Team:Berlin/Project/Results

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         Results<br/>
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          <strong>iGEM Berlin 2014: A remote control for E. coli</strong><br/>
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          The following animaton visualizes the concept of using ferritin iron storage proteins as a magnetism mediating module.<br/>
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          <iframe src="//player.vimeo.com/video/108832894?byline=0&amp;portrait=0&amp;color=0ecd28" width="700" height="394" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>
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          This animation was developed by Florian Renner who is an science interested and very talented grafic designer based in munich. We thank Florian for his amazing job he did voluntarily for iGEM Berlin helping us to overcome the limitations of our budget.
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          As the first iGEM team from Berlin to take part in the competition, we decided to construct a simple BioBrick that enables synthetic biologists to remotely control the movement of the laboratory workhorse Escherichia coli. A seemingly simple and non-invasive mechanism for this remote control is the use of magnetic fields, which enable a vast variety of applications. In nature, these are already used by several mammals, as well as bacteria for orientation.
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          Remote-controlled E. coli cells could be used as “bacteria-based nanorobots” in order to maneuver them live in the intestine - targeting diseased tissue or even tumors. Combined with BioBricks from other iGEM teams a local, site-directed treatment of intestine cancer is envisioned[1]. Therefore, we work with the probiotic E. coli strain Nissle 1917, which already has an 80 year history as a treatment for chronically inflamed intestine tissue and is sold commonly as “Mutaflor”[2].
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          Our experiments should enable us to construct simple BioBricks capable to produce a diverse set of nanoparticles, including quantum dots, magnetic nanoparticles, semiconductor nanoparticles, noble metal nanoparticles and many more[3]. For example, cheap and efficient production of magnetic nanoparticles could be used in hyperthermal cancer therapy. Subsequently, we would like to investigate if our method can also be adapted to the synthesis of rare earth metals, which despite their abundance are not mineable. This would offer an alternative to the environmental hazardous mining operations that are common today.
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          A remote control for E. coli will enable a whole variety of application relevant for bioprocess engineering. Therefore one can imagine neglecting centrifugation for cell separation - simply use a magnet. Also, it should be possible to use high frequent oscillating magnetic fields for cell lysis or even use rotating magnetic fields for self-stirring cultures in bioreactors solving scale up limiting issues like tip speed.
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          Nature is the world’s most skilled engineer and has naturally occurring magnetotactic bacteria such as Magnetospirrilium magneticum. Under certain conditions, these organisms form magnetosomes, which are chains of magnetite nanoparticles. These function as an intracellular compass for the cell and even allow them to orientate along earth’s weak magnetic field.
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          As previous iGEM teams have shown, synthesizing fully functional magnetosomes in E. coli is highly difficult as more than 60 highly regulated genes are involved[4]. The Berlin iGEM team came up with an alternative strategy that does not rely on the formation of magnetosomes.
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          By knocking out the iron efflux transporter gene FieF and the iron uptake suppressor Fur, we want to increase the total iron level of the cytosol. By sequestering iron in a ferritin protein, iron crystals are formed and the cell is detoxified. In order to create ferromagnetic crystals, we will use intensive high-throughput growth medium optimization to discover the best conditions for the formation of magnetic nanoparticles in E. coli.
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          We will work with other metal binding proteins such as metallothioneins and phytochelatin synthases in order to achieve nanoparticle synthesis. Once we have discovered the best way to magnetize E. coli bacteria, we will build and characterize suitable BioBricks that can be used by any research lab or iGEM team in the world in order to remote control the cellular movement.
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        <strong>Involving the Community </strong><br/>
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          Although there are several scientific institutions located in Berlin which are conducting research in synthetic biology, there has never been an iGEM team from Berlin before. This is even more surprising as Berlin with its vibrant bio-arts and diy-biology community seems to be the perfect location for successful iGEM projects.
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          As an interconnected workforce, our team incorporates members from various scientific, cultural and creative backgrounds, which makes our team able to address complex issues from various persepctives. So far, iGEM Berlin consists of students from biotechnology, history, design, medicine, theoretical physics, informatics, and more.
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          So far our diverse team has been able to make valuable connections into the bio-arts scene of Berlin, working together with think tanks such as the Hybrid Plattform, as well as EU advisor Markus Schmidt and his Biofaction AG. Supported by the Hybrid Plattform, we organized a science and design workshop event on the 8/9.08.2014. During this event we conducted a series of short presentations about synthetic biology, as well as about prototyping and speculative design. Participants from different backgrounds designed and constructed interactions, which deal with the idea of a biological modularity. The resulting interactions addressed currently debating issues about the future of syntheic biology applications. Surpisingly the participants focused on topics like performance enhancement, transhumanism, alternative materials and housing as well as standardiziation. By explaining the basic principles of synthetic biology and approaching synthetic biology with a limited complexity synthetic biological speculation became easily accessible and reached wide variety of people.
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          In the beginning of September, we collaborated with the artists and scientists from the c-lab collectiv (UK) as well as the Artlaboratory - a berlin bio-arts space. In the Synthetic Biology Workshop artists and other people were introduced to synthetic biology and performed their own cloning experiment. The whole event came to an end in Berlins first Science Café event for synthetic biology organized by the iGEM Berlin Team. During this event, we had speakers from different backgrounds and we discussed chosen aspects of synthetic biology with participants openly over drinks and food. The artist Ping Lui from Cologne presented his speculative design of an oracle based on magnetotactic bacteria. Rüdiger Trojok, a infamous German biohacker presented his current project, Howard Boland shared his bioart projects and former iGEM involvement with us and Johann from our team gave a short presentation about iGEM and our project. These events were designed to have a high impact on the German understanding of synthetic biology and were a major success in Berlin.
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          One of the current major issues in synthetic biology is the laws and regulations concerning patents. iGEM generally refuses patents and promotes the idea of open source biology. However, as the success and applicability of synthetic biology depend on industry investments, there has to be a compromise in policy regulations. To discuss this topic in detail we teamed up with patent lawyers from the Adares Patentanwältekanzlei as well as Biocommons (Creative Commons license model for Synbio) activist Rüdiger Trojok to discuss patenting and fundamental principles of intellectual property.
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          In summary, we used art events and practical workshops to confront the German public with issues of synthetic biology. Furthermore, our project of creating a remote control for E. coli bears various practical applications as well as expands the possibilities of future functional biological systems.
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        <strong>References </strong><br/>
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          [1] https://2012.igem.org/Team:Penn/ProjectResults (11.07.2014)<br/>
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          [2] http://www.mutaflor.de/cms/ (11.07.2014)<br/>
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          [3] Park, T. J., Lee, S. Y., Heo, N. S. and Seo, T. S. (2010), In Vivo Synthesis of
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          Diverse Metal Nanoparticles by Recombinant Escherichia coli. Angew. Chem.
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          Int. Ed., 49: 7019–7024.<br/>
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          [4] https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit (11.07.14)<br/>
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      <strong>3.1 Basics</strong>
 
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      <strong>Advantages and basic principles of using magnetic fields</strong><br/>
 
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      In order to control E. coli remotely, we decided to use magnetic fields because of a few key reasons.
 
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      First, magnetic fields allow to control the cells by an external force field which means that cells do not have to be directly treated or media conditions have to be changed as it is the case in many chemotaxis assays.
 
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      Second, magnets are widely spread and electro magnets easily built as you can see in this video:
 
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      https://www.youtube.com/watch?v=wzXRFp0DDrU
 
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      The accessibility and safety of magnetic fields opens up the field for new innovation and ideas using remote controlled bacteria.
 
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      Third, magnetic fields do have a high energy density and are way more viable to transfer energy than other energy fields like electrical fields. However, the magnetic moment of an atom is the product of of the atoms orbital angular momentum and its electron spins. Atomic magnetism is based on unfilled electron orbits.
 
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      Nobel gases and alkyl halogenide are non-magnetic or “diamagnetic”. Other elements like metals may have an increased magnetic moment as long as their electron orbit are unfilled, meaning they are unbound. Mn2+, Fe3+ have a magnetic moment of about 5 µB, Cr2+, Mn3+, Fe2+ and Co3+ have a magnetic moment of 3 µB. [http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000000626/2_f-Kapitel1.pdf?hosts=]
 
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      Because of the variety of atomar magnetic properties, magnetism can be divided into different forms by looking at apparent forces and effects.
 
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      There is diamagnetism, antiferromagnetism, paramagnetism, ferrimagnetism, superparamagnetism and Ferromagnetism. Ferromagnetic forced are about 1000 times stronger than super paramagnetic forces. However, it turns out that creating ferromagnetic particels or residues is very difficult (see magnetite formation in magnetospirrilium bacteria). Also note that in a lot of biological papers, people tend to mix e.g. super paramagnetism with ferromagnetism [Various magnetic Nanoparticles Paper].
 
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      Magnetic properties are depended on the crystal structure of a metall particle. The magnetic moment is proportional to the aligment of the electron spins within an component. If electron spins are alignt magnetism can be observed. However on a nanoscale real ferromagnetism can only be noted after a critical particle size of 128 nm.[An-Hui Lu, An-Hui; E. L. Salabas; Ferdi Schüth (2007). "Magnetic Nanoparticles: Synthesis, Protection, Functionalization, and Application". Angew. Chem. Int. Ed. 46 (8): 1222–1244]
 
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      This is due to thermal fluctations that prevent the alignment of electron spins and therefore prevent the development of sufficient magnetic moments. Because of this phenomena all meassurements for magnetism are usually conducted at very low temperatures.
 
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      All magnetic effects that are observed for particles between 1 nm to 100 nm are considered superparamagnetic. Superparamagnetic nanoparticles only show magnetic effects when an external magentic field is applied. This field aligns the electron spins in the particle resulting in an magnetic moment mediated by an external magnetic field.
 
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      [Picture Atomarer Magnetismus]
 
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      <strong>3.2 Iron Homeostasis, E. coli Nissle and Knockouts</strong><br/>
 
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      As an essential element for almost all life iron is often necessary for the activity of certain proteins but can also be problematic because of its toxicity and poor solubility. Organisms have evolved to regulate their iron effectively and as iron in an organism is usually supplied in a limited condition pathogens evolved iron aquisation systems to outcompete other microorganism.
 
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      A very efficient iron aquisition system, which bacteria inlcuding E. coli use are siderophore mediated transport pathways. 
 
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      [Simon C. Andrews, Andrea K. Robinson, Francisco Rodriguez-Quinones; School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, UK; 2003]
 
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      Iron E.coli Link                                                 
 
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      <strong>3.3 Ferritin Strategy</strong><br/>
 
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      Ferritins as scaffolds for magnetic nanoparticle synthesis
 
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      In order to protect themselves against radical stress as well as the lack of co-factors, organisms evolved a high regulated and stable iron acquisition system, also known as iron homeostasis. [Iron Homeostasis of E. coli] To put it in a nutshell iron is taken up by iron transporters or siderophore mediated mechanism and is transporters through the outer membrane into the periplasm, in the periplasm it “changes” transporters and is transported through the inner membrane into the cytoplasm. It always gets released as Fe2+ into the cytoplasm.
 
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      In order to protect themselves against superoxide formation by the Fenton-Reaction a lot of organisms evolved iron storage proteins. One of the superfamily of these proteins is called ferritin. These ferritins are highly symmertrical protein nanocages synthesizing iron concentrates required for cells to make cofactors of iron proteins. Through their ability to cage in biominerals they were the first and most obvious scaffolds for the synthesis of magnetic nanoparticles. These natural metal storage homomers form solid particles inside of their protein shell. Ferritins are ubiquitous in nature and protect the cell from redox stress through iron overload and from iron deficiency. They consist of 24 protein subunits which can consists of a heavy (catalytical active) and light chain (catalytical inactive but stabilizing). Caged ferritin minerals can  have diameters as larg as 8-12 nm with thousands of iron and oxygen atoms. Between species ferritins have different affinity for phosphate. Phosphate is low in animal ferritin iron minerals (Fe:P = 8:1) whereas in bacterial and plant ferritins iron minerals are usually occurring in higher relations (Fe:P = 1:1).[1]
 
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      Mössbauer studies on the superparamagnetic character of bacterioferritins (bfr) revealed that the phosphate concentration in a ferritin iron mineral reduces superparamegntic effects heavily due to replacement of the iron bridges between the iron atoms with phosphate. As these bridges have a lower exchange constant the order temperature is reduced further. [2]
 
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      The hollow ferritin nanocages are used in the chemical industry as scaffolds for synthesis of magnetite particles as well as for delivery of magnetic resonance imaging (MRI) contrast agents, drug delivery and catalysis.
 
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      [1]<br/>
 
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      Ferritins for Chemistry and for Life.<br/>
 
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      Elizabeth C Theil, Rabindra K Behera, Takehiko Tosha
 
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      Children's Hospital Oakland Research Institute, University of California, Berkeley ; Department of Nutritional Science and Toxicology, University of California, Berkeley.
 
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      Coordination Chemistry Reviews (Impact Factor: 11.02). 01/2013; 257(2):579-586. DOI: 10.1016/j.ccr.2012.05.013
 
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      [2] Mössbauer studies of superparamagnetism in E. coli; Hawkins, C.; Williams, J. M.
 
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      Journal of Magnetism and Magnetic Materials, Volume 104, p. 1549-1550
 
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      <strong>iGEM Berlin Ferritin Library</strong><br/>
 
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      During our summer we collected a variety of ferritin-coding sequences from bacterial and mammalian sources. As ferritins are common among all organisms we categorized our ferritins in three major groups. (Table)
 
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      <strong>3.4 Inclusion body Strategy</strong><br/>
 
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      By talking to the Fussenegger group from the ETH Zurich, who published the superparamagnetism paper about ferritins we got the tip to look for another strategy as they experienced the limitations of ferritins. [1]
 
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      For this reason, we came up with a different strategy. Park et al came up with a different strategy for the synthesis of biogenic nanoparticles in E. coli. [2] A strategy where they produced impressive results showing one strategy to synthesize a whole array of diverse nanoparticles with E. coli. (See Figure 1)
 
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      Two heavy metal binging proteins were combined and co-expressed on one plasmid. Peptides called phytochelatins are produced in fungus and plants to detoxify the cell from harmful heavy metals. Structurally phytochelatins are (gamma-Glu-Cys)n-Gly (n=2-7) peptides and function as metal ion accumulators through formation of peptide-metal conjugates. In this study the phytochelatin synthase from Arabidopsis thaliana (Columbia leave) was used (ATPCS). The other peptid that was used in combination with ATPCS was a metallothionein from Pseudomonas Putida KT2240 strain (PPMT). Metallothioneins are low-molecular proteins with a high content of cysteine and bind well cadmium, zinc, nickel and copper.
 
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      For expression of ATPCS a trc promotor was used while PPMT was expressed using a T5 promotor. After co expressing both proteins in an standard E. coli strain(DH5alpha) for 4 h the culture broth was centrifuged and fresh metal rich LB media added. (1 – 5 mM of corresponding final metal concentration (see table 1.).
 
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      After further incubation at 37°C for about 6 - 12 hours the cultures and the biogenic synthesized nanoparticles can be harvested.
 
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      Park et al reported further that by incubating these ATPCS and PPMT co-expressing in 1.0 mM FeSO4 and MnCl2 magnetic nanoparticles where obtained and cell moved by high magnetic fields (see figure 2).
 
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      [1] Kim T, Moore D, Fussenegger M. Genetically programmed superparamagnetic
 
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      behavior of mammalian cells. J Biotechnol. 2012 Dec 31;162(2-3):237-45. doi:
 
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      10.1016/j.jbiotec.2012.09.019. Epub 2012 Oct 2. PubMed PMID: 23036923.
 
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      [2] Park, T. J., Lee, S. Y., Heo, N. S. and Seo, T. S. (2010), In Vivo Synthesis of Diverse Metal Nanoparticles by Recombinant Escherichia coli. Angew. Chem. Int. Ed., 49: 7019–7024. doi: 10.1002/anie.201001524
 
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      [3] Wu CM, Lin LY. Immobilization of metallothionein as a sensitive biosensor chip
 
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      for the detection of metal ions by surface plasmon resonance. Biosens
 
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      Bioelectron. 2004 Nov 1;20(4):864-71. PubMed PMID: 15522603.
 
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      <strong>3.5 Magnetic modelleing (Andres)</strong><br/>
 
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      <div class="project-number">3</div><div class="project-headline-float"><h2 class="green-text project-headline"> Our Results</h2></div>
 
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              Results, jo!
 
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                <h2 class="sub-content-project-headline">Week 1: 02.04.2014 – 06.04.2014</h2>
 
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                    Cultivation of E. coli Nissle 1917<br/>
 
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                    Genomic DNA extraction of E.coli Nissle strain<br/>
 
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                    Production of BfR, FTNA1 and FTNA2<br/>
 
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                    Restriction digest<br/>
 
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                    PCR Purification<br/>
 
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                    Ligation Assay<br/>
 
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                    Transformation into DH5α-Cells<br/>
 
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                <h2 class="sub-content-project-headline">Week 2: 07.04.2014 – 13.04.2014</h2>
 
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                    Colony PCR to check the results<br/>
 
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                    Bfr, FTNA 1, FTNA 2 primar designed for amplification<br/>
 
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                    Transformation of pQE_80L into DH5α<br/>
 
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                    Cultivation of BfR, FTNA 1, FTNA 2 in LB<br/>
 
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                <h2 class="sub-content-project-headline">Week 3: 14.04.2014 – 20.04.2014</h2>
 
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                    Miniprep of the cells  from Week 2 <br/>
 
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                    DNA concentration determination and sequencing<br/>
 
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                    Expression of BfR, FTNA 1, FTNA 2 and induction with IPTG<br/>
 
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                    Production of a Mutaflor-Supression culture and streaking<br/>
 
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                <h2 class="sub-content-project-headline">Week 4: 21.04.2014 – 27. 04.2014 </h2>
 
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                    Minirep
 
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                <h2 class="sub-content-project-headline">Week 5: 28.04.2014 – 04.05.2014</h2>
 
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                    PCR Plasmid/Primar and Parameter check with Q5 Polymerase and Phusion Polymerase<br/>
 
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                    Miniprep of [pKD46+ DH5α] and [pKD4 + DH5 α]<br/>
 
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                    Genomic DNA extraction from Pseudomonas putida<br/>
 
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                    Enzyme digestion of different plasmids<br/>
 
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                <h2 class="sub-content-project-headline">Week 6: 05.05.2014 – 11.05.2014</h2>
 
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                    Preculture of strains from Budisa strain databse in LB medium and Midiprep<br/>
 
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                    Canamycin cassette PCR of pKD4<br/>
 
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                                        Restriction digest of Plasmid pKD4 and pKD46v<br/>
 
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                <h2 class="sub-content-project-headline">Week 7: 12.05.2014 – 18.05.2014</h2>
 
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                    Biotransformation of Ferritin and pKD46 in Nissle and DH5 α strains
 
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                <h2 class="sub-content-project-headline">Week 8: 19.05.2014 – 25.05.2014</h2>
 
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                    Gel extraction of FieF PCR<br/>
 
-
                   
 
-
                    Gene Knockout of FieF in [RV + pKD46] and [WM10+pKD46]<br/>
 
-
                   
 
-
                    Transformation of pKD46 in Nissle and MG 1655<br/>
 
-
                   
 
-
                    PCR of ATPCS and PPMT<br/>
 
-
                   
 
-
                    Digestion of pQE_80L for cloning<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 9: 26.05.2014 – 01.06.2014</h2>
 
-
                    Production of LB plates<br/>
 
-
                   
 
-
                    AMB-1 and Microfluidic Chip were picked up from Max-Plank Institute<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 10: 02.06.2014 – 08.06.2014</h2>
 
-
                    Colony PCR and analytical gel electrophoresis for identifying the right clones<br/>
 
-
                   
 
-
                    PCR of ATPCS and PPMT to identify the correct amplification parameter.<br/>
 
-
                   
 
-
                    Colony PCR for Knockout.<br/>
 
-
                   
 
-
                    PCR of ATPCS and PPMT with Q5 High Fidelity Mastermix.<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 11: 09.06.2014 – 15.06.2014</h2>
 
-
Refine the PCR of PPMT and ATPCS with DMSO<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 12: 16.06.2014 – 22.06.2014</h2>
 
-
PCR amplification of ATPCS from cDNA<br/>
 
-
Colony PCR to seperate cells with FieF Knockout<br/>
 
-
Restrcition digest of pQE_80L and ATPCS-PCR Fragment<br/>
 
-
Test expression of Ferritin in RV308 (pSB1C3_Ferritin) and Nissle (pSB1C3_Ferritin)<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 13: 23.06.2014 – 29.06.2014</h2>
 
-
Amplification of ATPCS from cDNA and PCR Purification<br/>
 
-
Preparation of Nissle, Nissle + Ferritin, RV 308, Rv 308 + Ferritin pre-cultures<br/>
 
-
Transformation of human Ferritin on PC514 to Nissle and RV 308<br/>
 
-
Induction of Ferritin expression with IPTG<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 14: 30.06.2014 – 06.07.2014</h2>
 
-
Colony PCR and Ligation of ATPCS<br/>
 
-
Knockout of FieF and FUR in RV308 and Nissle<br/>
 
-
Transformation of  RFP device and Ferritin in RV308, Nissle and WM110 strains.<br/>
 
-
PCR amplification of knockout cassette FUR/FieF<br/>
 
-
Expression of RV308 (RFP) and RV308 (RFP + Ferritin) after Induction with IPTG<br/>
 
-
              </div>
 
-
                <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 15: 07.07.2014 – 13.07.2014</h2>
 
-
Preparation of cryostocks and pre-cultures of ATPCS clone 1-10, WM 110, RV 308, Nissle<br/>
 
-
PCR of PPMT with goTaq Polymerase<br/>
 
-
Miniprep of ATPCS clone number 3<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 16: 14.07.2014-20.07.2014</h2>
 
-
Midiprep of pQE_80L , PMA-T_PPMT, pKD46  <br/>
 
-
Digestion of pQE_80L with Hind III and SacI<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 17: 21.07.2014-27.07.2014</h2>
 
-
Miniprep and Restriction of pBADex-mYFP Venus (Amp); pEx-HisII (Amp); pJS418_Phagemid (dummy) (Cm)<br/>
 
-
Ligation of PPMT Fragment from pMAC_PPMT into pEX_HisII<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 18: 28.07.2014-3.08.2014</h2>
 
-
Degradation test of prepped TB-Expression Plasmids <br/>
 
-
Transformation of pEX_His_PPMT in MG1655, DH5α, DH10B strains<br/>
 
-
Colony PCR of the PPMT clones<br/>
 
-
Miniprep and Sequencing of pEX_His_PPMT in DH5 α<br/>
 
-
Ligation of ATPCS PCR Fragment into pQE_80 L<br/>
 
-
Colony PCR of pQE_80L_ATPCS<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 19: 04.08.2014 -10.08.2014</h2>
 
-
Preculture of ATPCS clones for Sequencing <br/>
 
-
PCR of BamHI_PPMT_GS, GS_ATPCS_HindIII, BamHi_HuFerritin_HindIII<br/>
 
-
Transformation of  BFR M52H in DH10B.<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 20: 11.08.2014 - 17.08.2014</h2>
 
-
Prepare chemically competent cells<br/>
 
-
Generation of Heme-free BFR by Site-directed Mutagenesis<br/>
 
-
Digestion of various PCR fragements for cloning into pQE_80L<br/>
 
-
Colony PCR of pQE_80L<br/>
 
-
Clone Sequencing<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 21: 18.08.2014 – 24.08.2014</h2>
 
-
SDS-PAGE with Coomasie staining for identification of protein expression<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 22: 25.08.2014 – 31.08.2014</h2>
 
-
Calibration curve for iron concentration measurement<br/>
 
-
              </div>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 23: 15.09.2014 – 21.09.2014</h2>
 
-
Preparing cultures for fluorescence microscopy<br/>
 
-
Constructing pQE_80L_T5_ATPCS_lac_PPMT<br/>
 
-
Digest and Dephosphorylation of vector pQE_80L_ATPCS<br/>
 
-
PCR of Biobrick parts (BB0-BB3)<br/>
 
-
Digest of pSB1C3-Ferritin<br/>
 
-
              </div> 
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 24: 22.09.2014 – 28.09.2014</h2>
 
-
Preparation of pre-cultures<br/>
 
-
Checking insertion of gene in ATPCS_PPMT clones by colony PCR<br/>
 
-
Digestion of miniprepped pSB1C3_Ferritin (Calgary) for extraction of vector for Biobrick preparation<br/>
 
-
Mutagenesis of ATPCS in different plasmid_ATPCS construct<br/>
 
-
Berlin Vector – pQE-80L-JBFS- huFerritin Assembly PCR<br/>
 
-
Isolation of plasmid DNA of pQE80L_ATPCSMut_GS_PPMT and pQE80L_ATPCS_PPMT <br/>
 
-
Repeat PCR of Biobricks<br/>
 
-
              </div> 
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 25: 29.09.2014 – 05.10.2014</h2>
 
-
Digestion of Biobrick parts<br/>
 
-
Ligation of Biobrick parts with pSB1C3 backbone<br/>
 
-
Plasmid Digestion and checked with PCR<br/>
 
-
              </div> 
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">Week 25 06.10.2014 – 12.10.2014</h2>
 
-
                  Colony PCR<br/>
 
-
                  Miniprep of cultures and preparation of sequencing samples<br/>
 
-
                  Preculture of knockouts<br/>
 
-
                  PCR of pSB1C3 backbone<br/>
 
-
                  Extraction of PCR Product (pSB1C3 linearised)<br/>
 
-
                  Iron concentration measurement in knockout strains<br/>
 
-
              </div>                                                                                                           
 
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<!--- ////////////////// Notebook////////////////// -->
 
-
<div class="container">
 
-
 
 
-
  <div class="row">
 
-
    <div class="col-xs-12">
 
-
      <div class="project-number">5</div><div class="project-headline-float"><h2 class="green-text project-headline"> Lab Journal</h2></div>
 
-
    </div>
 
-
  </div>
 
-
 
 
-
  <div class="row">
 
-
    <!--<div class="col-sm-4 hidden-xs">
 
-
          <img src="img/blog/Team_Berlin_bacteria.png" class="img-responsive" style="margin: 0 auto;"/>
 
-
    </div>-->
 
-
    <div class="col-xs-12 col-sm-12 blog-text" style="margin-bottom:40px;">
 
-
      <p>   
 
-
        <a name="notebook">&nbsp;</a>
 
-
              <div class="sub-content-project">
 
-
                <h2 class="sub-content-project-headline">04/02 Wednesday - Cultivating E. coli Nissle 1917</h2>
 
-
                LB plates were produced without antibiotic. Therefore 10 ml MQ-H<sub>2</sub>O were sterile filtered in 15 ml falcon tube. 1 capsule Mutaflor 331800 was solved in the sterile water.
 
-
                The E. coli Nissle solution was incubated at 37°C and 200 rpm for 1 h and crossed out at 4 plates to get different dilution of cells.
 
-
              </html>
 
-
                {| class="wikitable"
 
-
                |-
 
-
                ! dilution !! E. coli Nissle solution !! H<sub>2</sub>O !! dilution factor
 
-
                |-
 
-
                | I || 2 µl || 1998 µl || 1:10<sup>3</sup>
 
-
                |-
 
-
                | II || 100 µl from dilution I || 900 µl ||1:10<sup>4</sup>
 
-
                |-
 
-
                | III || 10 µl from dilution II || 990 µl || 1:10<sup>5</sup>
 
-
                |}
 
-
            <html>
 
-
            </div> 
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 04/03 Thursday - Genomic DNA extraction of ECN - first step </h2>
 
-
 
-
            For extraction of the genomic DNA of E. coli Nissle, 2 E. coli colonies were oicked from LB plate (dilution 1:10<sup>3</sup>) and used for inocculation of 6 ml LB precultures. These were grown over night at 37°C and 200 rpm.
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 04/04 Friday - Genomic DNA extraction of ECN - second step</h2>
 
-
 
-
            For preperation of the genomic DNA 1 ml of each preculture was taken and a genomic extraction performed using the Wizard Genomic DNA purification Kit. See instructions of the purification Kit by Promega. Genomic DNA was stored at 12°C in fridge.
 
-
 
-
            As E. coli Nissle is a natural organism without resistence genes both precultures were streaked out on LB, LB+KAN and LB+AMP. All plates were incuvated over the weekend at 37°C.
 
-
 
-
            DNA concentration was meassured by 260 nm using Goldi. DNA was diluted 1:40 in a UV cuvette and DNA absorption meassured at 260/28 nm in goldi.<br/>
 
-
'''For genomic DNA:'''
 
-
</html>           
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | 1: || 1390 ng/µl
 
-
            |-
 
-
            | 2: || 988 ng/µl
 
-
            |}
 
-
<html>
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 04/05 Saturday - Genomic DNA extraction of ECN - results </h2>
 
-
 
-
            Bacteria growth only on LB plate indicates that there was no contamination with AMP or KAN restinatant E. coli. This doesn´t mean that there is no contamination at all. See for sure on PCR.
 
-
<br/>
 
-
</html> 
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! LB !! LB+KAN !! LB+AMP
 
-
            |-
 
-
            | + || - || -
 
-
            |}
 
-
            <html> 
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">                   
 
-
            <h2 class="sub-content-project-headline"> 04/06 Sunday </h2>
 
-
</html>
 
-
 
-
            <strong>Production of BfR, FTNA1 and FTNA2</strong>
 
-
            <em>Restriction digest</em>
 
-
            After 2 purifications of plasmids:
 
-
<html>           
 
-
<br/>
 
-
</html>
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | p1 || 84ng/µl || 10µl
 
-
            |-
 
-
            | p2 || 72,2ng/µl || 10µl
 
-
            |-
 
-
            | p3 ||  54,8ng/µl || 23µl
 
-
            |}
 
-
 
-
            <strong>Restriction program</strong>
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            |  || 1x || 4x
 
-
            |-
 
-
            | plasmid P2 || 3µl || 12µl
 
-
            |-
 
-
            | BamHI (FD) ||  1µl || 4µl
 
-
            |-
 
-
            | HindIII (FD) ||  1µl || 4µl
 
-
            |-
 
-
            | Buffer (FD) ||  2µl || 8µl
 
-
            |-
 
-
            | H<sub>2</sub>O ||  13µl || 52µl
 
-
            |}
 
-
 
-
            --> 37°C for 1h (restriction)
 
-
            --> 80°C for 10min (deactivation)
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | PCR || 6,38µl || 4,56µl || 2,71µl
 
-
            |-
 
-
            | BamHI (FD) ||  1µl || 1µl || 1µl
 
-
            |-
 
-
            | HindIII (FD) ||  1µl || 1µl || 1µl
 
-
            |-
 
-
            | Buffer (FD) ||  2µl || 2µl || 2µl
 
-
            |-
 
-
            | H<sub>2</sub>O ||  19,62µl || 21,44µl || 23,29µl
 
-
            |}
 
-
 
-
            --> 37°C for 1h (restriction)
 
-
            --> 80°C for 10min (deactivation)
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | Plasmid || 1 || 2 || 3
 
-
            |-
 
-
            | P ||  10µl || 10µl || 18µl
 
-
            |-
 
-
            | BamHI (FD) ||  1µl || 1µl || 1µl
 
-
            |-
 
-
            | HindIII (FD) ||  1µl || 1µl || 1µl
 
-
            |-
 
-
            | Buffer (FD) ||  2µl || 2µl || 3µl
 
-
            |-
 
-
            | nuc.free H<sub>2</sub>O ||  6µl || 6µl || 7µl
 
-
            |}
 
-
 
-
            --> 37°C for 1h (restriction)
 
-
            --> 80°C for 10min (deactivation)
 
-
 
-
            <em>PCR Purification (without isopropanol)</em>
 
-
 
-
            Elution buffer 20µl; 1min incubated
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | plasmid P1-3 || 45,3ng/µl
 
-
            |-
 
-
            | BfR || 12,9ng/µl
 
-
            |-
 
-
            | FTNA1 || 34,4 ng/µl
 
-
            |-
 
-
            | FTNA2 || 29,9ng/µl
 
-
            |}
 
-
 
-
            <em>Ligation Assay</em>
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! - !! Control !! BFR !! BFR !! BFR !! FTNA1 !! FTNA1 !! FTNA1 !! FTNA2 !! FTNA2 !! FTNA2 !! BFR_E !! BFR_E !! BFR_E
 
-
            |-
 
-
            | Dilution || - || 1x || 3x || 5x||1x|| 3x || 5x||1x || 3x || 5x ||1x || 3x || 5x
 
-
            |-
 
-
            | Vector DNA || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1 || 1,1
 
-
            |-
 
-
            | Insert DNA || 0 || 0,4 || 1,6 || 2,0 || 0,10 || 0,47 || 0,79 || 0,18 || 0,52 || 0,90 || 0,40 || 1,16 || 2,0
 
-
            |-
 
-
            | Buffer || 1 || 1 || 1 || 1 || 1 || 1 || 1 || 1 || 1 || 1 || 1 || 1 || 1
 
-
            |-
 
-
            | T4 DNA-Ligase || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25 || 0,25
 
-
            |-
 
-
            | H<sub>2</sub>O || 7,65 || 7,25 || 6,5 || 5,65 || 7,5 || 7,20 || 6,85 || 7,50 || 7,20 || 6,85 || 7,25 || 6,50 || 5,65
 
-
            |-
 
-
            |}
 
-
            <strong>Transformation</strong>
 
-
            --> Transformation of 5µl Sample into DH5α-Cells
 
-
            --> Incubation o/n at 37°C after streating out on LB+amp plates using sterile beads
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! BFR !! FTNA1 !! FTNA2
 
-
            |-
 
-
            | 5,2ng || 5,51ng || 5,43ng
 
-
            |-
 
-
            | 15,6ng || 16,5ng || 16,27ng
 
-
            |-
 
-
            | 26,0ng || 27,4ng || 27,13ng
 
-
            |}
 
-
 
-
<html>           
 
-
            </div>
 
-
 
-
            <div class="sub-content-project">               
 
-
            <h2 class="sub-content-project-headline"> 04/07 Monday - Cloning Results </h2>
 
-
</html>
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Sample !! CFU
 
-
            |-
 
-
            | Control || 13
 
-
            |-
 
-
            | tBFR 1 || 121
 
-
            |-
 
-
            | tBFR 3 || 38
 
-
            |-
 
-
            | tBFR 5 || 664
 
-
            |-
 
-
            | BFR 1 || 87
 
-
            |-
 
-
            | BFR 3 || 151
 
-
            |-
 
-
            | BFR 5 || 150
 
-
            |-
 
-
            | FTNA1 1 || 65
 
-
            |-
 
-
            | FTNA1 3 || 131
 
-
            |-
 
-
            | FTNA1 6 || 191
 
-
            |-
 
-
            | FTNA2 1 || 84
 
-
            |-
 
-
            | FTNA2 3 || 114
 
-
            |-
 
-
            | FTNA2 5 || 151
 
-
            |}
 
-
            --> picked 5 colos per construct for coloPCR (50µl TE-buffer; 96°C; 10min)
 
-
            --> rescue plate
 
-
 
-
            '''colPCR Programm'''
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! - !! 1x !! Mastermix 23x
 
-
            |-
 
-
            | nuc.free H<sub>2</sub>O || 13,7µl || 315,1µl
 
-
            |-
 
-
            | 10x Dream Taq Buffer || 2µl || 46µl
 
-
            |-
 
-
            | 25mM MgCl<sub>2</sub> || 1,2µl || 27,6µl
 
-
            |-
 
-
            | 10mM dNTPs || 0,5µl || 11,5µl
 
-
            |-
 
-
            | Primer T5 prom (PB16) || 0,5µl || 11,5µl
 
-
            |-
 
-
            | Primer T5 term (PB17) || 0,5µl || 11,5µl
 
-
            |-
 
-
            |
 
-
            |-
 
-
            | boiled colos || 1µl + 18,4ml Mastermix
 
-
            |-
 
-
            | Taq Polymerase || 0,5µl
 
-
            |}
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Temperature !! Time
 
-
            |-
 
-
            | 95°C || 3'
 
-
            |-
 
-
            |30 cycles
 
-
            |-
 
-
            | 95°C || 30''
 
-
            |-
 
-
            | 55°C || 30''
 
-
            |-
 
-
            | 72°C || 1'
 
-
            |-
 
-
            |
 
-
            |-
 
-
            | 72°C || 10'
 
-
            |-
 
-
            | 12°C || hold
 
-
            |}
 
-
<html>           
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">               
 
-
            <h2 class="sub-content-project-headline"> 04/08 Tuesday - Amplification of ferritin genes </h2>
 
-
 
-
            Primer designed for amplification:
 
-
<br/>
 
-
</html>
 
-
            '''primer Bfr:'''
 
-
 
-
            FW: 5'  GC  G| G A T C C AAAGGTGATACTAAAGTTATAAATTATCTC(GC 23,33% Tm = 57,5)  3'  OK
 
-
 
-
            RW: 5'  GC  A| A G C T T TCAACCTTCTTCGCG(GC 50% Tm = 58,5)  3'                    OK
 
-
 
-
            '''primer FtnA1:'''
 
-
 
-
            FW: 5'  GC  G| G A T C C GCAACCGCTGGAATG(GC 60%  Tm = 60,5) 3'                    OK
 
-
 
-
            RW: 5'  GC  A| A G C T T TCAATGCAGCTGATGC(GC 50,0% Tm = 58,5)  3'                OK
 
-
 
-
            '''primer FtnA2:'''
 
-
 
-
            FW: 5'  GC  G| G A T C C CTGAAACCAGAAATGATTG(GC 36,8%  Tm = 65,1)  3'            OK
 
-
 
-
            RW: 5'  GC  A| A G C T T TTAGTTTTGTGTGTCGAGG(GC 42,1%  Tm = 56,8)  3'            OK
 
-
 
-
 
-
            Using the Thermoscientific  PCR mastermix phusion polymerase, 2x 50 µl reactions per amplification:
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | Nuc-free H<sub>2</sub>O || 39,5 µl
 
-
            |-
 
-
            | 2x mastermix || 50,0 µl
 
-
            |-
 
-
            | FW primer ||  5,0 µl
 
-
            |-
 
-
            | RW primer ||  5,0 µl
 
-
            |-
 
-
            | template DNA ||  0,5 µl
 
-
            |}
 
-
 
-
 
-
            '''PCR programs:'''
 
-
            {| class="wikitable"
 
-
            |-
 
-
            |  || 98°C || 10s || 1x
 
-
            |-
 
-
            |  || 98°C || 5s || 30x
 
-
            |-
 
-
            |primer|| Bfr/ FtnA1/ FtnA2 || 60,5°C/ 58,9°C/ 56,1°C || 30x
 
-
            |-
 
-
            | || 72°C || 10s || 30x
 
-
            |-
 
-
            | 72°C || 60s || Beispiel || 1x
 
-
            |}
 
-
 
-
 
-
 
-
            <strong>Transformation of pQE_80L into DH5alpha</strong><br/>
 
-
 
-
            Plasmid from plasmid database of TU workgroup by Prof. Budisa was taken: <br/>
 
-
            plasmid ID: 4; concentration = 308 ng/µl<br/>
 
-
 
-
            Unthaw 50 µl aliquot of DH5alpha or BL21 DE3 gold on ice for 10 min.Than Use 308 ng and 616 ng of plasmids to bind on Ca<big>2+</big>-surface of the cell membranes. Heat shock was performed for 30-90 s. The cells were incubated on ice for 2 min and than there was added 950 µl LB media. The cells were incubated at 37°C for 60 min. After this 70 µl of transformed E. coli suspension was streacked out onto a plate with the appropriate selection marker. The plate was incubated over night at 37°C. To prepare preculture 2 colonies were picked and added into 5 ml LB media + 5 µl AMP. The precultures were incubated over night at 37°C and 200 rpm.
 
-
  <html>
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">           
 
-
            <h2 class="sub-content-project-headline"> 04/10 Thursday - Expression of Ferritin in LB </h2>
 
-
</html>
 
-
            →Innoculate 20ml LB + amp with 1ml of a preculture<br />
 
-
 
-
            {|
 
-
            |-
 
-
            ! Title !! No. !! Wavelength !! Absobance !! Volume
 
-
            |-
 
-
            | BfR || 1 || 600nm || 0,529A || 1,51ml
 
-
            |-
 
-
            | FTNA1|| 2 || 600nm || 0,307A || 3,25ml
 
-
            |-
 
-
            | FTNA2 || 3 || 600nm || 0,605A || 1,32ml
 
-
            |}
 
-
            →Incubation for 2h until OD<sub>600</sub>=0,6-08<br />
 
-
            {|
 
-
            |-
 
-
            ! Title !! No. !! Wavelength !! Absobance
 
-
            |-
 
-
            | BfR || 1 || 600nm || 0,825A
 
-
            |-
 
-
            | FTNA1|| 2 || 600nm || 0,883A
 
-
            |-
 
-
            | FTNA2 || 3 || 600nm || 0,859A
 
-
            |}
 
-
            → Take SDS Sample non-induced<br />
 
-
            →Induce with 20µl IPTG<br />
 
-
            →Add Fe<sup>2+</sup><br />
 
-
            →Expression: 4h at 22°C<br />
 
-
            <html>
 
-
            Cultivation was aborted because of heat development
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">                                                              .                                   
 
-
            <h2 class="sub-content-project-headline"> 04/14 Monday - Miniprep </h2>
 
-
            Miniprep of the cell-seperation streak out of the cloning procedure from december 2013<br />
 
-
</html>
 
-
            '''Miniprep-Kit of ThermoScientific'''<br />
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! - !! Title !! Concentration in ng/µl
 
-
            |-
 
-
            | A4 || BfR || 66
 
-
            |-
 
-
            | B3 || FTNA1 || 138
 
-
            |-
 
-
            | C5 || FTNA2 || 88
 
-
            |-
 
-
            | D2 || BfR_Electro || 144
 
-
            |}
 
-
 
-
            <strong><big>'''DNA Concentration Determination'''</big></strong>
 
-
            {|
 
-
            |-
 
-
            | Dilution Factor || 20
 
-
            |-
 
-
            | Integration Time || 1s
 
-
            |-
 
-
            | Factor || 50
 
-
            |-
 
-
            | Units || µg/ml
 
-
            |}
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! - !! Title !! No. !! 260nm !! 280nm !! 320nm !! Ratio !! Conc.
 
-
            |-
 
-
            | A4 || BfR || 1 || 0,056 || -0,022|| -0,010 || 2,05 || 66
 
-
            |-
 
-
            | B3 || FTNA1 || 2 || 0,135 || 0,067 || -0,003 || 1,96 || 138
 
-
            |-
 
-
            | C5 || FTNA2 || 3 || 0,078 || 0,035|| -0,008 || 2,00 || 86
 
-
            |-
 
-
            | D2 || BfR-Electro || 4 || 0,150 || 0,078 || 0,006 || 2,02 || 144
 
-
            |}
 
-
<html>           
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">                               
 
-
            <h2 class="sub-content-project-headline"> 04/16 Wednesday - Sequencing </h2>
 
-
            Preparation of the sequencing for the Samples from 16.01.2013<br/>
 
-
</html>
 
-
            {|
 
-
            |-
 
-
            | T5 prom. Primer || 3µl
 
-
            |-
 
-
            | Plasmid || 12µl
 
-
            |}
 
-
            {|
 
-
            |-
 
-
            | A4 || 6µl
 
-
            |-
 
-
            | B3 || 6µl
 
-
            |-
 
-
            | C5 || 6µl
 
-
            |-
 
-
            | D2 || 6µl
 
-
            |} 
 
-
<html>         
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">                                   
 
-
            <h2 class="sub-content-project-headline"> 04/17 Thursday - Expression of BfR and FTNA1/2 </h2>
 
-
            4x sterile 250ml Erlenmeyer<br />
 
-
            +50ml LB<br />
 
-
            +50µl amp<br />
 
-
            +2,5ml preculture<br />
 
-
            Incubation: 1h at 30°C
 
-
</html>
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! No. !! Title !! Wavelength !! Absorbance
 
-
            |-
 
-
            | 1 || BfR || 600nm || 0,909A
 
-
            |-
 
-
            | 2 || FTNA1 || 600nm || 0,980A
 
-
            |-
 
-
            | 3 || FTNA2 || 600nm || 0,930A
 
-
            |-
 
-
            | 4 || BfR+20?? || 600nm || 0,970A
 
-
            |}
 
-
<html>           
 
-
            →Take SDS-Sample<br />
 
-
            →Induction with 50µl IPTG<br />
 
-
            →Addition of 0,0525g Fe-citrate (20mM dissolved in 1ml sterile Water)<br />
 
-
            →Incubation for 3h at 30°C<br />
 
-
            →continue incubation o/n<br />
 
-
            →Centrifuge with 6800g for 5min<br />
 
-
            </div>
 
-
 
-
            <div class="sub-content-project">       
 
-
            <h2 class="sub-content-project-headline"> 04/18 Friday - Production of LB-Plates </h2>
 
-
 
-
            <em>Production of a Mutaflor-Supression-culture</em>
 
-
            →10ml sterile LB<br />
 
-
            →Add the content of a Mutaflor capsula (white pouder)<br />
 
-
            Incubation: 37°C at 220rpm<br />
 
-
            <em>Production of Dilutions of the Supression-culture and out streaking</em>
 
-
            →1µl of the supression-culture to 999µl LB (1:1000)<br />
 
-
            →100µl of that dilution to 900µl LB (1:10<sup>4</sup>)<br />
 
-
            →10µl of that dilution to 990µl LB (1:10<sup>5</sup>)<br />
 
-
            →Streak out 50µl of each culture on LB with sterile beads<br />
 
-
            Incubation: 37°C
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 04/24 Thursday - Mini-Prep </h2>
 
-
</html>
 
-
            {| class="wikitable"
 
-
            |-
 
-
            | 1 || PSB || D40 || 9fP || CR/LB
 
-
            |-
 
-
            | 2 || PSB || D20 || 9fP || CR/LB
 
-
            |-
 
-
            | 3 || PSB || D40 || fs || LB/CR
 
-
            |-
 
-
            | 4 || PSB || D40 || LB/CR
 
-
            |-
 
-
            | 5 || PSB || AB || Turyu || CR/LB
 
-
            |-
 
-
            | 6 || PSB || D48 || 9fP || CB/CR
 
-
            |}
 
-
            <html>
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 04/28 Monday -PCR Plasmid/ Primer and Parameter Check </h2>
 
-
            (Salah and Christina)<br />
 
-
 
-
            Check of:<br />
 
-
            -Plasmids/Primer<br />
 
-
            -Annealing temperature<br />
 
-
            -Phusion and Q5 Polymerase
 
-
</html>
 
-
            <em>Plasmids</em>
 
-
 
-
            iGEM Plasmid pkD4 (Stock 200ng/µl) =>1:200 diluted = 1ng/µl
 
-
 
-
            WH (Willi Hauke) Plasmid pkD4 (0,72ng/µl)
 
-
 
-
            <em>Primer</em>
 
-
 
-
            P1 FieF (iGEM)                                  fwd tnaA KO (WH)
 
-
 
-
            P2 FieF (iGEM)                                  rev  tnaA KO (WH)
 
-
 
-
 
-
            <em>Combinations</em>
 
-
 
-
            (4 combinations with Phusion; 4 combinations with Q5 )
 
-
 
-
 
-
            {| border="2"
 
-
            |
 
-
            | '''Plasmid'''
 
-
            | '''Primer'''
 
-
            | '''Primer'''
 
-
            |-
 
-
            | '''1. '''
 
-
            | iGEM Plasmid
 
-
            | P1 (iGEM)
 
-
            | P2 (iGEM)
 
-
            |-
 
-
            | '''2. '''
 
-
            | WH Plasmid 
 
-
            | fwd tnaA KO
 
-
            | rev  tnaA KO            '''POSITIVCONTROL'''
 
-
            |-
 
-
            | '''3. '''
 
-
            | iGEM Plasmid
 
-
            | fwd tnaA KO
 
-
            | rev  tnaA KO
 
-
            |-
 
-
            | '''4. '''
 
-
            | WH Plasmid
 
-
            | P1 (iGEM)
 
-
            | P2 (iGEM)
 
-
            |}
 
-
 
-
            Each of the four combinations was prepared 3 times => for Gradient PCR
 
-
 
-
           
 
-
 
-
            <em>Phusion Polymerase PCR Assay</em>
 
-
 
-
            20µl Reaction
 
-
            {| class="wikitable"
 
-
            |-
 
-
            !  !! Plasmid !! Primer !! Primer
 
-
            |-
 
-
            | 1. || iGEM Plasmid || P1 (iGEM) || P2 (iGEM)
 
-
            |-
 
-
            | 2. || WH Plasmid || fwd tnaA KO || rev  tnaA KO            POSITIVCONTROL
 
-
            |-
 
-
            | 3. || iGEM Plasmid || fwd tnaA KO || rev  tnaA KO
 
-
            |-
 
-
            | 4. || WH Plasmid || P1 (iGEM) || P2 (iGEM)
 
-
            |-
 
-
 
-
            |}
 
-
 
-
 
-
 
-
            <em>Q5 Polymerase PCR Assay</em>
 
-
 
-
            20µl Reaction
 
-
            {| {{table}}
 
-
            | align="center" style="background:#f0f0f0;"|'''5xQ5 Reaction Puffer (G2 runder Behälter)'''
 
-
            | align="center" style="background:#f0f0f0;"|'''4µl'''
 
-
            | align="center" style="background:#f0f0f0;"|'''1x'''
 
-
            |-
 
-
            | 10mM dNTPs ||0,4µl||200µM
 
-
            |-
 
-
            | 10µM forward Primer||1µl||0,5µM
 
-
            |-
 
-
            | 10µM reverse Primer||1µl||0,5µM
 
-
            |-
 
-
            | Template DNA||1µl||1pg-1ng sein
 
-
            |-
 
-
            | Q5 High Fidelity DNA Polymerase||0,2µl||0,02U/µl
 
-
            |-
 
-
            | GC enhancer||4 µl||
 
-
            |-
 
-
            | Nuclease-Free Water ||to 20µl||
 
-
            |-
 
-
            | ||||
 
-
            |-
 
-
            | ||8,4µl||
 
-
            |-
 
-
            |
 
-
            |}
 
-
 
-
            <em>FUR PCR Assay</em>
 
-
<br/>
 
-
            (Along with the above mentioned PCR Assays another Gradient PCR with FUR-Primer is performed)<br/>
 
-
 
-
            Aliquot of the FUR Primer (100µM) 1:10 diluted =>10µM<br/>
 
-
 
-
            20µl Reaction with Phusion-Polymerase (see above)<br/>
 
-
 
-
            with WH Plasmid and P1 FUR &amp; P2 FUR Primer<br/>
 
-
 
-
           
 
-
 
-
            <em>Gradient PCR Program</em>
 
-
 
-
            Thermocycling Conditions for the Gradient PCR <br/>
 
-
 
-
            Programm-NAME: Q5 grad trp KO<br/>
 
-
 
-
            {| {{table}}
 
-
            | align="center" style="background:#f0f0f0;"|'''Step'''
 
-
            | align="center" style="background:#f0f0f0;"|'''TEMP'''
 
-
            | align="center" style="background:#f0f0f0;"|'''TIME'''
 
-
            |-
 
-
            | Initial Denaturation||98°C||30 sec
 
-
            |-
 
-
            | 5 Cycles||98°C||8 sec
 
-
            |-
 
-
            | ||64±5°C||25 sec    GRADIENT
 
-
            |-
 
-
            | ||72°C||Trp ko: 1528bpà45s
 
-
            |-
 
-
            | 25 Cycles||98°C||8 sec
 
-
            |-
 
-
            | ||72°C||70 sec
 
-
            |-
 
-
            | Final Extension||72°C||2 min
 
-
            |-
 
-
            | Hold||8°C||
 
-
            |-
 
-
            |
 
-
            |}
 
-
 
-
 
-
            <em>Gel-Electrophoresis</em>
 
-
 
-
            1% Agarose Gel<br/>
 
-
 
-
            5µl Sample +1µl loading dye (1:6)<br/>
 
-
 
-
            8µl diluted GeneRuler Mix ladder<br/>
 
-
 
-
            MODE: 90V 25min<br/>
 
-
 
-
           
 
-
 
-
            '''Sample label:'''
 
-
 
-
           
 
-
 
-
            P = with Phusion Polymerase<br/>
 
-
 
-
            Q = with Q5 Polymerase<br/>
 
-
 
-
            1 = 1. Kombination<br/>
 
-
 
-
            2 = 2. Kombination<br/>
 
-
 
-
            3 = 3. Kombination<br/>
 
-
 
-
            4 = 4. Kombination<br/>
 
-
 
-
           
 
-
 
-
            '''Gradient'''
 
-
 
-
            1 = 59°C
 
-
 
-
            4 = 63°C
 
-
 
-
            8 = 69°C
 
-
 
-
            {| {{table}}
 
-
            | align="center" style="background:#f0f0f0;"|'''Gel 1 Phusion'''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            |-
 
-
            | P FUR||P1||P1||P1||P2||P2||P2||Marker||P3||P3||P3||P4||P4||P4
 
-
            |-
 
-
            | ||||||||||||||||||||||||||
 
-
            |-
 
-
            | 8||1||4||8||1||4||8||||1||4||8||1||4||8
 
-
            |-
 
-
            | Gel 2 Q5||||||||||||||||||||||||||
 
-
            |-
 
-
            | ||Q1||Q1||Q1||Q2||Q2||Q2||Marker||Q3||Q3||Q3||Q4||Q4||Q4
 
-
            |-
 
-
            | ||||||||||||||||||||||||||
 
-
            |-
 
-
            | ||1||4||8||1||4||8||||1||4||8||1||4||8
 
-
            |-
 
-
            |
 
-
            |}
 
-
 
-
 
-
           
 
-
 
-
            <strong>Results</strong>
 
-
 
-
 
-
            {| {{table}}
 
-
            | align="center" style="background:#f0f0f0;"|'''Gel 1 Phusion Result:'''
 
-
            | align="center" style="background:#f0f0f0;"|'''For FUR-Primer no Amplifikation'''
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | ||For iGEM-Plasmid no Amplifikation
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | ||Combination 2 (WH Plasmid & Primer)= only non-specific amplification
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | ||Combination 4 (WH Plasmid & iGEM Primer)=Bands for 59°C and 63°C + non-specific amplification
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | align="center" style="background:#f0f0f0;"|'''Gel 2 Q5 Result:'''||For iGEM-Plasmid no Amplifikation
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | ||Combination 2  (WH Plasmid & Primer) = bands for all three annealing temperature observed+non-specific amplification
 
-
            |-
 
-
            | ||
 
-
            |-
 
-
            | ||Combination 4 (WH Plasmid & iGEM Primer)= Bands at all three annealing temperature+non-specific amplification
 
-
            |-
 
-
            |
 
-
            |}
 
-
<html>
 
-
            <br/>
 
-
            <img src="https://static.igem.org/mediawiki/2014/2/2c/Team_berlin_0001.jpg" alt="" />
 
-
            <br />
 
-
            iGEM Plasmid not to be used anymore.
 
-
            FUR need to be checked again.
 
-
            </div>
 
-
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 04/29 Tuesday - Mini-Prep </h2>
 
-
            (Aritra)<br />
 
-
            [pKD46 + DH5α]→ 155ng/µl<br />
 
-
            [pKD4 + DH5α]→ 302ng/µl<br />
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/02 Friday - Genomic DNA extraction from Psedomonas putida </h2>
 
-
            (Johann)<br />
 
-
 
-
            -->see Protocol Wizard ® Genomic DNA Purification Kit
 
-
 
-
                - Strain from VLB Martin Senz PHO Psedomonas putida KT2242  B_0712  from 29.04.2014 culture<br/>
 
-
                - 2 days in 30°C  Shaking Incubator.<br/>
 
-
                - Mikro 22R Centrifuge Hettich (16000g)<br/>
 
-
 
-
            Final DNA Concentration measured after purification = 95ng/µl
 
-
            </div>
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 02.05.2014 - DNA Digestion to test Plasmids </h2>
 
-
</html>
 
-
            {| {{table}}
 
-
            | align="center" style="background:#f0f0f0;"|'''Samples'''
 
-
            | align="center" style="background:#f0f0f0;"|'''Conc. DNA (ng/µl)'''
 
-
            | align="center" style="background:#f0f0f0;"|'''Enzymes used'''
 
-
            | align="center" style="background:#f0f0f0;"|'''Expected band length'''
 
-
            | align="center" style="background:#f0f0f0;"|'''Evaluation'''
 
-
            |-
 
-
            | pKD4||302||Xbal||1874,1393||Possible plasmid, failed
 
-
            |-
 
-
            | pKD46||40||EcoRI||4820,1509||Failed
 
-
            |-
 
-
            | pKD46||39||EcoRI||4820,1509||Failed
 
-
            |-
 
-
            | pKD4||60||Xbal||1874,1393||Possible(passed); whole plasmid
 
-
            |-
 
-
            | pSBAC3||88||SpeI/EcoRI||2047,22||Possible (passed); smallpattern
 
-
            |-
 
-
            | pSBAC3-D20-GFP||115||SpeI/EcoRI||2047,957||whole plasmid; failed
 
-
            |-
 
-
            | pSBAC3-D40-Bfr||86||SpeI/EcoRI||2047, 774||Whole plasmid; failed
 
-
            |-
 
-
            | pSBAC3-D40-GFP||80||SpeI/EcoRI||2047,1014||Whole plasmid; failed
 
-
            |-
 
-
            | pSBAC3-AB-Tyrosin||110||SpeI/EcoRI||2047,3319||Failed
 
-
            |-
 
-
            | pSBAC3-D40||164||SpeI/EcoRI||2047,267||Failed
 
-
            |-
 
-
            | pSBAC3-D40-GFP-ssr||106||SpeI/EcoRI||2047,1032||Passed; whole plasmid
 
-
            |-
 
-
            |
 
-
            |}
 
-
            <strong>Gel Electrophoresis</strong>
 
-
            '''Key:'''<br>
 
-
            -band1: Ladder<br />
 
-
            -band5:Ladder<br />
 
-
            -residual bands, see table above
 
-
        <html> 
 
-
<br/>
 
-
            <img src="https://static.igem.org/mediawiki/2014/5/5b/Team_berlin_0002.png" alt="" /><br/>
 
-
            <em>Results</em>
 
-
 
-
            pKD4 with 60(ng/µl) best candidate for PCR.
 
-
            </div>
 
-
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/05 Monday - Preculture of strains from Budisa strain database in LB Medium </h2>
 
-
         
 
-
 
-
            1. BU31 (pKD4) in 50 ml LB+Kanamycin+Ampicillin  37°C 220 rpm<br/>
 
-
            2. BU32 (pKD46) in 50 ml LB+Ampicillin 30°C 240rpm<br/>
 
-
            3. BU31 (pKD46) in LB plate+Ampicillin  30°C <br/>
 
-
 
-
            <strong>Midiprep</strong>
 
-
           
 
-
 
-
            Midiprep of BU31 (pKD4) and BU32 (pKD46) from strain Database.<br/>
 
-
 
-
            Concentration pKD4 = 104 ng/µl<br/>
 
-
 
-
            Concentartion pKD46 = 161 ng/µl<br/>
 
-
            </div>
 
-
 
-
 
-
 
-
            <div class="sub-content-project">                         
 
-
            <h2 class="sub-content-project-headline"> 05/06 Tuesday - Gel-Electrophoresis </h2>
 
-
       
 
-
            Kanamycin Cassette PCR (pKD4 from MidiPrep 05.05.2014 104ng/µl Christina)<br />
 
-
</html>
 
-
            '''Key:'''<br />
 
-
            - 1st: Ladder<br />
 
-
 
-
            - 2nd and 3rd: Fief<br />
 
-
 
-
            - 4th: Negative control<br />
 
-
            - 7th and 8th: FUR<br />
 
-
            <html>
 
-
            <img src="https://static.igem.org/mediawiki/2014/c/c3/Team_berlin_0003.jpg" alt="" />
 
-
            <br/>
 
-
            <em>Results</em>
 
-
            FieF worked well; FUR no bands
 
-
 
-
</html>           
 
-
            <strong>Restriction digest of Plasmid pKD4 and pKD46</strong>
 
-
            {| {{table}}
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            | align="center" style="background:#f0f0f0;"|''''''
 
-
            |-
 
-
            | ||pKD4||pKD46
 
-
            |-
 
-
            | Plamid ||19.2µl||12.5µl
 
-
            |-
 
-
            | Digestion Enzym||Xbal 1µl||Xmal 1µl
 
-
            |-
 
-
            | nuclease free H2O||24.8µl||31.5µl
 
-
            |-
 
-
            | 10xFO green Buffer||5µl||5µl
 
-
            |-
 
-
            | Total||50µl||50µl
 
-
            |-
 
-
            |
 
-
            |}
 
-
              - Both the reaction mix incubated at 37°C for 1 hr.
 
-
              - After that another 1 hr at RT.
 
-
 
-
 
-
 
-
 
-
            <em>Gel-Electrophoresis</em>
 
-
            - 20µl of both the samples together with whole plasmids loaded on 1% Agarose Gel<br />
 
-
            <strong>Results</strong>
 
-
            '''Key:'''<br />
 
-
            -1st: pKD4 (XbaI digested)<br />
 
-
            -2nd: pKD4 (undigested)<br />
 
-
            - 3rd: Ladder<br />
 
-
            - 4th: pKD46 (undigested)<br />
 
-
            -5th: pKD46 (XmaI digested)<br />
 
-
 
-
 
-
            <em>Gel Extraction</em>
 
-
            -Used GeneJet GelExtraction Kit by Thermo Scientific
 
-
            <strong>Results</strong>
 
-
            DNA Concentration: 16ng/µl
 
-
<html>           
 
-
            </div>
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/16 Friday - Biotransformation of Ferritin and pKD46 in Nissle and DH5-α strain </h2>
 
-
            concentration Ferritin 120ng/µl<br>
 
-
            concentration pKD 46 95 ng/µl<br/>
 
-
</html>
 
-
            Protocol
 
-
            *electro competent cells of DH5α and Nissle were thawed on ice
 
-
            *0.4µl of Ferritin and 0.53 µl of pKD46 was added to the cells
 
-
            *cells with DNA were transferred to cuvettes for electroporation, then 950ml (LB-medium) was added to the cells immediately
 
-
            *incubation at 37°C for ferritin, 30°C for pKd46 for 1 h with shaking
 
-
            *the cells were plated on Amp plates for pKD46 and CM for Ferritin
 
-
            *Transformation did not work.
 
-
            <html>
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/21 Wednesday - PCR Gel-Extraction of FieF </h2>
 
-
 
-
 
-
            1% Agarosegel + 0,5µl EtBr<br />
 
-
            45µl Sample+9µl Loading Dye<br />
 
-
            8µl Ladder<br />
 
-
  </html>
 
-
            --> Gel-Extraction Kit used with 50µl nuclease-free water for elution<br />
 
-
            <strong>Gene Knockout of FieF</strong>
 
-
            (Salah)
 
-
            <em>Preparation of the preculture</em>
 
-
            '''Used Precultures:'''<br />
 
-
            - RV +pKD46<br />
 
-
            - WM10 +pKD46<br />
 
-
            The precultures was diluted to OD<sub>600</sub>=0,1 and then incubated for 2h at 30°C until they reach OD<sub>600</sub>=0,6<br />
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Title !! Wavelength !! Absorbance
 
-
            |-
 
-
            | Reference || 600nm || 0,000A
 
-
            |-
 
-
            | RV+pKD46 || 600nm || 0,066A
 
-
            |-
 
-
            | WM10+pKD46 || 600nm || 0,050A
 
-
            |}
 
-
            (The culture was diluted 1/10 for the OD measurement)<br />
 
-
            →The precultures are ready for the Rekombinase induction with Arabinose
 
-
            <em>Induction with Arabinose</em>
 
-
            The cultures have been induced with 500µl arabinose (1M)
 
-
            →After the induction, the cultures have to be incubated for further 30min at 30°C
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Title !! Wavelength !! Absorbance
 
-
            |-
 
-
            | Reference || 600nm || 0,000A
 
-
            |-
 
-
            | RV+pKD46 || 600nm || 0,084A
 
-
            |-
 
-
            | WM10+pKD46 || 600nm || 0,067A
 
-
            |}
 
-
            →From now on the cultures need to be cooled on ice
 
-
            <em>Preparation for the Electroporation</em>
 
-
 
-
            <em>Electroporation</em>
 
-
            '''Electroporation-Program: Ec1'''<br />
 
-
            -Amount of DNA sample: 75-150ng<br />
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Sample !! Conc !! Used Volume !! Strain !! Electroporation Time
 
-
            |-
 
-
            | FieF1 || 42ng/µl || 2µl (84ng) || RV || 4,4ms
 
-
            |-
 
-
            | FieF2 || 9ng/µl || 10µl (90ng) || RV || 4,1ms
 
-
            |-
 
-
            | FieF1 || 42ng/µl || 2µl (84ng) || WM10 || 4,3ms
 
-
            |-
 
-
            | FieF2 || 9ng/µl || 10µl (90ng) || WM10 || 4,8ms
 
-
            |}
 
-
            After the transformation, the cultures was immediately prepared with 950µl SOC and incubated for 60min at 30°C without antibiotics --> recovery
 
-
            <em>Selection-cultures</em>
 
-
            The selection of positive clones is done by using LB plates with kan+amp<br />
 
-
            Incubation: 30°C o/n
 
-
    <html>     
 
-
            </div>
 
-
 
-
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/22 Thursday - Transformation of pKD46 </h2>
 
-
          </html>
 
-
            <em>Preparation of the preculture</em>
 
-
            '''Used Precultures:'''<br />
 
-
            - MG1655<br />
 
-
            - Nissle<br />
 
-
            The precultures was diluted to OD<sub>600</sub>=0,1 and then incubated for 2h at 30°C until they reach OD<sub>600</sub>=0,6<br />
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Title !! Wavelength !! Absorbance
 
-
            |-
 
-
            | Reference || 600nm || 0,000A
 
-
            |-
 
-
            | MG1655 || 600nm || 0,062A
 
-
            |-
 
-
            | NIssle || 600nm || 0,054A
 
-
            |}
 
-
            (The culture was diluted 1/10 for the OD measurement)<br />
 
-
 
-
            →From now on the cultures need to be cooled on ice
 
-
            <em>Preparation for the Electroporation</em>
 
-
 
-
            <em>Electroporation</em>
 
-
            '''Electroporation-Program: Ec1'''<br />
 
-
            -Amount of DNA sample: 75-150ng<br />
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Sample !! Conc !! Used Volume !! Strain !! Electroporation Time
 
-
            |-
 
-
            | MG1655 1 || 42ng/µl || 2µl (84ng) || RV || 5,4ms
 
-
            |-
 
-
            | MG1655 2 || 9ng/µl || 10µl (90ng) || RV || 5,8ms
 
-
            |-
 
-
            | Nissle 1 || 42ng/µl || 2µl (84ng) || WM10 || 0,7ms (thrown away)
 
-
            |-
 
-
            | Nissle 2 || 9ng/µl || 10µl (90ng) || WM10 || 5,8ms
 
-
            |}
 
-
            After the transformation, the cultures was immediately prepared with 950µl SOC and incubated for 60min at 30°C without antibiotics --> recovery
 
-
            <em>Selection-cultures</em>
 
-
            The selection of positive clones is done by using LB plates with amp<br />
 
-
            Incubation: 30°C o/n
 
-
 
-
            <strong> PCR of ATPCS and PPMT </strong>
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! Mastermix !! ATPCS !! PPMT
 
-
            |-
 
-
            | nuc.free water|| 18.9 || 17.5
 
-
            |-
 
-
            | 2x Fusion Mastermix || 25 || 25
 
-
            |-
 
-
            | Fw Primar || 2.5 || 2.5
 
-
            |-
 
-
            | Rw Primar || 2.5|| 2.5
 
-
            |-
 
-
            | template DNA || 1.1 || 2.5
 
-
            |}
 
-
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! ATPCS !! Programm
 
-
            |-
 
-
            | 98°C || 10
 
-
            |-
 
-
            | 98°C|| 5 30 cycles
 
-
            |-
 
-
            | 62°C|| 5  30 cycles
 
-
            |-
 
-
            | 72°C || 5  30 cycles
 
-
            |-
 
-
            | 72°C||  60 secs
 
-
            |-
 
-
            | 8°C|| store
 
-
            |}
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! PPMT!! Programm
 
-
            |-
 
-
            | 98°C || 10
 
-
            |-
 
-
            | 98°C|| 5 30 cycles
 
-
            |-
 
-
            | 63,1°C|| 5  30 cycles
 
-
            |-
 
-
            | 72°C || 21  30 cycles
 
-
            |-
 
-
            | 72°C||  60 secs
 
-
            |-
 
-
            | 8°C|| store
 
-
            |}
 
-
 
-
            ATPCS 1469 bp; PPMT 234 bp
 
-
            --> wrong Programm
 
-
  <html>         
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/23 Friday - Digestion of Vector for Cloning </h2>
 
-
            Plasmid: pQE80L<br />
 
-
 
-
            Old Plasmid of Johann: <br />
 
-
            -P1≈1000ng<br/>
 
-
            -P3≈400ng<br/>
 
-
</html>
 
-
            {| class="wikitable"
 
-
            |-
 
-
            ! P3 !! !! P1 !!
 
-
            |-
 
-
            | SacI || 1µl || SacI || 1µl
 
-
            |-
 
-
            | HindIII || 1µl || BamHI || 1µl
 
-
            |-
 
-
            | Buffer || 2µl || Buffer || 2µl
 
-
            |-
 
-
            | Plasmid 1 || 4µl || Plasmid 3 || 16µl
 
-
            |-
 
-
            | nuc.water || 12µl || nuc. water || 0µl
 
-
            |}
 
-
            --> Incubation: 1,5h at 37°C<br />
 
-
            --> Deactivation: 20min at 80°C
 
-
            <html>
 
-
            </div>
 
-
 
-
 
-
            <div class="sub-content-project">
 
-
            <h2 class="sub-content-project-headline"> 05/27 Tuesday - Production of LB Plates </h2>
 
-
       
 
-
 
-
            LB Agar Plates prepared:<br/>
 
-
 
-
            4x with Ampicillin  (25µl in 25ml)<br/>
 
-
 
-
            4x with Ampicillin+ Kanamycin  (25µl+25µl in 25ml)<br/>
 
-
 
-
            4x Cm (25µl in 25ml)
 
-
            </div> 
 
-
 
-
              <div class="sub-content-project">           
 
-
              <h2 class="sub-content-project-headline"> 05/28 Wednesday </h2>
 
-
              Picked up from MPI: AMB-1 and Microfluidic Chip. (From  the two AMB-1 cultures, one is in the freeze and the other one in the RT-Incubator)<br/>
 
-
 
-
              Digestion of pQE80L: <br/>
 
-
 
-
              Marker: 2 log DNA ladder 5µl<br/>
 
-
 
-
              Sample 1: P1 Sacl-BamHI 10µl<br/>
 
-
 
-
              Sample 2: P3 Sacl-HindIII 10µl<br/>
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/02 Monday - Colony PCR and analytical gel electrophoresis for identifying the right clones </h2>
 
-
</html>
 
-
              Primer: C1  C2<br/>
 
-
 
-
                      C2  C5<br/>
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Components'''
 
-
              | align="center" style="background:#f0f0f0;"|'''20 µL Reaktion'''
 
-
              |-
 
-
              | ||
 
-
              |-
 
-
              | ||
 
-
              |-
 
-
              | Nuc. Free water||13.7
 
-
              |-
 
-
              | 10x Dream Taq Polymerase Puffer||2
 
-
              |-
 
-
              | 25mM MgCl2||1.2
 
-
              |-
 
-
              | 10mM dNTPs||0.5
 
-
              |-
 
-
              | 10mM FW Primer||0.5
 
-
              |-
 
-
              | 10mM RW Primer||0.5
 
-
              |-
 
-
              | Colony||1
 
-
              |-
 
-
              | Taq DNA Pol||0.6
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Denaturation'''
 
-
              | align="center" style="background:#f0f0f0;"|'''95°C'''
 
-
              | align="center" style="background:#f0f0f0;"|'''10min'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              |-
 
-
              | Denaturation||95°C||30sec||
 
-
              |-
 
-
              | Annealing||55°C||30 sec||
 
-
              |-
 
-
              | Extension||72°C||X min||30x
 
-
              |-
 
-
              | Extension||72°C||10 min||
 
-
              |-
 
-
              | End||12||hold||
 
-
              |-
 
-
              |
 
-
              |}
 
-
<html>
 
-
              Backup plates done. Cells given direct to PCR. 11 colonies selected.<br/>
 
-
 
-
              Colony PCR  with some of the clones performed. (All negative)
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/03 Tuesday - Strategy 2: PCR of ATPCS 2PPMT </h2>
 
-
</html>
 
-
              <em>PCR Assay</em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! - !! Sample1(PPMT) !! Sample2(ATPCS)
 
-
              |-
 
-
              | nuc. free water || 17,5µl || 18,9µl
 
-
              |-
 
-
              | FW Primer || 2,5µl || 2,5µl
 
-
              |-
 
-
              | RW Primer || 2,5µl || 2,5µl
 
-
              |-
 
-
              | 2x Phusion Mastermix || 25µl || 25µl
 
-
              |-
 
-
              | Template DNA || 2,5µl (250ng) || 1,1µl (250ng)
 
-
              |}
 
-
 
-
              <em>PCR Program</em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! PPMT (234bp) !! !! ATPCS (1469bp) !!
 
-
              |-
 
-
              | 98°C || 10' || 98°C || 10'
 
-
              |-
 
-
              |30cycles start
 
-
              |-
 
-
              | 98°C || 5" || 98°C || 5"
 
-
              |-
 
-
              | 62°C || 5" || 63°C || 5"
 
-
              |-
 
-
              | 72°C || 10" || 72°C || 45"
 
-
              |-
 
-
              |30cycles stop
 
-
              |-
 
-
              | 72°C || 1' || 72°C || 1'
 
-
              |-
 
-
              | 8°C || hold || 8°C || hold
 
-
              |}
 
-
              <em>Gel-Electrophoresis</em>
 
-
              '''Key:''' <br />
 
-
              2nd band= Ladder<br />
 
-
              3rd band= PPMT<br />
 
-
              5th band= ATPCS<br />
 
-
<html>
 
-
<img src="https://static.igem.org/mediawiki/2014/c/c3/Team_berlin_0004.jpg" alt="" />
 
-
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">                 
 
-
              <h2 class="sub-content-project-headline"> 06/04 Wednesday - PCR amplification of ATPCS and PPMT </h2>
 
-
 
-
              (see under protocol "Amplification BamHI_PPMT_Sacl and Sacl_ATPCS_HindIII"
 
-
 
-
              After Gel: 1 Band visible for ATPCS around 1500bp (expected); no band for PPMT
 
-
 
-
              Purification of the ATPCS-PCR product from gel.
 
-
 
-
              conc. of ATPCS-fragment 6ng/microL
 
-
 
-
              freezed at -20°C on 1st floor
 
-
<img src="https://static.igem.org/mediawiki/2014/f/fa/Team_berlin_0005.jpg" alt="" />
 
-
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 04.06.2014 - Colony PCR for Knockout </h2>
 
-
 
-
              6 clones were picked from 2 Agar plates; Agar plates labelled with numbers with RED
 
-
</html>
 
-
              3 PCR:  a) Primers C1, C3
 
-
 
-
                      b) Primers C2, C4
 
-
 
-
                      c) Primers C1, C5
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''BandNr:'''
 
-
              | align="center" style="background:#f0f0f0;"|'''Clone Nr:'''
 
-
              | align="center" style="background:#f0f0f0;"|'''PCR type'''
 
-
              | align="center" style="background:#f0f0f0;"|'''Primers'''
 
-
              |-
 
-
              | 1||6||C||C1,C5
 
-
              |-
 
-
              | 2||1||A||C1,C3
 
-
              |-
 
-
              | 3||2||A||C1, C3
 
-
              |-
 
-
              | 4||3||A||C1, C3
 
-
              |-
 
-
              | 5||4||A||C1, C3
 
-
              |-
 
-
              | 6||5||A||C1, C3
 
-
              |-
 
-
              | 7||6||A||C1, C3
 
-
              |-
 
-
              | 8||1||B||C2,C4
 
-
              |-
 
-
              | 9||2||B||C2,C4
 
-
              |-
 
-
              | 10||Marker||||
 
-
              |-
 
-
              | 11||3||B||C2,C4
 
-
              |-
 
-
              | 12||4||B||C2,C4
 
-
              |-
 
-
              | 13||5||B||C2,C4
 
-
              |-
 
-
              | 14||6||B||C2,C4
 
-
              |-
 
-
              | 15||1||C||C1,C5
 
-
              |-
 
-
              | 16||2||C||C2,C4
 
-
              |-
 
-
              | 17||3||C||C2,C4
 
-
              |-
 
-
              | 18||4||C||C2,C4
 
-
              |-
 
-
              | 19||5||C||C2,C4
 
-
              |-
 
-
              |
 
-
              |}
 
-
<html>
 
-
              Results: all samples with same primers are identical
 
-
 
-
              PCR A: one band an dimer (900-800bp)
 
-
 
-
              PCR B: one band (1200bp)
 
-
 
-
              PCR C: two bands (800 and 400 bp)
 
-
             
 
-
              - 2 of the colonies are quite luckily mix colonies that contains our knockout, bands are shown for wildtype and 2 show amplification for kanR cassette
 
-
              - they should be transfered to a new plate for single colony test
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">           
 
-
              <h2 class="sub-content-project-headline"> 06/05 Thursday - New PCR protocol for ATPCS and PPMT with Q5 High Fidelity MasterMix </h2>
 
-
</html>
 
-
              '''PPMT PCR Reaction:'''
 
-
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Component'''
 
-
              | align="center" style="background:#f0f0f0;"|'''25µl'''
 
-
              | align="center" style="background:#f0f0f0;"|'''Final Conc.'''
 
-
              |-
 
-
              | 2x Q5 MM||12. Mai||1x
 
-
              |-
 
-
              | 10µM FW Primer||02. Mai||0,5µM
 
-
              |-
 
-
              | 10µM RW Primer||2,5||0,5µM
 
-
              |-
 
-
              | 95ng/µL Putida genomic DNA||2.63 (250ng)||9.99 ng/µL
 
-
              |-
 
-
              | Nuc. Free water||Apr 87||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              '''ATPCS PCR Reaktion
 
-
 
-
              result'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Component'''
 
-
              | align="center" style="background:#f0f0f0;"|'''25µl'''
 
-
              | align="center" style="background:#f0f0f0;"|'''Final Conc.'''
 
-
              |-
 
-
              | 2x Q5 MM||1.,5||1x
 
-
              |-
 
-
              | 10µM FW Primer||Jan 25||0,5µM
 
-
              |-
 
-
              | 10µM RW Primer||Jan 25||0,5µM
 
-
              |-
 
-
              | 230ng/µL Arabidopsis  cDNA||1.1 (250ng)||10 ng/µL
 
-
              |-
 
-
              | Nuc. Free water||08. Sep||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              PCR Program
 
-
              '''PPMT 234 bp 
 
-
              result'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''denaturing'''
 
-
              | align="center" style="background:#f0f0f0;"|'''98°C'''
 
-
              | align="center" style="background:#f0f0f0;"|'''180sec'''
 
-
              |-
 
-
              | Denaturing||98°C||10 sec
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | Annealing            30x||||
 
-
              |-
 
-
              | ||64°C||30 sec
 
-
              |-
 
-
              | Elongation||72°C||20 sec
 
-
              |-
 
-
              | Final Elongation||72°C||2min
 
-
              |-
 
-
              | Store||8°C||
 
-
              |-
 
-
              |
 
-
              |}
 
-
              '''ATPCS 1469bp
 
-
              result'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''denaturing'''
 
-
              | align="center" style="background:#f0f0f0;"|'''98°C'''
 
-
              | align="center" style="background:#f0f0f0;"|'''30 sec'''
 
-
              |-
 
-
              | Denaturing||98°C||10 sec
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | Annealing              30x||||
 
-
              |-
 
-
              | ||62°C||30 sec
 
-
              |-
 
-
              | Elongation||72°C||60 sec
 
-
              |-
 
-
              | Final Elongation||72°C||2min
 
-
              |-
 
-
              | Store||8°C||
 
-
              |-
 
-
              |
 
-
              |}
 
-
      <html>       
 
-
              </div>
 
-
 
-
              <div class="sub-content-project"> 
 
-
              <h2 class="sub-content-project-headline"> 05.06.2014 </h2>
 
-
 
-
              Cryostocks: RV 308 ferritin (Cm)<br/>
 
-
 
-
                                Nissle ferritin (Cm)<br/>
 
-
 
-
              500 µl 7%DMSO+ 500 µl Cell Culture medium => -80°C <br/>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">           
 
-
              <h2 class="sub-content-project-headline"> 06/06 Friday - PCR for ATPCS and PPMT with Q5 High Fidelity MasterMix </h2>
 
-
 
-
              PPMT PCR Reaction:<br/>
 
-
</html>
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Component'''
 
-
              | align="center" style="background:#f0f0f0;"|'''25µl'''
 
-
              | align="center" style="background:#f0f0f0;"|'''25µl'''
 
-
              | align="center" style="background:#f0f0f0;"|'''Final Conc.'''
 
-
              |-
 
-
              | 2x Q5 MM||12. Mai||12,5||1x
 
-
              |-
 
-
              | 10µM FW Primer||02. Mai||Jan 25||0,5µM
 
-
              |-
 
-
              | 10µM RW Primer||2,5||Jan 25||0,5µM
 
-
              |-
 
-
              | 95ng/µL Putida genomic DNA||5,26 (500ng)||5,26 (500 ng)||
 
-
              |-
 
-
              | Nuc. Free water||Apr 87||4,74||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              ATPCS PCR Reaction<br/>
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Component'''
 
-
              | align="center" style="background:#f0f0f0;"|'''25µl'''
 
-
              | align="center" style="background:#f0f0f0;"|'''Final Conc.'''
 
-
              |-
 
-
              | 2x Q5 MM||12. Mai||1x
 
-
              |-
 
-
              | 10µM FW Primer||Jan 25||0,5µM
 
-
              |-
 
-
              | 10µM RW Primer||Jan 25||0,5µM
 
-
              |-
 
-
              | 230ng/µL Arabidopsis cDNA||2.2 (500ng)||
 
-
              |-
 
-
              | Nuc. Free water||08. Sep||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              PCR programm<br/>
 
-
 
-
              PPMT 234 bp<br/>
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''denaturing'''
 
-
              | align="center" style="background:#f0f0f0;"|'''98°C'''
 
-
              | align="center" style="background:#f0f0f0;"|'''120sec'''
 
-
              |-
 
-
              | Denaturing||98°C||10 sec
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | Annealing 30x||||
 
-
              |-
 
-
              | ||64°C||30 sec
 
-
              |-
 
-
              | Elongation||72°C||20 sec
 
-
              |-
 
-
              | Final Elongation||72°C||2min
 
-
              |-
 
-
              | Store||8°C||
 
-
              |-
 
-
              |
 
-
              |}
 
-
              ATPCS 1469bp
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''denaturing'''
 
-
              | align="center" style="background:#f0f0f0;"|'''98°C'''
 
-
              | align="center" style="background:#f0f0f0;"|'''30 sec'''
 
-
              |-
 
-
              | Denaturing||98°C||10 sec
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | Annealing 30x||||
 
-
              |-
 
-
              | ||62°C||30 sec
 
-
              |-
 
-
              | Elongation||72°C||60 sec
 
-
              |-
 
-
              | Final Elongation||72°C||2min
 
-
              |-
 
-
              | Store||8°C||
 
-
              |-
 
-
              |
 
-
              |}
 
-
<html>
 
-
              10µl of PCR reaction + 2µl 6XDNA loading dye was loaded onto a 1 % agarose gel<br/>
 
-
 
-
              ATPCS (one clear thick epxacted band at Test of purity and quality of genomic DNA by running it through a 1% agarose gel1400 bp)<br/>
 
-
 
-
              PPMT1 (no band)<br/>
 
-
 
-
              PPMT2 (no band)<br/>
 
-
<br/>>
 
-
             
 
-
</html>
 
-
              '''Test of genomic DNA of P.Putida for purity and quality by running it on a 1% agarose gel'''
 
-
<br/>
 
-
              - looks fine on a gel. One clear band over 10 000 bp<br/>
 
-
 
-
           
 
-
 
-
              '''!!! Improve PPMT !!!:'''
 
-
 
-
              Try using DMSO (NEB PCR grad) and set Annealingtemperature down to 55°C<br/>
 
-
 
-
              Try different DMSO conc. : 0; 1; 5; 8  %
 
-
              <html>
 
-
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/11 Wednesday - Continuation of work from 06.06.2014: PCR for (ATPCS and) PPMT with Q5 </h2>
 
-
 
-
             
 
-
 
-
              PPMT PCR without success last weak. Therefore the temperature of the annealing step should reduce from 64°C up to 55°C in the pcr programm.<br/>
 
-
 
-
             
 
-
</html>
 
-
              '''1) corrected pcr programm for PPMT'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''T [°C]'''
 
-
              | align="center" style="background:#f0f0f0;"|'''t [s]'''
 
-
              |-
 
-
              | Denaturating||98||120
 
-
              |-
 
-
              | Denaturating||98||10
 
-
              |-
 
-
              | Annealing||55||30
 
-
              |-
 
-
              | Elongation||72||60
 
-
              |-
 
-
              | Final Elongation||72||120
 
-
              |-
 
-
              | Store||8||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              '''2) PPMT pcr reaction'''
 
-
 
-
              Different samples with concentrations on DMSO 0%, 1%, 5%, 8% were prepared. Use 99,97% DMSO the samples were prepared with the following pattern:
 
-
              The final volume is 25μl.<br/>
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''#1 [μl]'''
 
-
              | align="center" style="background:#f0f0f0;"|'''#2 [μl]'''
 
-
              |-
 
-
              | Q5 MM||12,5||12,5
 
-
              |-
 
-
              | 10 μl FW Primer||2,5||1,25
 
-
              |-
 
-
              | 10 μl RW Primer||2,5||1,25
 
-
              |-
 
-
              | Putida genomic DNA 95 ng/μl|| 5,26|| 5,26
 
-
              |-
 
-
              | dazu 1.: DMSO,||0||0
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              |            nuclease free H<sub>2</sub>O||2,24||4,74
 
-
              |-
 
-
              | dazu 2.: DMSO,||0,25||0,25
 
-
              |-
 
-
              |            nuclease free H<sub>2</sub>O||1,99||4,49
 
-
              |-
 
-
              | dazu 3.: DMSO,||1,25||1,25
 
-
              |-
 
-
              |            nuclease free H<sub>2</sub>O||0,99||3,49
 
-
              |-
 
-
              | dazu 4.: DMSO,||2||2
 
-
              |-
 
-
              |            nuclease free H<sub>2</sub>O||0,24||2,74
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              '''the 7 samples were labeled by the following schema:'''
 
-
 
-
              PPMT.1.1, PPMT.1.2, PPMT.1.3, PPMT.1.4 (Primer je 2,5μl, DMSO Konz. 0,1,5,8 %)
 
-
 
-
              PPMT.2.2, PPMT.2.3., PPMT.2.4 (Primer je 1,25μl, DMSO Konz. 1,5,8 %)
 
-
        <html>     
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">       
 
-
              <h2 class="sub-content-project-headline"> 06/12 Thursday - PCR of PPMT </h2>
 
-
              Amplification of PPMT with DMSO<br />
 
-
              ''(Continuation of work from 06.06.2014: PCR for PPMT with Q5''
 
-
 
-
              For Protocol please see Labjournal from 11.06.2014<br/>
 
-
 
-
             
 
-
 
-
    </html>           
 
-
 
-
              '''following labeling for 8 samples was used:'''
 
-
 
-
              PPMT.1.1, PPMT.1.2, PPMT.1.3, PPMT.1.4 (Primer je 2,5μl, DMSO Konz. 0,1,5,8 %)
 
-
 
-
              PPMT 2.1, PPMT.2.2, PPMT.2.3., PPMT.2.4 (Primer je 1,25μl, DMSO Konz. 0,1,5,8 %)
 
-
 
-
             
 
-
 
-
              <em>Gel Electrophoresis</em>
 
-
 
-
              1µl loading buffer+5 µl sample  loaded on 1% agarose gel; 90V<br />
 
-
 
-
              (rest of sample in iGEM freezer)
 
-
 
-
             
 
-
           
 
-
 
-
 
-
              <strong>Results</strong>
 
-
 
-
              contamination from water (band 3000bp for every sample)<br/>
 
-
 
-
              with higher DMSO conc. (5% and 8%) bands from visible
 
-
<html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/17 Tuesday - PCR Amplification of ATPCS from cDNA </h2>
 
-
 
-
              <em>PCR-pipetting scheme</em>
 
-
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Volume [µl] !! Chemicals
 
-
              |-
 
-
              | 12,5 || 2x Q5 Mastermix
 
-
              |-
 
-
              | 1,25 || 10µM fwd Primer
 
-
              |-
 
-
              | 1,25 || 10µM rev Primer
 
-
              |-
 
-
              | 2,2 || Arabinopsis Thaliana cDNA
 
-
              |-
 
-
              | 8,9 || nucl.free H<sub>2</sub>O
 
-
              |-
 
-
              | 26,1µl total volume
 
-
              |-
 
-
              |}
 
-
 
-
              <em>PCR-program</em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! PCR-step !! Temperature [°C] !! Time [sec]
 
-
              |-
 
-
              | Denaturation || 98 || 30
 
-
              |-
 
-
              |"30 cycles start"
 
-
              |-
 
-
              | Denaturation || 98 || 10
 
-
              |-
 
-
              | Annealing || 62 || 30
 
-
              |-
 
-
              | Elongation || 72 || 60
 
-
              |-
 
-
              |"30 cycles stop"
 
-
              |-
 
-
              | Final Elongation || 72 || 120
 
-
              |-
 
-
              | Store || 8 ||
 
-
              |}
 
-
 
-
<html>
 
-
 
-
              <strong>PCR Purification of ATPCS</strong>
 
-
              - Kit Purification<br />
 
-
              - Elutionbuffer: 30µl<br />
 
-
              <img src="https://static.igem.org/mediawiki/2014/f/f0/Team_berlin_0006.jpg" alt="" /><br/>
 
-
 
-
              - Final concentration: 69 µg/ml
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/18 Wednesday - PCR of drag outs to separate cells for FieF Knockout  </h2>
 
-
</html>
 
-
              Pick up 7 single colonies + 20µl d. H<sub>2</sub>O each (on ice) <br>
 
-
              --> Labeling: K1, K2, K3, K4, K5, K6, K7 <br>
 
-
              PCR for each colony with Primer combinations: C1-C3, C2-C4, C1-C5 --> 7x3= 21 Samples<br/>
 
-
 
-
              <em>PCR Assay</em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Amount [µl] !! Chemical
 
-
              |-
 
-
              | 1 || Sample (Colony)
 
-
              |-
 
-
              | 13,5 || d. H<sub>2</sub>O
 
-
              |-
 
-
              | 2 || 10x Dream Taq Polymerasebuffer
 
-
              |-
 
-
              | 1,2 || 25mM MgCl<sub>2</sub>
 
-
              |-
 
-
              | 0,5 || 10µM fwd Primer
 
-
              |-
 
-
              | 0,5 || 10µM rev Primer
 
-
              |-
 
-
              | 0,5 || 10mM dNTPs
 
-
              |-
 
-
              | 0,6 || Taq DNA Polymerasse
 
-
              |}
 
-
 
-
              <em>PCR Program</em>
 
-
              Colony-PCR: Elongation Time : 1,2 Min, Annealing Temp.: 55°C <br>
 
-
<html>
 
-
              <em>Gel Electrophoresis<em><br/>
 
-
              <img src="https://static.igem.org/mediawiki/2014/7/71/Team_berlin_0007.jpg" alt="" /><br/>
 
-
              <strong>Result</strong>
 
-
              RV-strain is not appropriate for Fief-Knockout. Unknown genome leads to unspecific binding of designed primers, too many bonds in gel electrophoresis picture.
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/19 Thursday </h2>
 
-
 
-
              Continue working with colonies: K1, K5, K6, K7 from 18.06.2014<br/>
 
-
</html>
 
-
              PCR-programme:
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Amount [µl] !! Chemical
 
-
              |-
 
-
              | 1 || Sample (Colony)
 
-
              |-
 
-
              | 13,5 || d. H<sub>2</sub>O
 
-
              |-
 
-
              | 2 || 10x Dream Taq Polymerasebuffer
 
-
              |-
 
-
              | 1,2 || 25mM MgCl<sub>2</sub>
 
-
              |-
 
-
              | 0,5 || 10µM fwd Primer C1
 
-
              |-
 
-
              | 0,5 || 10µM rev Primer C4
 
-
              |-
 
-
              | 0,5 || 10mM dNTPs
 
-
              |-
 
-
              | 0,6 || Taq DNA Polymerasse
 
-
              |}
 
-
 
-
              PCR-programme: <br>
 
-
              Elongation time: 2Min, Annealing Temperature: 56°C<br/>
 
-
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 1 of 4 </strong>
 
-
 
-
              '''Aim''':
 
-
              Test the possibility of Magnetization of E.coli cells by the expression of human Ferritin:
 
-
 
-
 
-
              '''Procedure''':
 
-
 
-
              To evaluate the effect of Ferritin  on the Magnetization different cultures were compared:<br/>
 
-
 
-
 
-
              For Both RV308 and Nissle
 
-
              {| class="wikitable"
 
-
              |-
 
-
              !Culture !! 1 !! 2 !! 3 !! 4
 
-
              |-
 
-
              |Plasimd || +|| -|| +|| +
 
-
              |-
 
-
              |iron || +|| +|| -|| +
 
-
              |-
 
-
              |induction || +|| +|| +|| -
 
-
              |}
 
-
 
-
 
-
 
-
              - Transform the Human Ferritin gen carried on the Plasmid PC514 provided from (iGEM Team of Calgary university, Canada) to E. coli strains
 
-
              (Nissle and  RV308) via electroporation, plate on (Amp) plates for selection.
 
-
<html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/20 Friday Restriction digest of pQE_80L and ATPCS-PCR fragment </h2>
 
-
</html>
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''''
 
-
              | align="center" style="background:#f0f0f0;"|'''1x'''
 
-
              | align="center" style="background:#f0f0f0;"|'''5x Mastermix'''
 
-
              | align="center" style="background:#f0f0f0;"|'''pQE_80L'''
 
-
              |-
 
-
              | H2O nucfree||23,1µl||115,5µl||2µl
 
-
              |-
 
-
              | 10x green FD buffer||2µl||10µl||2µl
 
-
              |-
 
-
              | DNA||2,89µl||14,5µl||14µl
 
-
              |-
 
-
              | BamHI||1µl||0µl||1µl
 
-
              |-
 
-
              | SacI||1µl||0µl||1µl
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              5x Mastermix = Mastermix for ATPCS <br />
 
-
 
-
              Enzymes were added to each single aliqout and not into the Mastermix<br />
 
-
 
-
 
-
              '''Incubation:''' for 1,5 h at 37 °C<br />
 
-
 
-
              '''Deactivation:''' 80°C for 5 min<br />
 
-
 
-
 
-
              ''I used the wrong restriction enzymes as I got confused with the PCR fragment. Digestion with SacI and HindIII is needed not  BamHI.
 
-
              ''Repeat PCR for ATPCS as well as restriction digest!
 
-
 
-
             
 
-
 
-
              <strong>Test expression of Ferritin in RV308 (pSB1C3_Ferrtin) and Nissle (pSB1C3_Ferrtin)</strong>
 
-
 
-
              5ml overnight culture used as an inoculum.<br/>
 
-
 
-
              4 ml culture were diluted to 40 ml with LB and grown for 1 h at 37°C until an OD600 of 0.7 and 0.8 was reached.<br/>
 
-
 
-
              Non-induced SDS sample was taken and induced with 1 mM IPTG<br/>
 
-
 
-
              After expression for 3 h induced SDS sample was taken.
 
-
              <em>SDS PAGE</em>
 
-
              Ferritin band ecpected at 21kDa<br />
 
-
 
-
              '''Key:'''<br />
 
-
              - 1st band: Nissle (non induced)<br />
 
-
              - 2nd band: RV308 (non induced)<br />
 
-
              - 3rd band: Ladder<br />
 
-
              - 4th band: Nissle (induced)<br />
 
-
              - 5th band: RV308 (induced)
 
-
<html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/25 Wednesday - Amplification of ATPCS (cDNA) </h2>
 
-
              <em>PCR-pipetting scheme</em>
 
-
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Volume [µl] !! Chemicals
 
-
              |-
 
-
              | 12,5 || 2x Q5 Mastermix
 
-
              |-
 
-
              | 1,25 || 10µM fwd Primer
 
-
              |-
 
-
              | 1,25 || 10µM rev Primer
 
-
              |-
 
-
              | 1,5 || Arabinopsis Thaliana cDNA
 
-
              |-
 
-
              | 8,9 || nucl.free H<sub>2</sub>O
 
-
              |-
 
-
              | 25,4µl total volume
 
-
              |-
 
-
              |}
 
-
 
-
              <em>PCR-program</em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! PCR-step !! Temperature [°C] !! Time [sec]
 
-
              |-
 
-
              | Denaturation || 98 || 30
 
-
              |-
 
-
              |"30 cycles start"
 
-
              |-
 
-
              | Denaturation || 98 || 10
 
-
              |-
 
-
              | Annealing || 62 || 30
 
-
              |-
 
-
              | Elongation || 72 || 60
 
-
              |-
 
-
              |"30 cycles stop"
 
-
              |-
 
-
              | Final Elongation || 72 || 120
 
-
              |-
 
-
              | Store || 8 ||
 
-
              |}
 
-
 
-
              <em>PCR Purification</em>
 
-
              -Purification Kit <br>
 
-
 
-
              →DNA concentration measurement showed, that the Absorbance ratio of 260nm:280nm is quite low, which means that targeted DNA got contaminated.
 
-
 
-
              <strong>'''Preparation of pre-culture'''</strong>
 
-
              '''Strains:'''<br />
 
-
              - e.coli nissle<br />
 
-
              - e.coli nissle + ferritin<br />
 
-
              - RV308<br />
 
-
              - RV308 + ferritin<br />
 
-
 
-
              <em>Assay</em>
 
-
              - 5ml LB media + 1 picked clone of the pre-day<br />
 
-
              - Addition of 5µl CN37 to the strains with ferritin<br />
 
-
 
-
              '''Incubation:''' 37°C; 170rpm; o/n
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/27 Friday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 2 of 4 </strong>
 
-
 
-
              - Preculture of 1 positive clone over night ( preculture: 7 ml LB+ 7µL Amp + 1 Clone)
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/28 Saturday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 3 of 4 </strong>
 
-
</html>
 
-
 
-
              - Transfer the Precultures (OD= 0.4-0.5) to 25, 50 mL flasks (half filled with LB) and cultivate them at 37°C for 3 hours
 
-
              RV308 (+,+,+) & (-,+,+) And Nissle (+,+,+) were cultivated in 50 mL flasks<br/>
 
-
 
-
 
-
              Strain:  OD<br/>
 
-
              RV308    0,78<br/>
 
-
              Nissle  0,86<br/>
 
-
 
-
              - Induction with (20µl (50 ML flasks)/10µl (25 ML flasks)) IPTG (concentation 1 M).<br/>
 
-
              - Add FeCl2 and MnCl2 (100µL in 50ml flasks/ 50µl in 25ml flasks) Incubation over night at 37C°<br/>
 
-
 
-
 
-
              Strain:  OD<br/>
 
-
              RV308    2.56<br/>
 
-
              Nissle  2.8<br/>
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/29 Sunday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 1st Experiment part 4 of 4 </strong>
 
-
 
-
              -Sampling for testing the Ferritin content via SDS-Page, different ODs were taken in consideration! <br/>
 
-
 
-
              -Prepare the sample for SDS-gel by centrifuation and discard the supernatant then add (60µl Dis.water + 15 SDS+ MH-EtoH), boil for 10 min at 94°C.<br/>
 
-
             
 
-
              - Test the Magnetization using an permanent magnet under light microscope. <br/>
 
-
</html>
 
-
 
-
              '''Evaluation''':
 
-
 
-
              '''SDS Page''':  was not clear!
 
-
 
-
              '''Magnetization :
 
-
              '''
 
-
 
-
              '''RV308'''                                           
 
-
              {| class="wikitable"
 
-
              |-
 
-
              !Culture !! 1 !! 2 !! 3 !! 4
 
-
              |-
 
-
              |Plasimd  || +|| -|| +|| +
 
-
              |-
 
-
              |iron      || +|| +|| -|| +
 
-
              |-
 
-
              |induction || +|| +|| +|| -
 
-
              |-Magnetization|| yes|| No|| No|| yes (strong)}
 
-
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              !Culture !! 1 !! 2 !! 3 !! 4
 
-
              |-
 
-
              |Plasimd  || +|| -|| +|| +
 
-
              |-
 
-
              |iron      || +|| +|| -|| +
 
-
              |-
 
-
              |induction || +|| +|| +|| -
 
-
              |-Magnetization|| yes|| No|| No|| yes (strong)}.
 
-
              '''Nissle'''
 
-
        <html>     
 
-
              In samples with Iron aggregates were observed with strong Mag.effect.
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 06/30 Monday - Colony PCR and Ligation ATPCS </h2>
 
-
</html>
 
-
 
-
              <em>PCR pipetting scheme</em>
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Volume [µl] !! Chemicals
 
-
              |-
 
-
              | 13,7 || nucl.free H<sub>2</sub>O
 
-
              |-
 
-
              | 2 || 10x Dream Taq Buffer
 
-
              |-
 
-
              | 1,2 || 25mM MgCl<sub>2</sub>
 
-
              |-
 
-
              | 0,5 || 10mM dNTPs
 
-
              |-
 
-
              | 0,5 || 10µM fwd Primer
 
-
              |-
 
-
              | 0,5 || 10µM rev Primer
 
-
              |-
 
-
              | 1 || Sample (Colony)
 
-
              |-
 
-
              | 0,6 || Dream Taq DNA Polymerase
 
-
              |-
 
-
              |20µl Total Volume
 
-
              |-
 
-
              |}
 
-
 
-
              <em>PCR program</em>
 
-
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! PCR-step !! Temperature [°C] !! Time [sec]
 
-
              |-
 
-
              | Denaturating || 95 || 180
 
-
              |-
 
-
              |''30 cycles start''
 
-
              |-
 
-
              | Denaturating || 95 || 30
 
-
              |-
 
-
              |Annealing || 55 || 30
 
-
              |-
 
-
              |Elongation|| 72 || 120
 
-
              |-
 
-
              |'' 30cycles stop''
 
-
              |-
 
-
              |Final Elongation || 72 || 600
 
-
              |-
 
-
              | Store || 12 ||
 
-
              |}
 
-
 
-
              <em>Gel Electrophoresis</em>
 
-
              1% Agarose gel with EtBr; 8µl sample; 5µl Ladder<br />
 
-
              "Key:"<br />
 
-
              First band= Ladder<br />
 
-
      <html>       
 
-
              Each other band is a different picked clone (10 clones were picked)<br/>
 
-
              <img src="https://static.igem.org/mediawiki/2014/0/0a/Team_berlin_0008.jpg" alt="" />
 
-
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/01 Tuesday - ATPCS Ligation </h2>
 
-
 
-
              The ligation of ATPCS was checked with 1% Agarose gel (stained with ethidiumbromid) after colony pcr.
 
-
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/02 Wednesday - Knockout of Fief and Fur in RV308 and Nissle </h2>
 
-
 
-
              To pepare the knockout 5 µl CM solution (pFerritin with canamycin resistance cassette)and 500 µl culture solution were added to 5 ml LB media. For each stain two samples were determined (RV1/2 and N1/2). The samples were incubated at 37°C up to an OD<sub>600</sub> of 0.53-0.55.
 
-
              After incubation 1 ml of each culture was transfered in sterile eppi and washed for 7 min at 7000 rpm and 4°C. The supernatant was descarded, the pellet was resuspended in 1 ml sterile H<sub>2</sub>O and washed for 7 min at 7000 rpm and 4°C and descarded the supernatant.
 
-
 
-
              The pellet of N1 was resuspended in 25 µl pRFP (c = 41 ng/µl) and 25 µl sterile H<sub>2</sub>O. The pellets of N2 and RV1/2 were resuspended in 2 µl pRFP and 50 µl sterile H<sub>2</sub>O. 50 µl of each suspension were transfered in electroporation cuvette and electroporated for a few sec (table below). Directly after this, 1 ml fresh LB media (37°C) was added, the suspension was transfered in a sterile eppi and incubated at 37°C at 600 rpm. The cultures were recovered, deleted on CM+Amp plates and incubated at 37°C ove night.
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Überschrift !! [kV] !! [ms]
 
-
              |-
 
-
              | N1 || 1,8 || 2,3
 
-
              |-
 
-
              | N2 || 1,2 || 5,4
 
-
              |-
 
-
              | RV1 || 1,2 || 5,3
 
-
              |-
 
-
              | RV2 || 1,5 || 5,3
 
-
              |}
 
-
 
-
 
-
 
-
              <strong>Transformation of stains RV, Nissle, WM</strong><br/>
 
-
 
-
              The stains RV308[ferritin], Nissle[ferritin], RV308, Nissle and WM110 were transformed with RFP. RV308[ferritin] and Nissle[ferritin] were deleted on CM+Amp plates and 5 ml culture was added with CM/Amp and incubated at 37°C. The transformed strains RV308, Nissle and WM110 were deleted on Amp plates and 5 ml culture was added with Amp and incubated at 37°C.
 
-
<br/>
 
-
 
-
 
-
              <strong>Results of transformation</strong><br/>
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! stain !! colonies on plate !! cells in culture
 
-
              |-
 
-
              | Nissle1 + RFP || 3 || Yes
 
-
              |-
 
-
              | Nissle2 + RFP || 19 || Yes
 
-
              |-
 
-
              | WM110 1 + RFP || 0 || Yes
 
-
              |-
 
-
              | WM110 2 + RFP || n.d. || Yes
 
-
              |-
 
-
              | RV308 1 + RFP || 0 || Yes
 
-
              |-
 
-
              | RV308 2 + RFP || 87 || Yes
 
-
              |-
 
-
              | Nissle[ferritin]1 + RFP || 10<sup>8</sup> || No
 
-
              |-
 
-
              | Nissle[ferritin]2 + RFP || 0 || No
 
-
              |-
 
-
              | RV308[ferritin] 1 + RFP || 330 || Yes
 
-
              |-
 
-
              | RV308[ferritin] 2 + RFP || 300 || Yes
 
-
              |}
 
-
<html>
 
-
              The cultures of WM110 1 + RFP and WM110 2 + RFP were deleted on Amp plates and incubated at 37°C. Moreover 5 ml precultures from RV308 + RFP + Amp and RV308[ferritin] + RFP + CM+Amp were prepared.
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/03 Thursday - PCR amplification of knockout cassette FUR/FieF </h2>
 
-
 
-
              The pcr preparation was performed at the pattern in the table below.<br/>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! pcr preparation !! FUR (25µl) !! FieF (50µl)
 
-
              |-
 
-
              | Os High Fedility 2x Mastermix || 12,5 µl || 25 µl
 
-
              |-
 
-
              | forward primer 10mM || 1,25 µl || 2 µl
 
-
              |-
 
-
              | reverse primer 10mM || 1,25 µl || 2,5 µl
 
-
              |-
 
-
              | pkD4 plasmid DNA 1 ng/µl || 1 µl || 1 µl
 
-
              |-
 
-
              | nuclease-free H<sub>2</sub>O || to 25 µl || to 50 µl
 
-
              |}
 
-
 
-
              The amplification was performed with the programm in the table below.<br/>
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! step !! T [°C] !! t [sec]
 
-
              |-
 
-
              | initial denaturation || 98 || 30
 
-
              |-
 
-
              | 5 cycles || 98/ 63/ 72 || 8/ 25/ 45
 
-
              |-
 
-
              | 25 cycles || 98/ 72 || 8/ 70
 
-
              |-
 
-
              | final elongation || 72 || 120
 
-
              |}
 
-
              --> hold at 8°C
 
-
 
-
              The amplification results were analysed in agarose gelelectrophorese (1% agarose; 0,5µl Gel Red; 10x diluted ladder; 6x loading dye).
 
-
<html>
 
-
              </div>
 
-
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/04 Friday - Expression von RV308 (RFP) und RV308 (RFP + Ferritin) </h2>
 
-
 
-
             
 
-
 
-
              50 ml LB + 50 µl Amp inoculated with 5 ml overnight culture of RV308 (RFP)<br/>
 
-
 
-
             
 
-
 
-
              50 ml LB + 50 µl Amp/Cm inoculated with 5 ml overnight culture of RV308 (RFP + Ferritin)<br/>
 
-
 
-
             
 
-
 
-
              After a OD of 0.6-0.7 was reached 50 ml cultures were portioned into 4 sterile 100 ml flasks so that there was a final volume of 10 ml in each flask.<br/>
 
-
 
-
             
 
-
 
-
              The cultures were then cultred the following:<br/>
 
-
</html>
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''RV308 (RFP)'''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''RV308 (RFP + Ferritin)'''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              | align="center" style="background:#f0f0f0;"|'''              '''
 
-
              |-
 
-
              | Induced 1 mM IPTG||+||-||+||-||||+||-||+||-
 
-
              |-
 
-
              | Fe/Mn each 1 mM*||+||+||-||-||||+||+||-||-
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              *Fe/Mn were solubilized by autoclaving and 1M stock solution<br/>
 
-
<html>
 
-
             
 
-
 
-
              Altough not planned IPTG and metal ion solutions were added simultaneously due to time constraints. It was planned to add metal ions 2h after induction
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/07 Monday - Preculture prepared of: </h2>
 
-
             
 
-
 
-
              1. ATPCS Klon 1 - 10 (Amp)  --> check if anything grew and contact Johann<br/>
 
-
 
-
              2. WM110 (RFP), RV308 (RFP), Nissle (RFP), RV308 (Ferritin + RFP) --> make Cryostock for each<br/>
 
-
 
-
             
 
-
 
-
              Overgrown WM110 (RFP) plate streaked out again, please take out and put in cool room<br/>
 
-
 
-
             
 
-
 
-
              Rune:<br/>
 
-
 
-
              PCR of PPMT and ATPCS
 
-
 
-
     
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">                                     
 
-
              <h2 class="sub-content-project-headline"> 07/09 Wednesday - PCR for  PPMT with goTaq (Promega) </h2>
 
-
 
-
 
-
              25 mikrol reaction:<br/>
 
-
 
-
              12,5 mikrol goTaqMastermix<br/>
 
-
 
-
              1,25 mikrol fw Primer 10mikrom<br/>
 
-
 
-
              1,25 mikrol b Primer 10mikrom<br/>
 
-
 
-
              1,0 mikrol DNA Template PPMT <br/>
 
-
 
-
              9,0 mikrol nucleasefreies Wasser<br/>
 
-
 
-
              '''Mit folgenden PCR-Programm Parametern:'''
 
-
 
-
              Denaturation  98°C  10 min<br/>
 
-
              Denaturation loop 98°C  1 min<br/>
 
-
              Annealing Temp loop 56°C  1 min<br/>
 
-
              Elongation Time loop  72°C  1 min<br/>
 
-
              Final Elongation  72°C  5 min<br/>
 
-
              Storage 8°C infinite<br/>
 
-
 
-
              <strong> Miniprep </strong>
 
-
              Miniprep of ATPCS clone number 3 = 94ng/µl and sent for Sequencing
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/17 Thursday - Midiprep </h2>
 
-
              #pQE_80L = 183 ng/µl<br/>
 
-
              #pMA-T_PPMT =321ng/µl<br/>
 
-
              #pKD46 = 218ng/µl<br/>
 
-
 
-
              <strong>Digestion</big></strong><br/>
 
-
              Digestion pQE_80L with HindIII and SacI<br>
 
-
              deactivated at 80°C for 10 mins
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/24 Thursday - miniPrep + restriktion PPMT und iGEM plasmids </h2>
 
-
 
-
              Plasmide:
 
-
 
-
              1. pBADex-mYFP Venus (Amp)<br/>
 
-
 
-
              2. pEx-HISII (Amp)<br/>
 
-
 
-
              3. pJS418_phagemid(dummy) (Cm)<br/>
 
-
 
-
             
 
-
 
-
              Restriction-enzymes: XbaI | PstI (used SpeI instead :X)<br/>
 
-
 
-
              kit-miniprep<br/>
 
-
 
-
              1. 220ng/µl  2. 130ng/µl  3. 430ng/µl<br/>
 
-
 
-
              restriction:<br/>
 
-
 
-
              500 ng DNA + 1µl XbaI + 1µl PstI + 5µl 10x Buffer + ->50µl Wasser (x3) [ppmt x4]<br/>
 
-
 
-
              1. 2,3µl 2. 3,8µl 3. 1,2 µl PPMT 1,6µl<br/>
 
-
 
-
             
 
-
 
-
              2nd try w/ right enzyme:<br/>
 
-
 
-
              1,5 µg DNA + 0.5 µl enzymes + 3µl BUffer + -> 30 µl Wasser<br/>
 
-
 
-
              1. 6,5µl 2. 11 µl 3. 3,5 µl PPMT 4,5 µl (x3)<br/>
 
-
 
-
             
 
-
 
-
              Fragments: 1. 4043/700 2. 4450/55 3. 3800/861 PPMT 2400/251<br/>
 
-
 
-
              Gel1 L|3| 1 |1|2|2|2|P|3|3  Gel2 L|P|P|P<br/>
 
-
 
-
             
 
-
              Neu: Gel 1|2|3|L|P|P|P<br/>
 
-
 
-
              GelEx QiagenKit -> extrakte in grüner box im freezer<br/>
 
-
 
-
              Ligation 2 + P<br/>
 
-
 
-
              10µl Ansatz: 1µl BUffer + 0.5 µl Ligase + 1.4 µl PPMT + 7.14 µl pEX-HisII [78ng]
 
-
              </div>
 
-
 
-
 
-
                <div class="sub-content-project">         
 
-
              <h2 class="sub-content-project-headline"> 07/25 Friday </h2>
 
-
              1. Ordered Primer for cloning hu_Ferritin into pQE80L<br/>
 
-
 
-
              2.) Ligation of PPMT Fragment from pMAC_PPMT into pEX_HisII<br/>
 
-
 
-
             
 
-
 
-
              pMAC_PPMT and pEX_HisII were digested with HF PstI and HF XbaI (NEB)<br/>
 
-
 
-
              PPMT (Insert)  and cut pEX_HisII (Vector DNA) were purified via an Gel extraction<br/>
 
-
 
-
             
 
-
 
-
              Ligation was performed using NEB T4 DNA Ligase in molar ratios of (Insert:Vector) and 40 ng Vector were used.<br/>
 
-
 
-
              0:1    2:1      3:1    5:1<br/>
 
-
</html>
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Ratio'''
 
-
              | align="center" style="background:#f0f0f0;"|'''02:01'''
 
-
              | align="center" style="background:#f0f0f0;"|'''03:01'''
 
-
              | align="center" style="background:#f0f0f0;"|'''05:01'''
 
-
              |-
 
-
              | Amount Insert||4,04 ng||6,06 ng||10,1 ng
 
-
              |-
 
-
              |
 
-
              |}
 
-
<html>
 
-
              Ligase was deactivated and ligation transformed after weekend
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/28 Monday </h2>
 
-
 
-
              1. Degradation test of prepped TB-Expression Plasmids by running samples on agarose gel<br/>
 
-
 
-
              pBADex_MYFP_Venus  (no observable degradation)<br/>
 
-
 
-
              pEX_HisII (no observable degradation)<br/>
 
-
 
-
              pJS418_Phagemid (Dummy) (no observable degradation)<br/>
 
-
 
-
              Data:<br/>
 
-
 
-
              Fabian : 28072014_1<br/>
 
-
 
-
              2.Transformation of 0.2 µl pEX_His_PPMT ligation into DH5alpha, DH10b, and MG1655 via electroporation
 
-
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/29 Tuesday </h2>
 
-
 
-
              1.) Transformation worked and we got colonies for pEX_HisII_PPMT<br/>
 
-
 
-
              Colony PCR was performed (Sascha)<br/>
 
-
 
-
              See Standard Protocol<br/>
 
-
 
-
             
 
-
 
-
              2.) Ligation of ATPCS PCR Fragment into pQE_80L<br/>
 
-
 
-
             
 
-
 
-
              ATPCS PCR fragment and PQE80L Vector were digested with FD HindIII and FD SacI (ThermoScientific)<br/>
 
-
 
-
              ATPCS was purified via PCR purification and Vector DNA was purified via an Gel extraction<br/>
 
-
 
-
              Vector DNA was dephosphorylised using Fast-AP and deactivated<br/>
 
-
 
-
              Ligation was performed using NEB T4 DNA Ligase in molar ratios of (Insert:Vector) and 40 ng Vector were used.<br/>
 
-
 
-
              0:1    2:1      3:1    5:1
 
-
</html>
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''Ratio'''
 
-
              | align="center" style="background:#f0f0f0;"|'''02:01'''
 
-
              | align="center" style="background:#f0f0f0;"|'''03:01'''
 
-
              | align="center" style="background:#f0f0f0;"|'''05:01'''
 
-
              |-
 
-
              | Amount Insert||24,96 ng||37,41 ng||62,36 ng
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              Ligase was deactivated and ligation transformed next day
 
-
<br/><br/>
 
-
              <img src="https://static.igem.org/mediawiki/2014/1/11/Team_berlin_0009.jpg" alt="" /><br/>
 
-
 
-
              #pMAC_PPMT*
 
-
              #pQE_80L*
 
-
              #pSB1c3
 
-
              #pKD46*
 
-
<html>
 
-
              (*)Bands at 20 kbp for Promega prepped Plasmids.
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/30 Wednesday</h2>
 
-
              <strong> Results Colony PCR for pEX-HisII-PPMT clones </strong>
 
-
     
 
-
 
-
              preculture 4 and 5 in incubator for Miniprep and Sequencing<br/>
 
-
</html>
 
-
              <strong> Transformation </strong>
 
-
              <em>Chemical competent cells XL Blue </em>
 
-
              * 3 µl for each Ligation Assay
 
-
              * 10 min incubation on ice
 
-
              *60 s Heat schock
 
-
              * 2 min incubation on ice
 
-
              *950µl LB added
 
-
              *1h --> 37 °C for Recovery
 
-
              *platted on Amp-plates
 
-
              <em> Eporation </em>
 
-
              *0.2 µl Ligationassay in competent DH5α [iGEM]
 
-
              *1.7 kV
 
-
              * 1h; 37°C
 
-
              * platted on Amp plates
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 07/31 Thursday </h2>
 
-
              Miniprep for sequencing of pEx_His_ppmt in DH10B? 90-100 ng/µl<br/>
 
-
 
-
              Cryostock & miniprep of pjs418 in DH5a 518ng/µl<br/>
 
-
 
-
              PCR of 7 clones with pQe80l_ATPCS<br/>
 
-
 
-
              16 µl wasser<br/>
 
-
 
-
              2 green dreamtaq buffer<br/>
 
-
 
-
              0.5 dNTP<br/>
 
-
 
-
              0.5 primer (each)<br/>
 
-
 
-
              colony<br/>
 
-
 
-
              0.6 dream taq<br/>
 
-
 
-
             
 
-
 
-
              95° 3min<br/>
 
-
 
-
              95° 30s x30<br/>
 
-
 
-
              55° 30s x30<br/>
 
-
 
-
              72° 2min x30<br/>
 
-
 
-
              72° 10min<br/>
 
-
</html>
 
-
   
 
-
              Colonie PCR did not work--> no positive clones
 
-
              concentration after MiniPrep<br>
 
-
              * pJS418 = 518 ng/µl
 
-
              * Klone 4 = 90 ng/µl
 
-
              * Klone 5= 105 ng/µl
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/06 Wednesday </h2>
 
-
 
-
              PCR
 
-
</html>
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''BamHI_PPMT_GS'''
 
-
              | align="center" style="background:#f0f0f0;"|'''GS_ATPCS_HindIII'''
 
-
              | align="center" style="background:#f0f0f0;"|'''BamHI_HuFerritin_HindIII'''
 
-
              |-
 
-
              | Q5 2x Mastermix||12,5||12,5||25
 
-
              |-
 
-
              | 10  µM Primer fw||1,25||1,25||1,25
 
-
              |-
 
-
              | 10  µM Primer rev||1,25||1,25||1,25
 
-
              |-
 
-
              | template (1ng)|| 0,30|| 0,5|| 1
 
-
              |-
 
-
              | nucfree H2O|| 9,7|| 9,5|| 19
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              Program:
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''BamHI_PPMT_GS'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''GS_ATPCS_HindIII'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''BamHI_HuFerritin_HindIII'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              |-
 
-
              | 98||30''||  ||98||30''||  ||98||30''
 
-
              |-
 
-
              | ||||||||||||||
 
-
              |-
 
-
              | 98||10''||||98||10''||||98||10''
 
-
              |-
 
-
              | 58||30''||||56,3||30''||||58,6||30''
 
-
              |-
 
-
              | 72||12''||||72||60''||||72||45''
 
-
              |-
 
-
              | ||||||||||||||
 
-
              |-
 
-
              | 72||2'||||72||2'||||72||2'
 
-
              |-
 
-
              | 8||end||||8||end||||8||end
 
-
              |-
 
-
              |
 
-
              |}
 
-
<html>
 
-
              Analytical Gel
 
-
              Expacted Bands clearly seen for PPMT and Ferritin. Only little ATPCS band shows Primer Dimer inhibit PCR. Anyhow we will try a Gel extraction and after a Assembly PCR
 
-
 
-
 
-
              <strong> Generation of Heme-free BFR by Site-directed Mutagenesis, part 1 of 5 </strong><br/>
 
-
 
-
              <strong>Site-directed mutagenesis was performed by the QuickChange method </strong><br/>
 
-
 
-
              Primer design with http://www.bioinformatics.org/primerx/
 
-
 
-
              methionine (on position 52) was substituted by histidine
 
-
 
-
              BFR M52H
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/07 Thursday</h2>
 
-
 
-
              Analysing 2 colonies of pQE80L_ATPCS whether ATPCS was inserted by sequencing revealed no proper results.<br/>
 
-
 
-
              Tested by colony PCR (see protocols) using 55°C Annealing temp and 2' Elongation time (expected bands should be 2000bps).<br/>
 
-
 
-
              Gel showed PCR was about 500 bp big -> ATPCS NOT INSERTED.<br/>
 
-
 
-
              Outcome:BamHI_PPMT_GS    super<br>
 
-
              GS_ATPCS_HindIII  bad<br>
 
-
              BamHI_Ferritin    super
 
-
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/08 Friday - Gradienten PCR GS_ATPCS_HindIII </h2>
 
-
</html>
 
-
              '''PCR'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''3x GS_ATPCS_HindIII'''
 
-
              |-
 
-
              | Q5 2x Mastermix||12,5
 
-
              |-
 
-
              | 10  µM Primer fw||1,25
 
-
              |-
 
-
              | 10  µM Primer rev||1,25
 
-
              |-
 
-
              | template (1ng)|| 0,5
 
-
              |-
 
-
              | nucfree H2O|| 9,5
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              '''Program:'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''GS_ATPCS_HindIII'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              |-
 
-
              | 98°C||30''||
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | 98°C||10''||
 
-
              |-
 
-
              | 56,3-62°C||30''||34
 
-
              |-
 
-
              | 72°C||60''||
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | 72°C||2'||
 
-
              |-
 
-
              | 8°C||end||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              - preparative agarose gel 1% and gel ex of GS_ATPCS_HindIII bands at ca. 1490 bp<br/>
 
-
 
-
              - accidentally also loaded BamHI_PPMT_GS onto Gel and was also  extracted (elution with 25 µl elution buffer).<br/>
 
-
 
-
              - BamHI_Ferritin_HindIII was PCR purified<br/>
 
-
 
-
              - DNA concentration meassurement for  purificated pcr fragments:<br/>
 
-
 
-
              GS_ATPCS_HindIII = 33 ng/µl<br/>
 
-
 
-
              BamHI_PPMT_GS = 48 ng/µl<br/>
 
-
 
-
              BamHI_Ferritin_HindII = 125 ng/µl<br/>
 
-
 
-
              '''Assembly PCR'''
 
-
 
-
              An Assembly PCR was used to align BamHI_PPMT_GS with GS_ATPCS_HindIII and amplify the complementary structure in order to form a fusion protein coding sequence.<br/>
 
-
 
-
              Therefore, both fragments were added a templated equal molar amounts.<br/>
 
-
 
-
              Calcultation:<br/>
 
-
 
-
              bpATPCS = 1493<br/>
 
-
 
-
              bpPPMT = 255<br/>
 
-
 
-
              mATPCS/bpATPCS = mPPMT/bpPPMT<br/>
 
-
 
-
              mATPCS = (1ng * 1493) / 255<br/>
 
-
 
-
              mATPCS= 58 ng<br/>
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|'''BamHI_PPMT_GS_ATPCS_HindIII'''
 
-
              |-
 
-
              | Q5 2x Mastermix||25
 
-
              |-
 
-
              | 100  µM Primer fw||0.25 (not added till later to second PCR run)
 
-
              |-
 
-
              | 100  µM Primer rev||0.25 (not added till later to second PCR run)
 
-
              |-
 
-
              | template (1ng)|| 1,750 µl ATPCS + 0.208 µl PPMT
 
-
              |-
 
-
              | nucfree H2O|| 18.042
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              '''Program:'''
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''1. PCR BamHI_PPMT_GS_ATPCS_HindIII'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              |-
 
-
              | 98||30''|| 
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | 98||10''||
 
-
              |-
 
-
              | 68||30''|| 5
 
-
              |-
 
-
              | 72||55''||
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | 72||1'||
 
-
              |-
 
-
              | 8||end||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
              {| {{table}}
 
-
              | align="center" style="background:#f0f0f0;"|'''2. PCR BamHI_PPMT_GS_ATPCS_HindIII'''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              | align="center" style="background:#f0f0f0;"|''''''
 
-
              |-
 
-
              | 98||30''|| 
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | 98||10''||
 
-
              |-
 
-
              | 68||30''|| 30
 
-
              |-
 
-
              | 72||55''||
 
-
              |-
 
-
              | ||||
 
-
              |-
 
-
              | 72||2'||
 
-
              |-
 
-
              | 8||end||
 
-
              |-
 
-
              |
 
-
              |}
 
-
 
-
   
 
-
 
-
 
-
              <em> Transformation into DH10B </em>
 
-
              #BFR M52H
 
-
              # BFR M52H
 
-
              *Recover in LB--> 1h at 37°C
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/11 Monday - Plan-prepare fragments for digest </h2>
 
-
              Constructs aimed for
 
-
              </html>
 
-
              *In pQE_80L (Amp)    BamHI_PPMT_GS_ATPCS_Hind III  (PCR Construct available)
 
-
              Construct Size 1724 of 4731
 
-
 
-
              *In pQE_80L (Amp)    BamHI_FTH_FTL_Hind III  (PCR Construct available)
 
-
              Construct Size 1077 of 4731
 
-
 
-
              *In pQE_80L (Amp)  Sacl_ATPCS_Hind III    (PCR Construct not available)
 
-
              Construct Size 1400 of 4731
 
-
 
-
              *In pJS418 (CM)    XbaI_PPMT_PstI      (PCR Construct available)
 
-
              Construct Size 255 of 3800
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Q5 MasterMix !! 25μl
 
-
              |-
 
-
              | ATPCS SacI || 2.5
 
-
              |-
 
-
              | ATPCS Hind III|| 2.5
 
-
              |-
 
-
              | cDNA At. || 0.5
 
-
              |-
 
-
              | H<sub>2</sub>O || 19.5
 
-
              |-
 
-
 
-
              |}
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! PCR Programm !!
 
-
              |-
 
-
              | 98°C|| 30 sec
 
-
              |-
 
-
              | 98°C || 10 sec
 
-
              |-
 
-
              | 62°C 34cycles || 30 sec
 
-
              |-
 
-
              | 72°C || 60 sec
 
-
              |-
 
-
              | 72°C|| 2 mins
 
-
              |-
 
-
              | 4°C|| Store
 
-
              |}
 
-
 
-
 
-
              PCR Fragmente PPMT_GS_ATPCS+ATPCS+Purification (Gelex)<br/>
 
-
 
-
<html>
 
-
              After Gelex:<br/>
 
-
              PPMT  48ng/μl<br/>
 
-
 
-
              Ferritin 125ng/μl (Pur from PCR)<br/>
 
-
 
-
              ATPCS 33ng/μl <br/>
 
-
              </div>
 
-
 
-
 
-
                <div class="sub-content-project">           
 
-
              <h2 class="sub-content-project-headline"> 08/12 Tuesday - Preparing chemically competent cells </h2>
 
-
              V=100ml, 37°C<br/>
 
-
              BU36=DH10B
 
-
 
-
              OD at 600nm=0.461A <br/>
 
-
              DH10B competent cells<br/>
 
-
 
-
</html>
 
-
              '''''Digestion'''''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Inserts PCR Pur !! JBH1  PPMT_GS_ATPCS 1 !! JBH2  PPMT_GS_ATPCS 2 !! JBH3 Ferritin !! JSH  ATPCS
 
-
              |-
 
-
              | PCR Fragment  || 20|| 20 || 8|| 20
 
-
              |-
 
-
              | Buffer || 3 || 3|| 3 || 3
 
-
              |-
 
-
              | FD BamHI /FD SacI|| 1|| 1|| 1 || 1
 
-
              |-
 
-
              | FD Hind III || 1 || 1 || 1 || 1
 
-
              |-
 
-
              | nuclease free H<sub>2</sub>O || 5 || 5 || 17|| 5
 
-
 
-
              |}
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Vector !! VBH pQE_80L !! VSH pQE_80L SacI !! 2x PJS_418 !! 2x P_Mac_PPMT
 
-
              |-
 
-
              | Vector || 5.5 || 5.5|| 1.9|| 3.2
 
-
              |-
 
-
              | Enzyme 1|| 1 BamHI || 1 SacI || 1 FDxBa|| 1 FDxBa
 
-
              |-
 
-
              | Enzyme 2 || 1 HindIII || 1 HindIII || 1 FD PST || 1 FD PST1
 
-
              |-
 
-
              | Buffer || 3|| 3 || 2|| 2
 
-
              |-
 
-
              | Fast AP || 1|| 1 || 0 || 0
 
-
              |-
 
-
              | nuclease free H<sub>2</sub>O|| 18.5|| 18.5 || ||
 
-
              |}
 
-
 
-
 
-
              * 35 ng/L  PPMT ATPCS 1
 
-
              * 15ng/L  PPMT ATPCS 2
 
-
              * 25ng/L  ATPCS
 
-
              * 13ng/L  P_Mac_PPMT
 
-
              * 31ng/L  PJS_418
 
-
              <html>
 
-
<br/>
 
-
<img src="https://static.igem.org/mediawiki/2014/9/91/Team_berlin_0010.jpg" alt=""/><br/>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Ligation 5:1 !! JBH1 in VBH !! JBH2 in VBH !! JBH3 in VBH!! JSH in VSH !! PPMT in PJS_418
 
-
              |-
 
-
              | 10x T4 DNA ligase Buffer|| 1μl|| 1μl || 1μl || 1μl || 1μl
 
-
              |-
 
-
              | Vector || 1.42 || 1.42 || 1.42|| 1.33|| 1.29
 
-
              |-
 
-
              | Insert || 3.29 || 7.08 || 1.36 || 7.17 || 1.03
 
-
              |-
 
-
              | Nuclease free H<sub>2</sub>O || 3.79 || 0 || 5.72 || 0 || 6.18
 
-
              |-
 
-
              | T4 DNA ligase (NEB)|| 0.5 || 0.5 || 0.5 || 0.5 || 0.5
 
-
 
-
 
-
              |}
 
-
 
-
              Ampicillin  <br>
 
-
              JBH1 in VBH<br>
 
-
              JBH2 in VBH <br>
 
-
              JSH in VSH <br>
 
-
 
-
              Chloramphenicol <br>
 
-
              PPMT in PJS_418
 
-
 
-
              Transformation in DH10b (cc.c)<br>
 
-
              10<sup>6</sup> Kolonie for every approach  <br>
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">           
 
-
              <h2 class="sub-content-project-headline"> 08/13 Wednesday - pQE 80L Colony PCR </h2>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Mastermix !! 1x!! 35x !! 10x
 
-
              |-
 
-
              | nuclease free H<sub>2</sub>O|| 14 || 490 || 140
 
-
              |-
 
-
              | 10 dreamtaq|| 1 || 70|| 20
 
-
              |-
 
-
              | 25µM MgCl<sub>2</sub> || 1.2 || 42|| 12
 
-
              |-
 
-
              | 10mM dNTPs || 0.5|| 17.5 || 5
 
-
              |-
 
-
              | 10mM Forward Primar || 0.5|| 17.5|| 5
 
-
              |-
 
-
              | 10mM Reverse Primar || 0.5 || 17.5 || 5
 
-
              |-
 
-
              | Taq|| 0.3 || 10.5 || 3
 
-
              |
 
-
              |}
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! PCR Programm !!
 
-
              |-
 
-
              | 95°C|| 3 mins
 
-
              |-
 
-
              | 95°C || 30 secs
 
-
              |-
 
-
              |55°C|| 30 secs
 
-
              |-
 
-
              | 72°C|| 60 secs
 
-
              |-
 
-
              | 72°C || 10 min
 
-
              |-
 
-
              | 8°C|| Store
 
-
              |}
 
-
 
-
 
-
              Samples : <br>
 
-
              # PPMT GS ATPCS  size 1912
 
-
              # PPMT GS ATPCS  size 1912
 
-
              # ATPCS in pQE80L  size 1770
 
-
              # Ferritin in pQE80L  size 1376
 
-
              # PPMT in PJS  size 420
 
-
 
-
 
-
              pQE80L=300bp  <br>   
 
-
              pJS = 170bp<br>
 
-
 
-
              Sequence clones A - H + J<br>
 
-
 
-
 
-
 
-
              <strong> Generation of Heme-free BFR by Site-directed Mutagenesis, part 2 of 5 </strong>
 
-
 
-
 
-
              QuickChange Site-Directed Mutagenesis<br>
 
-
 
-
              20µL approach:
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Überschrift !! component
 
-
              |-
 
-
              | 2 µL || 10x Pfu Buffer (MgSO4)
 
-
              |-
 
-
              | 0,6 µL || 10µM forward Primer
 
-
              |-
 
-
              | 0,6 µL || 10µM reverse Primer
 
-
              |-
 
-
              | x µL || 30ng Template
 
-
              |-
 
-
              | 0,4 µL || dNTPs
 
-
              |-
 
-
              | 0,6 µL || Pfu Polymerase
 
-
              |-
 
-
              | to 20 µL || PCR Wasser
 
-
              |}
 
-
 
-
 
-
              Template BFR: <br/>
 
-
 
-
              0,5 µL              A4 (66ng/µL)<br/>
 
-
 
-
              0,2 µL    D2 (144ng/µL)<br/>
 
-
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! labeling !! Template !! Annealing Temp.
 
-
              |-
 
-
              | 17 || D2 (144ng/µL) || 71°C
 
-
              |-
 
-
              | 15 || D2 (144ng/µL) || 55°C
 
-
              |-
 
-
              | 67 || A4 (66ng/µL) || 71°C
 
-
              |-
 
-
              | 65 || A4 (66ng/µL) || 55°C
 
-
              |}
 
-
 
-
 
-
              PCR Program<br/>
 
-
 
-
              {|
 
-
              |-
 
-
              ! Temp !! time
 
-
              |-
 
-
              | 95°C  || 30sec
 
-
              |-
 
-
              | ________ || ______
 
-
              |-
 
-
              | 16 Cyclen ||
 
-
              |-
 
-
              | 95°C  ||  30sec
 
-
              |-
 
-
              | 55/71°C  || 1min
 
-
              |-
 
-
              | 68°C  || 5min
 
-
              |-
 
-
              | ________ || ______
 
-
              |-
 
-
              | 68°C || 10sec
 
-
              |-
 
-
              | 4°C  || finale
 
-
              |}
 
-
 
-
              Σ20µL -8µL fürs Gel= 12µL +1µL DpnI
 
-
 
-
 
-
              37°C 90min<br/>
 
-
 
-
              '''chemical Transformation (Fabian)
 
-
              '''
 
-
 
-
              in DH10b<br/>
 
-
<html>
 
-
 
-
              plating out on Amp plates
 
-
              </div>
 
-
 
-
 
-
                <div class="sub-content-project">       
 
-
              <h2 class="sub-content-project-headline"> 08/15 Friday - Clone Sequencing </h2>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Clone !! Name !! Construct present !! concentration after isolation
 
-
              |-
 
-
              | A|| pQE_80L_PPMT GS ATPCS || yes || 388ng/µL
 
-
              |-
 
-
              | B|| pQE_80L_PPMTGSATPCS || yes || 373ng/µL
 
-
              |-
 
-
              | C || pQE_80L_PPMTGSATPCS || yes|| 442ng/µL
 
-
              |-
 
-
              | D || pQE_80L_PPMTGSATPCS || no|| 389 ng/µL
 
-
              |-
 
-
              | E || pQE_80L_huFerritin || yes|| 490ng/µL
 
-
              |-
 
-
              | F|| pQE_80L_huFerritin || no|| 402ng/µL
 
-
              |-
 
-
              | G || pQE_80L_ATPCS|| yes || 497ng/µL
 
-
              |-
 
-
              | H || pQE_80L_ATPCS || yes  || 443 ng/µL
 
-
              |-
 
-
              | I || pJS418_PPMT|| yes || 596 ng/µL
 
-
              |}
 
-
 
-
<html>
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/19 Tuesday </h2>
 
-
 
-
              <strong> Generation of Heme-free BFR by Site-directed Mutagenesis, part 3 of 5 </strong>
 
-
 
-
              ÜN culture<br/>
 
-
 
-
              5ml LB + 5µL Amp →shakingincubator
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/20 Wednesday </h2>
 
-
 
-
              <strong> Generation of Heme-free BFR by Site-directed Mutagenesis, part 4 of 5 </strong>
 
-
 
-
 
-
              MiniPrep nach Protocol<br/>
 
-
              Photometer<br/>
 
-
              4µL Probe + 76µL dilution (Wasser)
 
-
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/21 Thursday </h2>
 
-
              <strong> Generation of Heme-free BFR by Site-directed Mutagenesis, part 5 of 5 </strong>
 
-
 
-
 
-
              Sequencing:
 
-
              <br />
 
-
              Primer PB 16
 
-
              <br />
 
-
              Crystocks:
 
-
              <br />
 
-
              ÜN culture
 
-
              <br />
 
-
              500µL culture + 500µL DMSO<br />
 
-
              2xclon  17<br />
 
-
              2xclon 67
 
-
<br/>
 
-
<img src="https://static.igem.org/mediawiki/2014/6/62/Team_berlin_0011.png" alt=""/><br/>
 
-
              </div>
 
-
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/22 Friday - SDS-PAGE with Coomasie staining </h2>
 
-
              Samples<br />
 
-
</html> 
 
-
              # Marker
 
-
              # Pellet ATPCS/PPMT
 
-
              #15:00 after induction ATPCS/PPMT
 
-
              #overnight ATPCS/PPMT
 
-
              #GS Pellet
 
-
              #PGSA after induction 15:00
 
-
              #GS P/A overnight
 
-
              #human Ferritin Pellet
 
-
              #human Ferritin after induction 15:00
 
-
              #human Ferritin overnight
 
-
 
-
 
-
              '''''Analysis of Expression'''''<br>
 
-
              Human Ferritin = 42 kDa (Potparam  Expasy)<br>
 
-
              ATPCS = 56.3 kDA (Potparam  Expasy)<br>
 
-
              PPMT = 7.9 kDA (Potparam  Expasy)<br>
 
-
              ATPCSGSPPMT = 64.3 kDa (Potparam Expasy)
 
-
        <html>     
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 08/29 Friday - Calibration curve for Iron concentration measurement </h2>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Überschrift !! Überschrift
 
-
              |-
 
-
              | 0.017A || 10 µg/ml
 
-
              |-
 
-
              | 0.105A || 50 µg/ml
 
-
              |-
 
-
              | 1.076A || 100 µg/ml
 
-
              |-
 
-
              | 2.095A || 150 µg/ml
 
-
              |-
 
-
              | 2.747A || 200 µg/ml
 
-
              |}
 
-
      <html>       
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/03 Wednesday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 1 of 8 </strong>
 
-
</html>
 
-
              '''Aim''':
 
-
              Test the possibility of Magnetization of E.coli cells by the expression of human Ferritin:
 
-
 
-
 
-
              '''Procedure''': ...
 
-
<html>
 
-
 
-
              -Precultures of Nissle and RV308 (wild types)
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/04 Thursday </h2>
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 2 of 8 </strong>
 
-
 
-
 
-
              -Prepare chemical competent cells ( Nissle and RV308) . see Protocol
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/05 Friday </h2>
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 3 of 8 </strong>
 
-
 
-
              -Chemical biotransforamtion (double Trafo, 200ng of each) of, red fluorescence protein carried on plasmid (kan) Human-Ferritin carried on PQE-80L (Amp) [was prepared by iGEM-Berlin using the '''Biobrick''' from Calgary, unlike does not contains polypeptide at the beginning].
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/06 Saturday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 4 of 8 </strong>
 
-
 
-
              -Positive colones for both RV308 and Nissle
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/11 Thursday </h2>
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 5 of 8 </strong>
 
-
              - Precultures of the transformed colones
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/12 Friday </h2>
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 6 of 8 </strong>
 
-
 
-
              - Transfer the precultures into 250ml filled until 100ml with LB and incubate them at 37°C
 
-
 
-
              Strain    OD<br />
 
-
              RV308    0.71<br />
 
-
              Nissle    0.6<br />
 
-
 
-
 
-
              - Induction with 100µl IPTG (1M), incubation over night at '''30°C''' and 200rpm
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/13 Saturday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 7 of 8 </strong>
 
-
 
-
              -samples were taken for protein analysis SDS-Page
 
-
 
-
              Strain    OD<br />
 
-
              RV308    6.2<br />
 
-
              Nissle    5.2<br />
 
-
 
-
              - adding  7ml of 1M Mn-citrate (wrongly) and incubated at 4°C over weekend
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/15 Monday </h2>
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, 2nd Experiment part 8 of 8 </strong>
 
-
</html>
 
-
 
-
              -Test the Magnetization using a permanent magnet under '''Fluorescent microscope.'''
 
-
 
-
              '''Evaluation'''
 
-
 
-
              -Cells grew
 
-
              -no red fluorescence observed
 
-
              -no Magnetization observed
 
-
 
-
              Possible Explanation:
 
-
              - Adding Mn ions instead of Fe could be effected the Magnetization
 
-
              - The red Fluorescence gen contains a cadaverin chain, this could explain the non-fluorescence.
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/16 Tuesday </h2>
 
-
 
-
              <strong> Preparing Cultures for flouruscence microscopy </strong><br/>
 
-
 
-
              E. coli Nissle 1917 (pQE_80L Hu_Ferritin + RFP) <br />
 
-
              E. coli RV308 (pQE_80L_HuFerritin + RFP)<br />
 
-
 
-
              Nissle OD600 = 5.08  <br />
 
-
              RV 308 OD600 = 5.81<br />
 
-
 
-
              take OD=1<br />
 
-
 
-
              wash in 1000 µl PBS three times ( centrifuge at 6000g for 2min, discard supertanent and resuspend pellet in PBS)
 
-
 
-
              finally resuspend pellet in 500 µl
 
-
 
-
              Put it into a cool box and take it over to the fluorescence microscope facility.
 
-
 
-
              <strong> Constructing PQE_80L_T5_ATPCS_lac_PPMT </strong><br/>
 
-
 
-
              Plasmid for Co-Expression of PPMT and ATPCS on one plasmid.
 
-
 
-
              Source:
 
-
              pJS418_PPMT (amplifying insert)
 
-
              pQE_80L_ATPCS (as target vector)
 
-
 
-
              <em> PCR of HindIII_lac_PPMT_HindIII </em>
 
-
</html>
 
-
              Construction of the HindIII_lac_PPMT_HindIII in pQE80L_Hind III
 
-
               
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! 3x HindIII_lac_PPMT_HindIII
 
-
              |-
 
-
              | Q5 2x Mastermix|| 12,5
 
-
              |-
 
-
              | 10 µM Primer fw|| 1,25
 
-
              |-
 
-
              | 10 µM Primer rev|| 1,25
 
-
              |-
 
-
              | template (1ng)|| 0,5
 
-
              |-
 
-
              | nucfree H2O|| 9,5
 
-
              |-
 
-
              |}
 
-
 
-
              <em> Program </em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Temperature!! Durattion in seconds!! Cycles
 
-
              |-
 
-
              | 98|| 30''||  1
 
-
              |-
 
-
              | 98|| 5''||  loop start
 
-
              |-
 
-
              | 62-65|| 15''|| loop 32
 
-
              |-
 
-
              | 72|| 10''|| loop end
 
-
              |-
 
-
              | 72|| 2'|| 1
 
-
              |-
 
-
              | 8|| infinite|| 1
 
-
              |}
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/17 Wednesday - Digest and Dephosphorylation of vector pQE_80L_ATPCS </h2>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! pQE80L_ATPCS digest!! 1x!! 3x
 
-
              |-
 
-
              | pQE_80L_ATPCS|| 2 µl || 7 µl
 
-
              |-
 
-
              | FD HindIII|| 1 µl || 3 µl
 
-
              |-
 
-
              | 10x FD Buffer|| 2µl || 7 µl
 
-
              |-
 
-
              | FastAP (Thermo)||  1 µl|| 3 µl
 
-
              |-
 
-
              | nucfree H2O|| 14 µl || 51 µl
 
-
 
-
              |}
 
-
<html>
 
-
              Gelextraction resulted in HindIII cut pQE80L_ATPCS 20 µl with 12 ng/µl
 
-
              <br />
 
-
 
-
              In parallel the PCR fragment HindIII_lac_PPMT_HindIII was purified and is ready for digest.
 
-
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/18 Thursday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 1 of 7 </strong>
 
-
 
-
</html>
 
-
              ''''''Aim'''
 
-
              '''
 
-
 
-
              -Double Trafo of the Human-Ferritin and fluorescence marker.<br />
 
-
 
-
              '''Procedure:'''…
 
-
 
-
              Stains: RV308, Nissle and DH0B (control)<br />
 
-
              -chemical Double-biotransformation of:<br />
 
-
              -0.5 µl of Human-ferrtin on PQE-80L(490 ng/µl) with (Amp)<br />
 
-
              -3 µl green fluorescence protein Nerm ASGP-R-GFP (83 ng/µl) with (Kan)<br />
 
-
 
-
              for control:<br />
 
-
              - 3 µl green fluorescence protein Nerm ASGP-R-GFP (83 ng/µl) with (Kan) is transformed into DH05<br />
 
-
              - Double Trafo of ('''pJS418_PPMT and pQE_80L_ATPCS)'''<br />
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/19 Friday </h2>
 
-
</html>
 
-
              '''PCR of BB0 - BB3 parts (Saba)'''
 
-
 
-
              {| class="wikitable sortable"
 
-
              |-
 
-
              ! compound !! V/µl (50µl total)
 
-
              |-
 
-
              | Q5 2xMM || 25.0
 
-
              |-
 
-
              | 10µM P_fv || 2.5
 
-
              |-
 
-
              | 10µM P_rev || 2.5
 
-
              |-
 
-
              | DNA (template 1ng)|| 2.0 (of diluted plasmid)
 
-
              |-
 
-
              | nuc.-free H2O || 28.0
 
-
              |-
 
-
              |}
 
-
 
-
              '''Primers'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Reaction !! fw Primer !! rev. Primer !! TmTm/°C !! Template !! bp
 
-
              |-
 
-
              | BB0 || BBa_K1438000_fw || BBa_K1438000_rev || 62 || pQE80L_BFR || 507
 
-
              |-
 
-
              | BB1 || BBa_K1438000_fw || BBa_K1438000_rev || 62 || pQE80L_BFR M52H || 507
 
-
              |-
 
-
              | BB2 || BBa_K1438002_fw || BBa_K1438002_rev || 68 || pQE80L_Hu-Fer || 1000
 
-
              |}
 
-
 
-
              '''PCR Programms'''
 
-
              '''BB0 & BB1'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! T/°C !! t/min !! cycles
 
-
              |-
 
-
              | 98 || 0:30 || 30
 
-
              |-
 
-
              | 98 || 0:10 || 30
 
-
              |-
 
-
              | 62 || 0:30 || 30
 
-
              |-
 
-
              | 72 || 0:15 || 30
 
-
              |-
 
-
              | 72 || 2:00 || 30
 
-
              |-
 
-
              | 8 || infinity || 30
 
-
              |}
 
-
 
-
              '''BB2'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! T/°C !! t/min !! cycles
 
-
              |-
 
-
              | 98 || 0:30 || 30
 
-
              |-
 
-
              | 98 || 0:10 || 30
 
-
              |-
 
-
              | 68 || 0:30 || 30
 
-
              |-
 
-
              | 72 || 0:40 || 30 (probably too long since ~1000bp and not 1408bp however worked well as seen on gel)
 
-
              |-
 
-
              | 72 || 2:00 || 30
 
-
              |-
 
-
              | 8 || infinity || 30
 
-
              |}<br/>
 
-
            <html> 
 
-
<img src="https://static.igem.org/mediawiki/2014/9/9c/Team_berlin_0012.jpg" alt=""/><br/>
 
-
 
-
              Biobricks derived from pQE80L constructs<br>
 
-
              BB1  BFR  191µg/ml<br>
 
-
              BB2  BFRM  173µg/ml <br>
 
-
              BB2  HuFerritin  166 µg/ml
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 2of 7 </strong>
 
-
              -No positive colones were detected for double-trafo expect these for control (transformation was successful in DH05).
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/20 Saturday - Digest of PSB1C3-Ferritin </h2>
 
-
 
-
              <strong>Plasmid:  PSB1C3 - ferritin with Peptid  120ng/µl </strong> <br/>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! component !! µL
 
-
              |-
 
-
              | NEB Xba1 || 2 µL
 
-
              |-
 
-
              | NEB Pst1 || 2 µL
 
-
              |-
 
-
              | NEB Buffer 3.1 || 20 µL
 
-
              |-
 
-
              | nucleasefree H<sub>2</sub>O || 151 µL
 
-
              |-
 
-
              | PSB1C3 Feriitin || 25 µL
 
-
              |-
 
-
              | total volume || 200µL
 
-
              |}
 
-
 
-
              37°C for 1,5h
 
-
              (inactivate for 20min at 80°C)
 
-
 
-
 
-
              <strong>Gel electrophoresis </strong>
 
-
              1% Agarose-Gel <br/>
 
-
              + 3 µL EthBr<br/>
 
-
 
-
              200µL Probe + 40 µL loading dye (6x)<br/>
 
-
 
-
              5 µL GenRuler-Mix<br/>
 
-
 
-
              no Gel-extraction, because nothing was seen on the gel, except the marker (GenRuler) <br/>
 
-
 
-
              (add Figure)<br/>
 
-
              Figure not in Dropbox<br/>
 
-
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 3 of 7 </strong>
 
-
              -Transformation of RF '''(red fluorescence protein)''' on with (Kan) into DH05
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/21 Sunday </h2>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 4 of 7 </strong>
 
-
 
-
              -Transformation was successful
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/22 Monday - Precultures </h2>
 
-
 
-
              Precultures of
 
-
 
-
              PSB1K3_RFP in DH10b (Kan)<br />
 
-
              pQE80L_ATPCS & pJS418_PPMT in Dh10b (Amp & Cm)<br />
 
-
              Clones with pQE80L_ATPCS'n'PPMT in DH10b (Amp)<br />
 
-
              PSB1C3_Ferritin in DH10b (Cm)
 
-
 
-
              <strong> Checking Insertion of gene by colony PCR </strong><br/>
 
-
              Performing PCR for clones of ATPCS-PPMT construct<br>
 
-
</html>               
 
-
              {| class="wikitable"
 
-
              |-
 
-
              !  !! 1x in µl !! 12x in µl  !! 10x in µl
 
-
              |-
 
-
              | nuclease free H<sub>2</sub>O|| 14|| 168 || 140
 
-
              |-
 
-
              | 10x DreamTaq buffer|| 2 || 24 || 20
 
-
              |-
 
-
              | 25mM MgCl<sub>2</sub>|| 1.2|| 14.4|| 12
 
-
              |-
 
-
              | 10mM dNTPs || 0.5|| 6 || 5
 
-
              |-
 
-
              | 10mM FW Primar<br>HindIII-lac-prom-fw || 0.5 || 6 || 5
 
-
              |-
 
-
              | 10mM RW Primar<br> PB17 (T7 term_rev) || 0.5 || 6 || 5
 
-
              |-
 
-
              | Taq Polymerase || 0.3 || 3.6 || 3
 
-
              |}
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Programm colony PCR !! Temp !! Time
 
-
              |-
 
-
              | Denaturing|| 95°C|| 7 min
 
-
              |-
 
-
              | Denaturing|| 95°C|| 30
 
-
              |-
 
-
              | Annealing || 69°C || 30
 
-
              |-
 
-
              | Elongation || 72°C || 1 min
 
-
              |-
 
-
              | Final Elongation || 72°C || 10 min
 
-
              |-
 
-
              | Store|| 8°C ||
 
-
 
-
              |}
 
-
<html>
 
-
              Dissolved colonies 4 and 6 which showed band at 400 bp were grown each in a cultivation tube with LB+Amp100 at 37°C
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/23 Tuesday - Mutagenesis of ATPCS </h2>
 
-
 
-
              The elimination of the XbaI restriction site of all our ATPCS containing constructs was achieved by quick change mutagenesis.<br/>
 
-
</html>
 
-
              ... Details Saba....
 
-
 
-
              After digest with DpnI the reaction was transformed into competent DH10b E. coli cells via heat shock transformation.<br />
 
-
              After streaking out all aliquots on LB-Amp Agar plates, they were incubated at 37 °C over night.<br/>
 
-
 
-
              <strong> Digest of miniprepped PSB1C3_Ferritin (Calgary) for extraction of vector for BioBrick preparation </strong>
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Components !! Volume in µl
 
-
              |-
 
-
              | NEB XbaI|| 2
 
-
              |-
 
-
              | NEB PstI || 1,5
 
-
              |-
 
-
              | NEB Buffer 3.1 || 5
 
-
              |-
 
-
              | nucfree H2O || 26,5
 
-
              |-
 
-
              | plasmid PSB1C3_ferritin (Calgary) || 15
 
-
              |-
 
-
              |  || 50 µl reaction
 
-
              |}
 
-
              <br />
 
-
              The reaction was incubated at 37 °C for 1,5 h.<br />
 
-
 
-
 
-
              The digested vector was purified using a 1% agarose gel and the Roth GelNebulizer purifiction kit. The vector band was expected at 2000 bp and the insert band at about 1000 bp.<br/>
 
-
 
-
              '''both colonies from Saba were grown --> Mini-prep (Johann) to harvest plasmid DNA'''
 
-
 
-
              Mutagenesis of ATPCS
 
-
              in
 
-
                pQE80L_ATPCS-GS-PPMT<br/>
 
-
                pQE80L_ATPCS_PPMT<br/>
 
-
                pQE80L_ATPCS<br/>
 
-
              3x PCR-Reactions<br/>
 
-
                Q5 MM  12.0µl<br/>
 
-
                PB_for SN_ATPCS_xbaI_Mut_for  1.25µl<br/>
 
-
                PB_rev SN_ATPCS_xbaI_Mut_rev  1.25µl<br/>
 
-
                nuc.-free H2O  10.5µl<br/>
 
-
                template (1ng)  ~ 1.0µl (dilations of original plasmids)<br/>
 
-
              Total 26µl<br/>
 
-
 
-
              '''PCR Programm'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! T/°C !! t/min
 
-
              |-
 
-
              | 98 || 0:30
 
-
              |-
 
-
              | 98 || 0:10
 
-
              |-
 
-
              | 69 || 0:30
 
-
              |-
 
-
              | 72 || :
 
-
              |-
 
-
              | 72 || 2:00
 
-
              |}
 
-
 
-
              Trafo of 5µl PCR-Product in DH10b cells --> incubation at 37 °C
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 5 of 7 </strong>
 
-
 
-
              - Preculture of DH05 with RF plasimd
 
-
<html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/24 Wednesday </h2>
 
-
 
-
              <strong> Berlin Vector - pQE-80L-JBFS-huFerritin Assembly PCR </strong>
 
-
 
-
              <strong> Running Gel Electrophoresis </strong>
 
-
</html>
 
-
              * 1% Agarose, Ethidium bromide
 
-
 
-
              * 50µL Assembly PCR product + 10µL 6*DNA dye
 
-
              * 10µL GeneRuler DNA Ladder Mix (ThermoScientific)
 
-
              * Gel Electrophoresis conditions 100V, 30min
 
-
              <html>
 
-
<br/>
 
-
            <img src="https://static.igem.org/mediawiki/2014/c/c9/Team_berlin_0013.jpg" alt=""/><br/>
 
-
 
-
              <strong>Gel Extraction </strong>
 
-
 
-
              Gel Extraction using GeneJET Gel Extraction Kit (ThermoScientific)
 
-
</html>
 
-
              * Determination of Concentration by Ultraviolet Spectrophotometry
 
-
 
-
              ?
 
-
 
-
              <strong>Double Digest </strong>
 
-
 
-
              * Digestion of 1μg of purified Insert DNA using FastDigest BamHI / HindIII
 
-
              * 1h at 37°C
 
-
              ?
 
-
 
-
              * Heat inactivation of FastDigest BamHI / HindIII, 15min at 80°C
 
-
 
-
              <strong>PCR purification </strong>
 
-
 
-
              * PCR purification of BamHI / HindIII digested insert using GeneJET PCR Purification Kit (ThermoScientific)
 
-
              * Determination of Concentration by Ultraviolet Spectrophotometry
 
-
 
-
              ?
 
-
 
-
              <strong>Ligation </strong>
 
-
 
-
              * Using the Molar Ligation Ratio 1:5 (1 times vector and 5 times insert)
 
-
 
-
 
-
              * 20min at RT
 
-
 
-
              <strong>Chemical Transformation </strong>
 
-
 
-
              * 100µL Aliquots of Chemically Competent Cells - DH10B ''E.coli'' + 10µL Ligation approach chilled on ice for 30 min
 
-
              * Heat shock for 1min at 42°C
 
-
              * Add 900µL preheated (37°C) LB
 
-
              * Incubate the cells for 1h at 37°C with shaking approx. 200rpm
 
-
              * Plate 200µL and spin down the rest and plate on LB Ampicillin, incubate overnight at 37°C
 
-
 
-
              <strong>Saba</strong>
 
-
              o/n culture of clones from successful pQE80L_ATPCS-mut_GS_PPMT and pQE80L_ATPCS-mut_PPMT transformation
 
-
              --> 37°C, 200pm, o/n 5-6 nl LB+AB (Amp)
 
-
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 6 of 7 </strong>
 
-
 
-
 
-
              - Miniprep of the Preculture, DNA concentration 71 ng/µl
 
-
 
-
              '''Chemical Biotransformation of:
 
-
              -'''3 µl of RFP 71 ng/µl'''
 
-
              -2 µl '''Ferritin jbfs_m (different ferrtin)(120 ng/µl) with  (Amp)''''''
 
-
 
-
 
-
              in RV308 and Nissle (2 plates each)
 
-
              <html>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 09/25 Thursday - PCR of Biobrick Parts </h2>
 
-
              <strong>Isolation of plasmid-DNA with Mini-Prep Kit of pQE80L_ATPCSMut_GS_PPMT and pQE80L_ATPCS_PPMT</strong>
 
-
</html>
 
-
              '''PCR of Biobrick-Parts 03,04,06 & 10-15'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! BB !! PB_fw !! PB_rew !! Tm/°C !! template !! bp !! part
 
-
              |-
 
-
              | 03 || BBa-K1438003_fw || BBa-K1438003_rew || 67 || pQE80L_PPMT_GS_ATPCS || 1715 || PPMT GS ATPCS
 
-
              |-
 
-
              | 04 || BBa-K1438004_fw || BBa-K1438003_rew || 65 || pQE80L_PPMT_ATPCS || 1408 || ATPCS
 
-
              |-
 
-
              | 10 || XbaI_T7_prom || for Lambda_Term_suffix_rew || 66 -->67 || pQE80L_BFR || 690 (+377bp-->cp) || BFR_cp
 
-
              |-
 
-
              | 11 || " || " || 66 -->67 || pQE80L_BFRM52H || 690 (+377bp) || BFRM52H_cp
 
-
              |-
 
-
              | 12 || " || " || 66 -->65 || pQE80L_FTH_FLH(HuFer) || 1337(+377bp) || FTH_FLH_cp
 
-
              |-
 
-
              | 13 || " || " || 66 -->67 || pQE80L_PPMT_GS_ATPCS || 1968(+377bp) || PPMT_GSATPCS_cp
 
-
              |-
 
-
              | 14 || " || " || 66 -->67 || pQE80L_PPMT_ATPCS || 2091(+377bp) || ATPCS_cp
 
-
              |-
 
-
              | 06 || " || " || 66 || pQE80L_fbfs_mil_Ferritin || 1403(+377bp) || fbfs_mil_Ferritin_cp
 
-
              |}
 
-
 
-
              '''PCR-Ansätze V/µl'''
 
-
                Q5 2xMM      25.0
 
-
                10µM PB_fw    2.5
 
-
                10µM PB_rew  2.5
 
-
                template      2.0 (~1ng)
 
-
                nuc.-free H2O 18.0
 
-
              '''PCR-Programm'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! T/°C !! t/min !! cycles
 
-
              |-
 
-
              | 98 || 30" || 30
 
-
              |-
 
-
              | 98 || 10" || "
 
-
              |-
 
-
              | 66/67 || 30" || "
 
-
              |-
 
-
              | 72 || 40"/12"/1' || "
 
-
              |-
 
-
              | 72 || 2' || "
 
-
              |-
 
-
              | 8 || infinity || "
 
-
              |}
 
-
 
-
              PCR purification of 1,2, 3 (Jbfs_mil_Ferritin_cp),BF-cp and BFM-cp biobrick parts
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! !! Concentration µg/ml
 
-
              |-
 
-
              | fbfs_mit_Ferritin1 || 42
 
-
              |-
 
-
              | fbfs_mit_Ferritin2 || 35
 
-
              |-
 
-
              | fbfs_mit_Ferritin3 || 42
 
-
              |-
 
-
              | ATPCS and PPMT || -12 too low
 
-
              |-
 
-
              | Bacterioferritin CP|| 56
 
-
              |-
 
-
              | BFM52H CP || 57
 
-
              |}
 
-
<html>
 
-
              <strong> Magnetization of E. coli by expression of human Ferritin, Bio-transformations, 3rd Experiment part 7 of 7 </strong><br/>
 
-
              - Double-trafo was successful in all RV308 plates  but not in Nissle
 
-
              </div>
 
-
 
-
 
-
 
-
                <div class="sub-content-project">                   
 
-
              <h2 class="sub-content-project-headline"> 09/30 Tuesday </h2>
 
-
              <strong>Ligation of Biobrick parts with PSBIC3 backbone (digested on 23.09.2014 by Johann</strong>
 
-
 
-
 
-
              Transformation into DH10b c.c.cells by chemical transformation<br/>
 
-
 
-
              5µl of each ligation was transformed to 100µl aligusted cells each<br/>
 
-
 
-
              --> after recovery at 37°C, 30min cells were plated on Cm/LB-Agar plates after centrifuging-->pelleting and resuspending in 100µl LB to plate all cells.
 
-
 
-
              --> incubation at 37°C, o/n
 
-
 
-
              <strong> Mini Prep von pSB 1U 3-RFP </strong>
 
-
              concentration 112 ng/µl<br>
 
-
 
-
              Preculture <br>
 
-
              pQE-80L-jbfs-Ferritin 5ml LB+5µl Amp at 37°C overnight
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">             
 
-
              <h2 class="sub-content-project-headline"> 10/01 Wednesday - Plasmid Digestion & PCR Probe </h2>
 
-
 
-
              <strong>Plasmid Digestion </strong>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Plasmid Digestion !!
 
-
              |-
 
-
              | NEB Buffer 3.1 || 5µl
 
-
              |-
 
-
              | NEB XbaI || 0.5µl
 
-
              |-
 
-
              | NEB PstI || 0.5µl
 
-
              |-
 
-
              | P_MA_T_PPMT 312ng/µl || 3.2µl
 
-
              |-
 
-
              | null. free water || 40.5µl
 
-
              |}
 
-
<html>
 
-
              <strong>PCR Probe </strong>
 
-
 
-
 
-
              <em>Ligation plates evaluated:</em><br/>
 
-
 
-
              All plates had clones except for BFR_cp from each plate transformation one clone was cultivated with LB/Cm (~5ml) o/n at 37°C
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">                 
 
-
              <h2 class="sub-content-project-headline"> 10/02 Thursday - Cultures were Mini-preped </h2>
 
-
 
-
              --> elution with 40µl EB
 
-
 
-
              --> DNA contration measurement
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 10/06 Monday- Colony PCR </h2>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Biobrick !! Sequenzierung !! Sequenz (?) !! (???)
 
-
              |-
 
-
              | BB0 || BFR || 100Y BFR M52H || -A ws ATGf (??)
 
-
              |-
 
-
              | BB1 || BFR M52H || 100% BFR || -A wr
 
-
              |-
 
-
              | BB2 || HFTN_LFFN (?) || 96Y HuFerritin (Rw Sep nötig) ?? ||
 
-
              |-
 
-
              | AnP || ATPCS || f 70% ok, aber Fragment f || PCR nochmal ... Gelex (?)
 
-
              |-
 
-
              | BFM1cp || BFR1cp || ? ||
 
-
              |-
 
-
              | BFM2cp || BFR2cp || ? ||
 
-
              |-
 
-
              | HuFecp || HuFerritin cp || ? ||
 
-
              |}
 
-
 
-
              <em>Colony-PCR of other clones</em>
 
-
 
-
              '''PCR-Programm'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! T/°C !! t/min !! cycles
 
-
              |-
 
-
              | 95 || 7' || 30
 
-
              |-
 
-
              | 95 || 30" || 30
 
-
              |-
 
-
              | 52 || 30" || 30
 
-
              |-
 
-
              | 72 || 1' || 30
 
-
              |-
 
-
              | 72 || 10" || 30
 
-
              |-
 
-
              | 8 || infinity || 30
 
-
              |}
 
-
 
-
              --> gel (1% Agarose)
 
-
 
-
              Clones 3, 5, 6, 7 and 13 were grown o/n in LB/Cm for Mini-prep on the following day. therefore 5µl of the disolved clones were used for each inoculation
 
-
 
-
              --> 37°C, 200rpm
 
-
 
-
 
-
<html>
 
-
              <strong>2x M9 Media Production</strong><br/>
 
-
              (Christina)<br />
 
-
 
-
              2X M9 mineral medium<br/>
 
-
 
-
              For 500 ml M9 minearal medium add to XXX ml sterile water:<br/>
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              | 100ml || M9 salt solution (10X) || Na<sub>2</sub>HPO<sub>4</sub> <br />
 
-
              KH<sub>2</sub>PO<sub>4</sub><br />
 
-
              NaCl<br />
 
-
              NH<sub>4</sub>Cl || 67.4mM<br />
 
-
              44.0mM<br />
 
-
              17.10mM<br />
 
-
              18.70mM
 
-
              |}
 
-
<html>
 
-
     
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">                 
 
-
              <h2 class="sub-content-project-headline"> 10/07 Tuesday </h2>
 
-
              <em>Mini-Prep of cultures (Ben) and preparation of sequencing samples (Saba):</em>
 
-
 
-
              9µl nuc.-free H2O + 3µl DNA + 3µl PB794<br>
 
-
<br/>
 
-
              <img src="https://static.igem.org/mediawiki/2014/c/c3/Team_berlin_0014.jpg" alt=""/><br/>
 
-
 
-
              <strong> Preculture of Knockouts </strong>
 
-
              * λΔ FieF +PCP 20 : 5ml LB+tet/amp (1:1000)
 
-
              * λΔ FUR  : 5ml  LB+tet/kan (1:1000)
 
-
              * MG1655 ΔFieF: 5ml LB + amp/kan (1:1000)<br>
 
-
              incubation at 30°C
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">                     
 
-
              <h2 class="sub-content-project-headline"> 10/08 Wednesday - PCR of PSB1C3 Backbone </h2>
 
-
 
-
              Q5 Mastermix 2x
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Component !! Volume in µl
 
-
              |-
 
-
              | Q5 Mastermix 2x || 25
 
-
              |-
 
-
              | Primer fw (PSB1C3 Suffix fw)|| 2,5
 
-
              |-
 
-
              | Primer rev (PS1C3 Prefix rev|| 2,5
 
-
              |-
 
-
              | template (PSB1C3_BBa_K1189018)|| 2
 
-
              |-
 
-
              | nuc free H2O|| 18
 
-
              |}
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Temperature in °C!! Time!! Nr. of cyles
 
-
              |-
 
-
              | 98|| 30''||
 
-
              |-
 
-
              | 98|| 5''|| loop start
 
-
              |-
 
-
              | 70|| 15''|| 30
 
-
              |-
 
-
              | 72|| 1'|| loop end
 
-
              |-
 
-
              | 72|| 2'||
 
-
              |-
 
-
              | 8|| infinit||
 
-
              |-
 
-
              |}
 
-
 
-
              <strong> Extraction of PCR Product (PSB1C3 linearised) </strong>
 
-
 
-
              After extracting the expected band at 2000 bp it was purified using the EMDMillipore Montage Gel Extraction Device.<br>
 
-
              Resulting in about 120 µl DNA extract in TAE buffer with an concentration of 9ng/µl<br>
 
-
 
-
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Digestion of PCR Product !!
 
-
              |-
 
-
              | NEB Buffer 3.1 || 15µl
 
-
              |-
 
-
              | NEB PstI|| 1.5µl
 
-
              |-
 
-
              | NEB XbaI || 1.5µl
 
-
              |-
 
-
              | nuc. free water || 83µl
 
-
              |-
 
-
              | PCR Product || 100µl
 
-
              |}
 
-
             
 
-
              * 1.5 hours at 37°C
 
-
              * PCR Purification
 
-
              * DNA concentraion measurement = 35ng/µl
 
-
 
-
              <strong> Ligation </strong>
 
-
              Calculation
 
-
              *BFM52H = 3.22µl
 
-
              *BF_cp= 6.7µl
 
-
              *jbfs_m = 8.06 µl
 
-
              *BB_AnP = 10.64 µl
 
-
              * HuFer = 9.45 µl
 
-
              <strong> Iron Concentration measurement </strong>
 
-
              278 mg FeSO<sub>4</sub>.7H<sub>2</sub>O dissolved in 10 ml d.H<sub>2</sub>O <br>
 
-
              λ FieF PCP<sub>2</sub> Amp  1:100 ---> 3.0 OD<br>
 
-
              iGEM BV125 tet 1:100 --> 3.0 OD <br>
 
-
              λ FieF PCP<sub>1</sub> Amp 1:20 -->3.26 OD
 
-
              iGEM BV125 tet 1:20---> 2.44<br>
 
-
              too high OD!
 
-
 
-
              Both samples diluted 1:2
 
-
              Samples
 
-
              #  FieF + 5µl 0.1 M Fe-stock solution
 
-
              # FieF + 15 µl 0.1 M Fe-Stock solution
 
-
              # BV + 5 µl 0.1M Fe-stock solution
 
-
              # BV + 15 µl 0.1 M Fe-stock solution
 
-
 
-
              Overnight incubation at 30°C on a shaker
 
-
      <html>
 
-
              </div>
 
-
 
-
              <div class="sub-content-project">         
 
-
              <h2 class="sub-content-project-headline"> 10/09 Thursday </h2>
 
-
              Mini Prep (using: AccuPrep Plasmid Mini Extraction Kit Ver. 2.0, Company: BIONEER), using 100µl Elution Buffer <br>
 
-
              and dsDNA Measurement: 4 µl Sample + 76µl MilliQ, blanked with MilliQ
 
-
</html>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Samplenumber !! Samplename !! dsDNA conc [ng/µl] !! Sample [µl] used for Sequencing !! nucl.free Water [µl] used for Sequencing
 
-
              |-
 
-
              | #1 || cp HuF || 111 || 9 || 3
 
-
              |-
 
-
              | #2 || AGSP || 107 || 9,4 || 2,6
 
-
              |-
 
-
              | #3 || AGSP || 59 || 12 || 0
 
-
              |-
 
-
              | #4 || AGSP || 64 || 12 || 0
 
-
              |-
 
-
              | #5 || jbfs_Fer || 54 || 12 || 0
 
-
              |-
 
-
              | #6 || A'n'P || 67 || 12 || 0
 
-
              |}
 
-
 
-
              For Sequencing:
 
-
              *total volume: 15µl
 
-
              *Primer used: PB795 3µl each Sequencing approach
 
-
              *Sample [µl] see table
 
-
              *nucl.free Water [µl] see table
 
-
 
-
              evaluation of Trafos ---> no growth --->Repeat Trafo in other cells
 
-
  <html>
 
-
              </div>
 
-
 
-
 
-
 
-
              <div class="sub-content-project">                 
 
-
              <h2 class="sub-content-project-headline"> 10/10 Friday - STRATEGY 1 - Knockout of FieF and FUR Genes </h2>
 
-
              <em> Detection PCR </em>
 
-
              kan-deletion-cassette for FieF and FUR Genes was transformed into 2 different strains (MG1655 and λ MAGE). Additionally pCP20 was already transformed into one of the λ MAGE Clones (has to be re-validated).<br />
 
-
              The positive clones have to be validated.<br />
 
-
 
-
              Detection-PCR of one clone of Plates 1-3:<br />
 
-
 
-
              Plate 1: MG1655 ΔFieF<br />
 
-
              Plate 2: λ ΔFieF + pCP20<br />
 
-
              Plate 3: λ ΔFUR<br />
 
-
 
-
              <em> Primer-Combinations </em>
 
-
</html>
 
-
              '''FieF'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              !- !! Combination !! WT length !! Clone length !! Annealing Temperature range
 
-
              |-
 
-
              | A ||C1+C2 || 2060bp || 2654bp || 58,4-60,1°C
 
-
              |-
 
-
              | B ||C1+C3 || 0 || 1046bp || 59,5-60,1°C
 
-
              |-
 
-
              | C ||C4+C2 || 0 || 1181bp || 57,5-58,4°C
 
-
              |-
 
-
              | D ||C1+C5 || 1134bp || 0 || 60,1-60,5°C
 
-
              |}
 
-
              --> Annealing Temperature: 57°C<br />
 
-
 
-
              '''FUR'''
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! - !!Combination !! WT length !! Clone length !! Annealing Temperature range
 
-
              |-
 
-
              | A ||C1+C2 || 1130bp || 2219bp || 59,5°C
 
-
              |-
 
-
              | B ||C1+C3 || 0 || 823bp || 59,5°C
 
-
              |-
 
-
              | C ||C4+C2 || 0 || 969bp || 57,5-59,5°C
 
-
              |-
 
-
              | D ||C1+C5 || 500bp || 0 || 59,5°C
 
-
              |}
 
-
              --> Annealing Temperature: 57°C
 
-
              <em> PCR-Assay </em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! - !! 1x !! Mastermix 15x
 
-
              |-
 
-
              | nuc.free H<sub>2</sub>O || 14,4µl || 216µl
 
-
              |-
 
-
              | 10x Dream Taq Buffer || 2µl || 30µl
 
-
              |-
 
-
              | 50mM MgCl<sub>2</sub> || 0,6µl || 9µl
 
-
              |-
 
-
              | 10mM dNTPs || 0,5µl || 7,5µl
 
-
              |-
 
-
              |
 
-
              |-
 
-
              | 10mM Primer Combination || 1µl
 
-
              |-
 
-
              | 10µl nuc.free H<sub>2</sub>O+ picked colony|| 1µl + 18,4ml Mastermix
 
-
              |-
 
-
              | Taq Polymerase || 0,5µl
 
-
              |}
 
-
 
-
              <em> PCR-Program </em>
 
-
              {| class="wikitable"
 
-
              |-
 
-
              ! Temperature !! Time
 
-
              |-
 
-
              | 95°C || 7'
 
-
              |-
 
-
              |30 cycles
 
-
              |-
 
-
              | 95°C || 30"
 
-
              |-
 
-
              | 57°C || 30"
 
-
              |-
 
-
              | 72°C || 2'40"
 
-
              |-
 
-
              |
 
-
              |-
 
-
              | 72°C || 5'
 
-
              |-
 
-
              | 12°C || hold
 
-
              |}
 
-
              <html>
 
-
              <em> Gel-Electrophoresis </em><br/>
 
-
              1% Agarose-Gel + 1µl GelRed; 90V; 30min<br />
 
-
<img src="https://static.igem.org/mediawiki/2014/9/92/Team_berlin_0015.jpg" alt=""/>
 
-
              </div>
 
-
 
-
 
-
              <div class="sub-content-project">
 
-
              <h2 class="sub-content-project-headline"> 10/14 Tuesday - Iron-Assay </h2>
 
-
              1. Day: inoculation of 5ml LB Media (+ Antibiotics)<br />
 
-
               
 
-
              * 37°C or 30°C/ON<br />
 
-
              <br />
 
-
              2.Day:inoculation of 10ml LB (1:10)<br />
 
-
              * 30°C or 37°C<br />
 
-
              * grow until OD<sub>600</sub> 0,6<br />
 
-
              * take 1ml<br />
 
-
              * centrifuge 2min at max. speed<br />
 
-
              * discard the supernatant <br />
 
-
              * wash with 1X M9 Media<br />
 
-
              <br />
 
-
              * 1XM9:<br />
 
-
              :500µL 2X M9+<br />
 
-
              :500µL sterile water<br />
 
-
              * wash 2x and recover 1mL 1XM9 Media<br />
 
-
              * diluted 1:1000 with 1X M9<br />
 
-
              * plate 20µL per well
 
-
 
-
 
-
 
-
              24well plate without Antibiotics
 
-
              <br />
 
-
              *A:MG1655 wt
 
-
              *B:Nissel 1917 wt
 
-
              *C:RV308 wt
 
-
              *D:DH10b
 
-
              <br />
 
-
              concentration of Fe-citrat
 
-
              <br />
 
-
              0    0,5    1    2    5    10mM
 
-
              </div>                 
 
-
    </div>
 
-
 
-
 
-
  </div>   
 
-
</div>
 
-
 
-
 
</section>   
</section>   
-
</div>
 

Revision as of 22:36, 15 October 2014

Explore our Project:

1. What is it all about?

2. Detailed Description

3. Our Results

4. Lab Summary

5. Lab Journal

6. Intellectual Property


3

Results

Results

Müller-Breslau-Str. 10
10623 Berlin
Phone: +49 1778800244
Mail: mail@igem.berlin
©2014 iGem Berlin, Layout/Umsetzung: Valerian Blos, Marius Wessel

Retrieved from "http://2014.igem.org/Team:Berlin/Project/Results"