. Enter "raspi-config", press Return and activate the camera with the displayed corresponding option.<br />
* To check if the camera works, enter "raspistill -t 5000 -o camera_test.jpg" in the terminal. An overlay shows a 5 second preview from the camera on the screen, then an image is taken and saved as "camera_test.jpg" in the current directory.<br />
* An issue concerning the Raspberry Pi camera is that it supports just a fixed-focus which is per default set to infinity. This can be solved by removing the glue dots fixing the lense und unscrewing it until the required distance is focused.<br />
* Download the source files for the backend server and the graphical user interface (GUI). To be able to compile the GUI, you need to install the Qt5-libraries. Follow [http://qt-project.org/wiki/Native_Build_of_Qt5_on_a_Raspberry_Pi this guide] on how to get the Qt source code, compile it and setup your environment correctly. Make sure that your Raspberry Pi is constantly running, since this process takes some time and must not be interrupted.<br />
* With the Qt-libraries installed, open a terminal and change to the directory where you put the source for the GUI (command "cd [path to source]"). Call "qmake" followed by "make" and you will start compilation of the program. When finished, you can launch the GUI with the command "./igem_GUI".<br />
* The backend - that will establish the connection between hardware and the user interface - requires you to install additional packages for Python which is a high-level general-purpose programming language and an interpreter that will ship with your system. Open the README in the "Backend" directory and follow the instructions.<br />
* You now should be able to launch the backend by calling "python takeimageserver.py &" from the terminal.<br />
* Now start the GUI. An input dialog will show up asking you to provide the IP address of the backend server or the Raspberry Pi, respectively. Since you are running the GUI and the backend on the same device, just press Enter to select the default entry which is the IP of the local host. After a few seconds, when the connection to the backend server has been established, the user interface gets enabled and you can start to take images and time lapse shootings. If the image is not focused you need to adjust the lense in front of the camera by rotating it. For the full list of features refer to the [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#watsonsoftware Software section] of this page.<br />
<br />
In case you want to run the GUI on a remote machine, e.g. your notebook, follow these additional steps:<br />
<br />
* Install the [http://qt-project.org/ Qt-libraries and QtCreator] on your system. This is just an installation - you do not have to compile it. Get the source code for the GUI and open the ".pro" file with QtCreator. After importing the project and selecting a built directory, click the green arrow on the left side. Compilation is started and as soon as it is finished the GUI will start. <br />
* In order to be able to connect to the Raspberry Pi you need to be connected to the same network. Therefore, make sure the Raspberry Pi USB wifi stick is working properly (see [https://2014.igem.org/Team:Aachen/Notebook/Engineering/WatsOn#pitrouble Troubleshooting & Useful Links]), and that you reside in the same network. Start the backend server on the Raspberry Pi. It will print the IP address on start up which you must enter in the GUI on your device running the GUI. Now you should be able to use all the features as if running the GUI on the Raspberry Pi.<br />
<br />
=== Troubleshooting & Useful Links ===<br />
<span class="anchor" id="pitrouble"></span><br />
<br />
* Display resolution: If your connected display is not working properly you may refer to<br />
** http://elinux.org/RPiconfig#Video<br />
** http://www.raspberrypi.org/forums/viewtopic.php?f=29&t=24679<br />
<br />
* Raspberry Pi Camera Module<br />
** http://elinux.org/Rpi_Camera_Module<br />
<br />
* Network configuration:<br />
** http://www.raspberrypi.org/documentation/configuration/wireless/README.md<br />
<br />
* General<br />
** [http://elinux.org/R-Pi_Troubleshooting Raspberry Pi Troubleshooting]<br />
** [http://raspberrywebserver.com/linux-basics/ Linux basics]<br />
** [http://www.raspberrypi.org/ Raspberry Pi Foundation]<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/SecretHappeningsTeam:Aachen/SecretHappenings2014-10-18T03:15:32Z<p>R.hanke: /* +++Newsticker from #Wikifreeze night+++ */</p>
<hr />
<div>__NOTOC__<br />
{{CSS/Main}}<br />
{{Team:Aachen/Stylesheet}}<br />
{{Team:Aachen/Header}}<br />
<html><br />
<style type="text/css"><br />
<br />
.secretimg {<br />
display: block;<br />
text-align: center;<br />
}<br />
<br />
.secretimg img {<br />
border: 3px solid #0069B3;<br />
border-radius: 20px;<br />
}<br />
</style><br />
</html><br />
= ''Mr. Holmes Secret Logbook'' =<br />
<br />
<span style="font-size: 22px">Please, please do not take this sub-page serious. It's probably everything - but not serious.</span><br />
<br />
In fact, most team members know that this website exists. But it silently documents all the funny aspects of our project.<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
First, even we as team Aachen 2014 - we're actually the first team of our university - performed experiments that didn't end well.<br />
<br />
<span class="secretimg">[[File:Aachen_si_1.jpg]]</span><br />
<br />
It's never a good sign if already the blank rather tries to escape than to stay.<br />
<br />
Especially with our own-minded experiments we had some rainy days in the lab<br />
<br />
<span class="secretimg">[[File:Aachen_si_2.jpg]]</span><br />
<br />
but also some bright moments, where we could spread peace, love and happiness :)<br />
<br />
<span class="secretimg">[[File:Aachen_si_3.jpg]]</span><br />
<br />
How many biologists does a computer scientist need to nail a camera?<br />
<br />
<span class="secretimg">[[File:Aachen_si_4.jpg]]</span><br />
<br />
Exact. 3.<br />
<br />
But not only the biological experiments created a high level of frustration, but also the hardware ...<br />
<br />
<span class="secretimg">[[File:Aachen_si_5.JPG]]</span><br />
<br />
... or software.<br />
<br />
<span class="secretimg">[[File:Aachen_si_6.jpg]]</span><br />
<br />
At times we really wanted to kill each other ...<br />
<br />
<span class="secretimg">[[File:Aachen_si_7.jpg]]</span><br />
<span class="secretimg">[[File:Aachen_si_10.jpg|500px]]</span><br />
<br />
... but we had those cool moment where stuff really worked out ...<br />
<br />
<span class="secretimg">[[File:Aachen_si_8.jpg]]</span><br />
<br />
... and just some other bright moments.<br />
<br />
Now at the day of wiki-freeze we're really tired ...<br />
<br />
<span class="secretimg">[[File:Aachen_si_9.jpg]]</span><br />
<br />
... but really, overall we had a fun time with our igem and loved to stand together for our project<br />
<br />
<span class="secretimg">[[File:Aachen_Team_Aachen_Teamfoto_small.jpg|900px]]</span><br />
<br />
<!-- == '''+++Newsticker from #Wikifreeze night+++''' ==<br />
* Congratuatlions - you deleted everything.<br />
* Fail!<br />
* That looks interesting o.O<br />
* One page does not take the newest editing: who created a second header file?!<br />
* Why is there a link to www.example.com on our landing page??<br />
* Nina: I just broke our landing page.<br />
* *coffee smell in the air* - did someone just fetch coffee without fetching me one?? - *evil face*<br />
* i just want to quickly delete our css<br />
* Why is that broken again? --><br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/User:NbaillyUser:Nbailly2014-10-18T03:14:35Z<p>R.hanke: /* */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<center><br />
{{Team:Aachen/TeamMembersBanner}}<br />
</center><br />
== ==<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/4/48/Aachen_team_member_Nina_01.jpg" width="200px" /></html><br />
<br />
'''Nina Bailly - Public Relations & Wiki'''<br />
<br />
''Molecular and Applied Biotechnology (B.Sc. student)''<br />
<br />
I'm making my current term more exciting by participating in our 2014 iGEM team at RWTH Aachen University, where I'm especially concerned with our team's PR work.<br />
<br />
When I'm not working on our iGEM project, I learn about patent law, do tai chi and work on my motorcycle license. In the remaining time (not so much this summer), I enjoy cooking and baking (Check out my [http://thegermanscorner.wordpress.com recipe blog]!). I also love reading fantasy novels while drinking tea and eating chocolate!<br />
<br />
<br />
'''Mainly involved in...'''<br />
* the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] school projects<br />
* public relations<br />
* wiki editing and coordination<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/User:NbaillyUser:Nbailly2014-10-18T03:14:26Z<p>R.hanke: /* */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<center><br />
{{Team:Aachen/TeamMembersBanner}}<br />
</center><br />
== ==<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/4/48/Aachen_team_member_Nina_01.jpg" width="200px" /></html><br />
<br />
'''Nina Bailly - Public Relations & Wiki'''<br />
<br />
''Molecular and Applied Biotechnology (B.Sc. student)''<br />
<br />
I'm making my current term more exciting by participating in our 2014 iGEM team at RWTH Aachen University, where I'm especially concerned with our team's PR work.<br />
<br />
When I'm not working on our iGEM project, I learn about patent law, do tai chi and work on my motorcycle license. In the remaining time (not so much this summer), I enjoy cooking and baking (Check out my [http://thegermanscorner.wordpress.com recipe blog]!). I also love reading fantasy novels while drinking tea and eating chocolate!<br />
<br />
<br />
<br />
'''Mainly involved in...'''<br />
* the [https://2014.igem.org/Team:Aachen/Collaborations/Kaiser-Karls-Gymnasium Kaiser-Karls-Gymnasium] and [https://2014.igem.org/Team:Aachen/Collaborations/Neanderlab NEAnderLab] school projects<br />
* public relations<br />
* wiki editing and coordination<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/User:AZimmermannUser:AZimmermann2014-10-18T03:13:55Z<p>R.hanke: /* */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
<center><br />
{{Team:Aachen/TeamMembersBanner}}<br />
</center><br />
== ==<br />
<br />
<html><img class="imgshadow" style="float: left;" src="https://static.igem.org/mediawiki/2014/8/88/Aachen_team_member_Arne_01.jpg" width="200px" /></html><br />
<br />
'''Arne Zimmermann - Planning & Coordination'''<br />
<br />
''Molecular and Applied Biotechnology (M.Sc. student)''<br />
<br />
I have finished my bachelor at the RWTH Aachen with my bachelor thesis in quantitative Biology.<br />
<br><br><br />
I have always had an interest in engineering, and see the iGEM project as the perfect opportunity to explore more of this field during my studies. In my spare time, I like to play and watch cricket and can never put down a good book.<br />
<br />
<br />
<br />
<br />
'''Mainly involved in...'''<br />
* main organization of our [https://2014.igem.org/Team:Aachen/Meetup Meetup]<br />
* head of project management & fundrainsing<br />
* organization and design of REACh clonings<br />
<br />
<br />
{{Team:Aachen/Footer}}</div>R.hankehttp://2014.igem.org/Team:Aachen/PartsTeam:Aachen/Parts2014-10-18T03:10:37Z<p>R.hanke: /* K1319004 */</p>
<hr />
<div>__NOTOC__<br />
{{Team:Aachen/Header}}<br />
= iGEM Team Aachen BioBricks =<br />
<br />
This page lists the collection of BioBricks developed by our team for the project ''Cellock Holmes - A Case of Identity''.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319000 K1319000]==<br />
<span class="anchor" id="partsK1319000"></span><br />
<br />
===RFC &#91;25&#93; Version of E0020===<br />
<br />
This part is an RFC [25]-compatible version of BBa_E0030. The start and stop codons have been removed to make it RFC [25]-compatible and the part is flanked by the RFC [25] prefix- and suffix-sequences.<br />
<br />
The coding sequence encodes EYFP (enhanced yellow fluorescent protein) which is derived from ''A. victoria'' GFP. The excitation is 512&nbsp;nm and the emission is 534 nm. This part was used to create the parts K1319001 and K1319002. It can also be used in a fusion protein instead of E0030 due to its RFC[25] compability.<br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319001 K1319001]==<br />
<span class="anchor" id="partsK1319001"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh1===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh1.<br />
<br />
Two mutations were introduced that eliminated fluorescence:<br />
* L90I<br />
* Y145W<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319013 K1319013] this is realized and the proteins are fused together with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins bring GFP and REACh1 in proximity to each other which allows GFP and REACh1 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh1 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows the release of a strong fluorescence signal, if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh1 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319001 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319013, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319001 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to create a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319013 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/5/56/Aachen_Graph2_13.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319013 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 9-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (9-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319001. The cutting results in a separation of GFP and REACh1 collapsing the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh1 and emitted as heat but rather as fluorescence with a wavelength of 511 nm.<br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319013 and K1319008 shows the functionality of K1319001. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319001. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 12,5. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319001, K1319013 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/b/bb/Aachen_K1319001_comparison_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319013}}}'''<br />{{{subtitle|The expressed fusion protein K1319013 exhibits a fluorescence more than 30 fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh1 is more than 30-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of >96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319013.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/7/74/Aachen_K1319013_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319013}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319013 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319013 K1319013] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319002 K1319002]==<br />
<span class="anchor" id="partsK1319002"></span><br />
<br />
===RFC [25] - compatible dark quencher based on K1319000 (E0030) called REACh2===<br />
<br />
This part is a RFC[25] dark quencher that is based upon K1319000 (the RFC[25] version of E0030/EYFP) called REACh2. <br />
<br />
Three mutations were introduced that eliminated fluorescence: <br />
* L90I <br />
* Y145W <br />
* H148R<br />
<br />
===References===<br />
* Ganesan S, Ameer-Beg SM, Ng TT, Vojnovic B, Wouters FS. A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP. Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4089-94. Epub 2006 Mar 6. PubMed PMID: 16537489; PubMed Central PMCID: PMC1449651. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449651/?report=classic PubMed Central]<br />
<br />
===Usage and Biology===<br />
This protein is designed to be a dark quencher for GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) in a FRET system. When used in a fusion protein with GFP it reduces the observed fluorescence of GFP drastically. In the biobrick [http://parts.igem.org/Part:BBa_K1319014 K1319014] this is realized and the proteins are fused with the linker [http://parts.igem.org/Part:BBa_K1319016 K1319016] which includes a specific TEV protease (available as [http://parts.igem.org/Part:BBa_K1319004 K1319004]) cleavage site. The fusion of the proteins brings GFP and REACh2 in proximity to each other which allows GFP and REACh2 to act as donors and acceptors in a FRET (Förster Energy Transfer System) system. GFPs emission energy is thereby taken up by REACh2 and released as thermal energy instead of visible light. This eliminates the GFP fluorescence and allows a release of a strong fluorescence signal if a TEV protease is expressed and the linker is cut. The cutting separates GFP and REACh2 cancelling the FRET interaction and providing a GFP fluorescence response.<br />
<br />
===Characterization===<br />
<br />
In order to characterize K1319002 it was expressed as a fusion protein together with GFP to show its quenching ability. This fusion protein, produced by K1319014, was located on the plasmid backbone pSB3K3. To show that the reduced fluorescence was due to the quenching ability of K1319002 and not based on a faulty expression, K1319008 was also introduced into the cells on a pSB1C3 backbone to allow for a double plasmid system. Both constructs were put into ''E. coli'' BL21 (DE3) and compared to [http://parts.igem.org/Part:BBa_I20260 I20260] and [http://parts.igem.org/Part:BBa_B0015 B0015]. B0015 was used as a negative control and I20260 was chosen as a positive control due to the expressed GFP being identical to the GFP being expressed in the fusion protein of K1319014 and having the same promoter, RBS, Terminator and plasmid backbone. <br />
<br />
The double plasmid system, B0015 and I20260 were measured in biological triplicates and after 2 h one set of triplicates of each of the three systems were induced with 50 µl 100mM IPTG in their 50 ml culture (500 ml shake flasks). Fluorescence measurement was performed with the [http://www.biotek.com/products/microplate_detection/synergymx_monochromator_based_multimode_microplate_reader.html Synergy Mx from BioTek] with an excitation wavelength of 496 ± 9 nm and emission wavelength of 516 ± 9 nm. The following graph shows the resulting fluorescence adjusted for the measured optical density to account for difference in growth of the cultures and to only show the fluorescence per cell.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
The strong fluorescence response (10-fold increase) after induction with IPTG shows the functionality of GFP inside the fusion protein. After the induction a TEV protease is produced which is specifically cutting the recognition sequence build inside the linker (K1319016) between GFP and K1319002. The cutting results in a separation of GFP and REACh2 resulting in a collapse of the FRET system between the two. This results in a fluorescence signal of GFP due to the fact that the emission is no longer absorbed by REACh2 and emitted as heat but rather as fluorescence with a wavelength of 511 nm. The overall fluorescence of the double plasmid system reaches the fluorescence level of the positive control indicating a total clavage of all fusion proteins by the produced TEV protease. <br />
<br />
The very low fluorescence in the non induced double plasmid system of K1319014 and K1319008 shows the functionality of K1319002. As established before, the GFP is being expressed correctly inside the fusion protein, therefore the reduction in fluorescence in the non induced double plasmid system is a direct result of the quenching ability of K1319002. The quenching, after subtraction of the background fluorescence, reduced the fluorescence of GFP by a factor of 10. This also includes the slight leakiness of the TEV protease.<br />
<br />
To eliminate the effect of the leakiness of the K1319008 construct in determining the quenching ability of K1319002, K1319014 was also compared against I20260 and B0015 on its own under the same condition as above (again in a biological triplicate).<br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/61/Aachen_K1319002_characterization_positive_negative.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and K1319014}}}'''<br />{{{subtitle|The expressed fusion protein K1319014 exhibits a fluorescence more than nearly 25-fold smaller as the positive control of I20260.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This experiments shows that the fluorescence of the fusion protein GFP-REACh2 is nearly 25-fold lower than normal GFP expression under identical circumstances (same backbone, promoter, RBS, terminator and cultivation circumstances). This demonstrates a quenching percentage of GFP of ~96 %!<br />
<br />
To prove that the measured constructs were the same as assumed the plasmids were tested with specially designed Check PCRs with one primer binding upstream on the plasmid backbone and one primer binding specifically inside the insert. The following results were obtained for K1319014.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/08/Aachen_K1319014_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319014}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
The PCR clearly shows that the used plasmid had the correct insert. After a positive identification of K1319014 the double plasmid system was also checked for the correct TEV protease plasmid K1319008.<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
|-<br />
|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<br />
This PCR also positively identified K1319008. Additionally both parts were sequenced. The sequencing data for [http://parts.igem.org/Part:BBa_K1319008 K1319008] and [http://parts.igem.org/Part:BBa_K1319014 K1319014] can be found in the parts registry.<br />
<br />
===characterization of K1319001 with the iGEM Team Aachen [https://2014.igem.org/Team:Aachen/Project/2D_Biosensor 2D Biosensor]===<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 40px; border:{{{border|0px solid #aaa}}};width:{{{width|500px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/6/6d/Aachen_K1319014%2B8_and_K1319013%2B8_pixelig_minus_bg.gif" width="500px"></html><br />
|-<br />
|'''{{{title|K1319013 + K1319008 and K1319014 + K1319008 non-induced (top) and induced (bottom) in sensor cells }}}'''<br />{{{subtitle|The induced double plasmid systems K1319013 + K1319008 and K1319014&nbsp;+&nbsp;K1319008 exhibit a clear fluorescence response in our sensor cells which in response to induction with 2 µl IPTG. }}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
To further characterize the REACh construct, they were introduced into the sensor cells which were then induced with 2&nbsp;µL IPTG with a concentration of 100&nbsp;mM. Subsequently, we took fluorescence measurement read-outs (GFP, excitation 496&nbsp;±&nbsp;9&nbsp;nm, emission&nbsp;516&nbsp;±&nbsp;9&nbsp;nm) roughly every 10&nbsp;min in the plate reader. The results were plotted in the heatmap shown on the left. <br />
<br />
The heatmap shows an increase of fluorescence from blue (no fluorescence) to red (high fluorescence). It is clearly visible that the induced chips are exhibiting a significantly higher fluorescence than the non-induced chips. This again shows that the constructs work as intended: The TEV protease cuts the linker so that the fusion protein is separated into GFP and a dark quencher, disabling the quenching. GFP has a clear fluorescence emission after the fusion protein has been successfully cut into two pieces by the TEV protease. <br />
<br />
<br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319003 K1319003]==<br />
<span class="anchor" id="partsK1319003"></span><br />
<br />
===human galectin-3, codon optimized for ''E. coli''===<br />
<br />
Galectin-3 is a 26 kDa protein that binds certain LPS patterns. It especially bind the O-section of the LPS.<br />
<br />
Galectins are proteins of the lectin family, which posess '''carbonhydrate recognition domains''' binding specifically to β-galactoside sugar residues. In humans, 10 different galectines have been identified, among which is galectin-3. <br />
<br />
Galectin-3 has a size of about 31&nbsp;kDA and is encoded by a single gene, LGALS3. It has many physiological functions, such as '''cell adhesion, cell growth and differentiation,''' and contributes to the development of '''cancer, inflammation, fibrosis and others'''.<br />
<br />
Human galectin-3 is a protein of the lectin-family that was shown to bind the LPS of multiple human pathogens.<br />
Some of them, including ''Pseudomonas&nbsp;aeruginosa'' protect themselves against the human immune system by mimicking the lipopolysaccharides (LPS) present on human erythrocytes. <br />
<br />
===Usage and Biology===<br />
<br />
K1319003 was used to create [http://parts.igem.org/Part:BBa_K1319020 K1319020], a Galectin-mRFP fusion protein with a C-terminal His tag in the [https://2014.igem.org/Team:Heidelberg/Team/Collaborations Heidelberger expression vector] pSBX1A3.<br />
<br />
We also cloned our K1319003 into the pET17 expression vector and expressed all combinations of fusion proteins in E.&nbsp;coli&nbsp;BL21(DE3). An SDS-PAGE showed that all fusion proteins were fully translated:<br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/5/52/Aachen_14-10-04_Expression_Pellets_iMO.png/425px-Aachen_14-10-04_Expression_Pellets_iMO.png" width="400px"></html><br />
|-<br />
|'''{{{title|Pellets of different fusion protein expressions}}}'''<br />{{{subtitle|Expression in the pET17 vector was much more leaky than the expression in the pSBX vectors.}}}<br />
|}<br />
</div><br />
</center><br />
<html></br></html><br />
<center><br />
<div class="figure" style="float:{{{align|center}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Aachen_Gal3_Expression.png/425px-Aachen_Gal3_Expression.png" width="400px"></html><br />
|-<br />
|'''{{{title|SDS-PAGE of K1319020 expression}}}'''<br />{{{subtitle|The fusion protein was fully translated to the correct molecular mass of 74&nbsp;kDa.}}}<br />
|}<br />
</div><br />
</center><br />
{{Team:Aachen/BlockSeparator}}<br />
<br />
==[http://parts.igem.org/Part:BBa_K1319004 K1319004]==<br />
<span class="anchor" id="partsK1319004"></span><br />
<br />
===TEV protease with anti-self cleavage mutation S219V, codon optimized for ''E. coli''===<br />
<br />
This part is a TEV protease in RFC25 that was optimized for expression in E. coli. The part contains the S219V anti-self cleavage mutation.<br />
<br />
The TEV Protease (also known as Tobaco Edge Virus nuclear inclusion a endopeptidase) is a highly sequence specific cysteine protease from the Tobacco Edge Virus (TEV). The protease is highly sequence specific. The consensus sequence for the cut is ENLYFQ\S with \ denoting the cleaved peptide bond. This sequence can be found in the part [http://parts.igem.org/Part:BBa_K1319016 K1319016]. <br />
<br />
ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
<br />
The TEV protease is commonly used as a biochemical tool to cleave affinity tags from purified proteins like [http://parts.igem.org/Part:BBa_K1319007 His-Tags]. The high specifity makes the protease relatively non-toxic ''in vitro'' and ''in vivo''. The molecular weight of the TEV protease is 27 kDa.<br />
<br />
===Usage and Biology===<br />
<br />
The TEV Protease was used and characterizes in the [http://parts.igem.org/Part:BBa_K1319008 K1319008] construct.<br />
<br />
To characterize the TEV protease we used the fusion protein [http://parts.igem.org/Part:BBa_K1319014 K1319014]. This fusion protein contains GFP ([http://parts.igem.org/Part:BBa_E0040 E0040]) bound to a dark quencher ([http://parts.igem.org/Part:BBa_K1319002 REACh2/K1319002]) over a [http://parts.igem.org/Part:BBa_K1319016 linker] which includes the TEV protease cleavage site. If the TEV protease successfully cuts the linker, GFP and its quencher would separate and the FRET (Förster Resonance Energy Transfer) system would be shut down. This would result in an increased GFP fluorescence.<br />
<br />
To demonstrate this behaviour a double plasmid system was designed using the biobrick K1319013 in a pSB3K3 backbone and K1319008 in a pSB1C3 backbone. Also [http://parts.igem.org/Part:BBa_I20260 I20260] was used as a positive control because it produces the same GFP as used in the fusion protein and is regulated by the same promoter, RBS and Terminator on the same plasmid backbone. [http://parts.igem.org/Part:BBa_B0015 B0015] was used as negative control. Induction of the double plasmid constructs occured after 2 h with 50 µl of 100mM IPTG in a 50 ml shake flask culture. <br />
<br />
<center><br />
<div class="figure" style="float:{{{align|center}}}; margin: 0px 10px 10px 0px; border:{{{border|0px solid #aaa}}};width:{{{width|800px}}};padding:10px 10px 0px 0px;"><br />
{|<br />
|<html> <img src="https://static.igem.org/mediawiki/2014/3/3e/Aachen_Graph2_14.PNG" width="800px"></html><br />
|-<br />
|'''{{{title|Comparison of the fluorescence adjusted for OD of I20260, B0015 and the double plasmid system K1319014 + K1319008}}}'''<br />{{{subtitle|After induction with IPTG after 2 h the double plasmid system produced a fast fluorescence response with an over 10-fold increase compared to the non induced state. I20260 served as positive control and B0015 as negative control.}}}<br />
|}<br />
</div><br />
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The increase in fluorescence after induction with IPTG is clear sign of funtional expression of the TEV protease. The difference between not induced and induced plasmid is proof that the increase in fluorescence is only attributed to the successful cleavage of the linker. Therefore this is proof of a functional expression of the TEV protease after induction with IPTG.<br />
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Furthermore we validated the used plasmid with a Check PCR with one primer binding upstream on the plasmid backbone and one specifically in the insert.<br />
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|<html> <img src="https://static.igem.org/mediawiki/2014/0/0c/Aachen_K1319008_Gel_Check_PCR.png" width="500px"></html><br />
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|'''{{{title|Check PCR for K1319008}}}'''<br />{{{subtitle|The length of the PCR product matches the length of the control plasmid.}}}<br />
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This validates that the construct is indeed the TEV protease and thereby the functionality of the TEV protease is established. The construct K1319008 was also sequenced. The sequencing data can be seen in the parts registry [http://parts.igem.org/Part:BBa_K1319008 here].<br />
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{{Team:Aachen/BlockSeparator}}<br />
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==[http://parts.igem.org/Part:BBa_K1319008 K1319008]==<br />
<span class="anchor" id="partsK1319008"></span><br />
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=== IPTG-induced and T7-driven expression of TEV protease ===<br />
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This protein generator produces TEV protease when induced with IPTG in a DE3 strain.<br />
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===Usage and Biology===<br />
More information about the characterization of this part is available on the parts registry page for [http://parts.igem.org/Part:BBa_K1319004 K1319004]. This part was alos used in the validation and characterization of the parts [http://parts.igem.org/Part:BBa_K1319001 K1319001] and [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
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This biobrick is used in our [https://2014.igem.org/Team:Aachen/Project/FRET_Reporter REACh construct].<br />
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{{Team:Aachen/BlockSeparator}}<br />
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==[http://parts.igem.org/Part:BBa_K1319010 K1319010]==<br />
<span class="anchor" id="partsK1319010"></span><br />
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=== Constitutive expression of K1319000 ===<br />
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This part expresses K1319000 behind a J23101 constitutive promoter.<br />
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{{Team:Aachen/BlockSeparator}}<br />
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==[http://parts.igem.org/Part:BBa_K1319011 K1319011]==<br />
<span class="anchor" id="partsK1319011"></span><br />
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=== Constitutive expression of K1319001 ===<br />
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This part expresses [http://parts.igem.org/Part:BBa_K1319001 K1319001] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
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{{Team:Aachen/BlockSeparator}}<br />
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== [http://parts.igem.org/Part:BBa_K1319012 K1319012] ==<br />
<span class="anchor" id="partsK1319012"></span><br />
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=== Constitutive expression of K1319002 ===<br />
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This part expresses [http://parts.igem.org/Part:BBa_K1319002 K1319002] behind a [http://parts.igem.org/Part:BBa_J23101 J23101] constitutive promoter.<br />
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{{Team:Aachen/BlockSeparator}}<br />
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== [http://parts.igem.org/Part:BBa_K1319013 K1319013] ==<br />
<span class="anchor" id="partsK1319013"></span><br />
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=== Constitutive expression of GFP-REACh1 fusion protein ===<br />
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This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319001 K1319001] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
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===Usage and Biology===<br />
More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319001 K1319001].<br />
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{{Team:Aachen/BlockSeparator}}<br />
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== [http://parts.igem.org/Part:BBa_K1319014 K1319014] ==<br />
<span class="anchor" id="partsK1319014"></span><br />
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===Constitutive expression of GFP-REACh2 fusion protein===<br />
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This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319002 K1319002] fusion protein (GFP-REACh1) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter. <br />
[http://parts.igem.org/Part:BBa_K1319002 K1319002] is a '''dark quencher''' that eliminates the fluorescence of the GFP-domain by Förster Resonance Energy Transfer (FRET), but does not exhibit strong fluorescence itself.<br />
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===Usage and Biology===<br />
The two domains can be separated from each other via a TEV protease cleavage site in the linker.<br />
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More information about the characterization of this part can be found on the part page of [http://parts.igem.org/Part:BBa_K1319002 K1319002].<br />
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{{Team:Aachen/BlockSeparator}}<br />
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== [http://parts.igem.org/Part:BBa_K1319015 K1319015] ==<br />
<span class="anchor" id="partsK1319015"></span><br />
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===Constitutive expression of GFP-EYFP fusion protein===<br />
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This part expresses a [http://parts.igem.org/Part:BBa_E0040 E0040].[http://parts.igem.org/Part:BBa_K1319000 K1319000] fusion protein (EGFP-EYFP) behind a [http://parts.igem.org/Part:BBa_J23101 J23101] promoter.<br />
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{{Team:Aachen/BlockSeparator}}<br />
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== [http://parts.igem.org/Part:BBa_K1319016 K1319016] ==<br />
<span class="anchor" id="partsK1319016"></span><br />
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===TEV protease cleavage site===<br />
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This sequence codes for a [http://parts.igem.org/Part:BBa_K1319004 TEV protease] cleavage site.<br />
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ENLYFQ\S is the optimal cleavage site with the highest activity but the protease is also active to a greater or lesser extent on a range of substrates. The highest cleavage is of sequences closest to the consensus EXLYΦQ\φ where X is any residue, Φ is any large or medium hydrophobic amino acid and φ is any small hydrophobic amino acid.<br />
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===Usage and Biology===<br />
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A TEV protease is available codon optimised for ''E. coli'' with the part [http://parts.igem.org/Part:BBa_K1319004 K1319004].<br />
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==[http://parts.igem.org/Part:BBa_K1319017 K1319017]==<br />
<span class="anchor" id="partsK1319017"></span><br />
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=== LasI induced iLOV ===<br />
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This device produces iLOV (K660004) in response to a quorum sensing input.<br />
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{{Team:Aachen/BlockSeparator}}<br />
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==[http://parts.igem.org/Part:BBa_K1319020 K1319020]==<br />
<span class="anchor" id="partsK1319020"></span><br />
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===Translational unit of mRFP-galectin3-His===<br />
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This part is a translational unit of a mRFP-galectin-3-his (B0032.E1010.K1319003.K1319016.B0015)<br />
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===Usage and Biology===<br />
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For more information about the characterization of this part check out [http://parts.igem.org/Part:BBa_K1319003 K1319003].<br />
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{{Team:Aachen/BlockSeparator}}<br />
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==[http://parts.igem.org/Part:BBa_K1319042 K1319042]==<br />
<span class="anchor" id="partsK1319042"></span><br />
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===IPTG inducible iLOV===<br />
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This part can be used for IPTG-induced expression of K660004 (iLOV).<br />
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{{Team:Aachen/BlockSeparator}}<br />
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===iGEM Team Aachen Biobrick overview===<br />
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<groupparts>iGEM14 Aachen</groupparts><br />
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{{Team:Aachen/Footer}}</div>R.hanke