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Team:UCL/Humans/Collab
From 2014.igem.org
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<h2>Our collaborations</h2> | <h2>Our collaborations</h2> | ||
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<h4>Edinburgh 2014 iGEM team: RewirED</h4> | <h4>Edinburgh 2014 iGEM team: RewirED</h4> | ||
How it all begun: | How it all begun: | ||
<img src="https://static.igem.org/mediawiki/2014/a/ac/UCL2014_collaboration-start.png" width="360" heigth="288"> | <img src="https://static.igem.org/mediawiki/2014/a/ac/UCL2014_collaboration-start.png" width="360" heigth="288"> | ||
| - | + | Making sense of antisense together! | |
<img src="https://static.igem.org/mediawiki/2014/d/db/UCL2014_collaboration-yeey.png" width="360" heigth="288"> | <img src="https://static.igem.org/mediawiki/2014/d/db/UCL2014_collaboration-yeey.png" width="360" heigth="288"> | ||
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| - | <p1>The <a href="https://2014.igem.org/Team:Edinburgh">RewirED Edinburgh Team</a> | + | <p1>The <a href="https://2014.igem.org/Team:Edinburgh">RewirED Edinburgh Team</a> Focused on the creation of a metabolic wiring system as a novel way of connecting logic gates in different bacterial strains. They developed <a href="https://2014.igem.org/Team:Edinburgh/modelling/software">a software tool to analyze sequences of antisense RNA for gene silencing</a> which identifies the optimal sequence (~100bp, covering RBS and start codon) and analyses the structure to find the most stable antisense RNA. <br> |
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| - | Focused on the creation of a metabolic wiring system as a novel way of connecting logic gates in different bacterial strains. They developed <a href="https://2014.igem.org/Team:Edinburgh/modelling/software">a software tool to analyze sequences of antisense RNA for gene silencing</a> which identifies the optimal sequence (~100bp, covering RBS and start codon) and analyses the structure to find the most stable antisense RNA. <br> | + | |
In this collaboration they provided the sequence of the antisense gene which, according to their model, has the fewest secondary structures in the core regions and analysed the behaviour of our design of an antisense gene. | In this collaboration they provided the sequence of the antisense gene which, according to their model, has the fewest secondary structures in the core regions and analysed the behaviour of our design of an antisense gene. | ||
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| - | From our side we provided real world data on the behaviour of the antisense gene silencing in order to test the accuracy of their model and efficacy of their software. Specifically we analysed the growth in different media of <i>E. coli</i> engineered with the antisense gene silencing biobrick. The silenced gene is core for the survival of E. coli and the reduction in growth corresponds to the efficacy of the antisense. We sent them all the data we gathered that they could then compare to their <i>in silico</i> prediction.<br> | + | From our side we provided real world data on the behaviour of the antisense gene silencing in order to test the accuracy of their model and efficacy of their software. Specifically we analysed the growth <!--link to results--> in different media of <i>E. coli</i> engineered with the antisense gene silencing biobrick <!--link to part-->. The silenced gene is core for the survival of E. coli and the reduction in growth corresponds to the efficacy of the antisense. We sent them all the data we gathered that they could then compare to their <i>in silico</i> prediction.<br> |
| - | The sequence we designed didn't effectivly repress growth in <i>E.coli</i> as modelled by the software. We designed new primers to amplify the sequence suggested by Edinburgh: a smaller fragment with better predicted functionality, and we are now in the stage of cloning and testing it to provide them with more data on their software's effectiveness. | + | The sequence we designed didn't effectivly repress growth in <i>E.coli</i> as modelled by the software. We designed new primers <!--New primer design link!--> to amplify the sequence suggested by Edinburgh: a smaller fragment with better predicted functionality, and we are now in the stage of cloning and testing it to provide them with more data on their software's effectiveness. |
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Identification of the optimal antisense RNA for ispB silencing | Identification of the optimal antisense RNA for ispB silencing | ||
| - | <img src="https://static.igem.org/mediawiki/2014/d/d0/UCL2014_ideal_asispB.png" width="90%" height=" | + | <img src="https://static.igem.org/mediawiki/2014/d/d0/UCL2014_ideal_asispB.png" width="90%" height="530"> |
<br><br> | <br><br> | ||
Analysis of our antisense RNA design for ispB silencing | Analysis of our antisense RNA design for ispB silencing | ||
| - | <img src="https://static.igem.org/mediawiki/2014/9/99/UCL2014_ourispBv1_structure.png" width="90%" height=" | + | <img src="https://static.igem.org/mediawiki/2014/9/99/UCL2014_ourispBv1_structure.png" width="90%" height="530"> |
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| + | <h4>Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa</h4> | ||
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| + | <p1>The <a href="http://met.itqb.unl.pt/">Microbial & Enzyme Technology Lab</a> led by Dr Lígia O. Martins at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, is one of the world leaders in bioremediation with microorganisms and enzymes. Their paper titled 'Synergistic action of azoreductase and laccase leads to maximal decolourization and detoxification of model dye-containing wastewaters' <a href="http://www.ncbi.nlm.nih.gov/pubmed/21890348">[1]</a> was the fundamental inspiration for our Goodbye AzoDye project. We are truly grateful for their initial support and guidance, and for sending us the following plasmids for our experiments:<br><br> | ||
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| + | <b>pAzoR (pLP-1)</b> containing the FMN-dependent NADH-azoreductase 1 gene. <a href="http://www.ncbi.nlm.nih.gov/pubmed/21655981">[2]</a><br> | ||
| + | <b>pCotA (pLOM10)</b> containing the Spore Coat Protein Laccase gene. <a href="http://www.ncbi.nlm.nih.gov/pubmed/11884407">[3]</a><br> | ||
| + | <b>p1B6</b> containing the mutant FMN-dependent NADH-azoreductase 1 gene <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=Improving+kinetic+PpAzoR">[4]</a><br> | ||
| + | <b>pBsDyp (pRC-2)</b> containing the Dye Decolourising Peroxidase BSU38260 gene. <a href="http://www.ncbi.nlm.nih.gov/pubmed/23820555">[5]</a><br> | ||
| + | <b>pPpDyp (pRC-1)</b> containing the Dye Decolourising Peroxidase PP_3248 gene.<a href="http://www.ncbi.nlm.nih.gov/pubmed/23820555">[5]</a><br> | ||
| + | </p1><br> | ||
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| + | <img src="https://static.igem.org/mediawiki/2014/3/3d/10491123_10204437153717396_7991059471759774917_n.jpg" width="360" height="288"> | ||
| + | <img src="https://static.igem.org/mediawiki/2014/5/53/Group.jpg" width="360" height="288"> | ||
| + | <img src="https://static.igem.org/mediawiki/2014/e/ed/Jointlogo.jpg" width="400" height="320"> | ||
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<h3>Central St Martins</h3> | <h3>Central St Martins</h3> | ||
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Revision as of 17:00, 17 October 2014
Our collaborations
Edinburgh 2014 iGEM team: RewirED
How it all begun:
Making sense of antisense together!
In this collaboration they provided the sequence of the antisense gene which, according to their model, has the fewest secondary structures in the core regions and analysed the behaviour of our design of an antisense gene.
From our side we provided real world data on the behaviour of the antisense gene silencing in order to test the accuracy of their model and efficacy of their software. Specifically we analysed the growth in different media of E. coli engineered with the antisense gene silencing biobrick . The silenced gene is core for the survival of E. coli and the reduction in growth corresponds to the efficacy of the antisense. We sent them all the data we gathered that they could then compare to their in silico prediction.
The sequence we designed didn't effectivly repress growth in E.coli as modelled by the software. We designed new primers to amplify the sequence suggested by Edinburgh: a smaller fragment with better predicted functionality, and we are now in the stage of cloning and testing it to provide them with more data on their software's effectiveness.
Identification of the optimal antisense RNA for ispB silencing
Analysis of our antisense RNA design for ispB silencing
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa
pAzoR (pLP-1) containing the FMN-dependent NADH-azoreductase 1 gene. [2]
pCotA (pLOM10) containing the Spore Coat Protein Laccase gene. [3]
p1B6 containing the mutant FMN-dependent NADH-azoreductase 1 gene [4]
pBsDyp (pRC-2) containing the Dye Decolourising Peroxidase BSU38260 gene. [5]
pPpDyp (pRC-1) containing the Dye Decolourising Peroxidase PP_3248 gene.[5]
Central St Martins
We approached the Central St Martins textiles department with our ideas of synthetic biology and science and they asked ‘When does technology like this become accessible?’ This question yielded a set of beautiful visualisation of the way our bacteria could be used to create art if controlled by light. These pieces by second year Textiles Design BA students Cameo Bondy and Barbara Czepiel exhibit the textiles that could be created if our bacteria contained optogenetic biobricks that switched their dye breakdown capacities on and off via light cues.
Natsai Audrey
A practicing independent designer and researcher, Natsai Audrey Chieza is a Design Futurist inspired by material innovation and technology. Natsai considers her creative pursuits with a strong interest in how the life sciences can enable new craft processes for a more robust environmental paradigm.
Natsai contributed a series of pieces to be displayed at the #UncolourMeCurious from her Faber Futures exhibition, exploring the use of bacteria to create pigments and dye fabrics, deviating from the standardisation of a petri dish.
Natsai has achieved measurable success in design research projects for Microsoft, Nissan, Unilever and EDF Energy. She has also exhibited in numerous design exhibitions and events across Europe including the Victoria & Albert Muesum, London; Audax Textile Museum, Tilburg; Salone Internazionale del Mobile di Milano, Milan; Designersblock LDF, London; EN VIE/ ALIVE, Paris; Science Gallery, Dublin; and Heimtextil, Frankfurt.
University of Westminster
UCL Igem Bioprocess Team visits Godfrey Kyazze, a Lecturer in Bioprocess Technology at University of Westminster. He is involved in water science research, using microbial fuel cells to produce electricity upon the degradation of azodyes.
Linden Gledhill
*Edo Content*
The Slade
For the exhibition The Slade School of Art provided us with Pigment Cases outlining the history of dyes. They illustrated how dyeing technology has moved through the ages and allowed the public to witness how far we have come.
