Team:Paris Bettencourt

From 2011.igem.org

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<h2>Welcome to the iGEM Paris Bettencourt 2011 wiki</h2>
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<h2 style="text-align:center; margin-top:0px;">Towards harnessing bacterial nanotubes by and for synthetic biology</h2>
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<h3>Using synthetic biology to investigate newly discovered biological phenomena</h3>
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<p>The recent discovery of <em>nanotubes between individual <i>B.subtilis</i></em> by Dubey and Ben-Yehuda spiked our interest. Through very detailed and advanced microscopy, they showed nanotubes forming between cells and that a wide rande of proteins could pass through this communication channel (GFP, calcein, antibiotics, ...). They also showed signs of communication between <i>B.subtilis</i> and <i>E.Coli</i>, another species entirely. With these synthetic-biology-friendly bacterium and a potentially non-specific cell-to-cell transportation system, the possibilities for designing new systems seem endless!</p>
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<p><i><span style="font-size:16px;color:#0009FF;">The interest:</span></i> A recent ground-breaking paper <a href="https://2011.igem.org/Team:Paris_Bettencourt#references">[1]</a> described a new cell-to-cell bacterial communication system: nanotubes. Through excellent electronic microscopy images, antibiotic resistance transfer, faint fluorescence transfer, and cross-antibiotic resistance, previously unknown exchange channels were revealed between B.subtilis cells and even between completely different species. Results suggest that protein and/or RNA can travel through these tubes. This discovery may lead to a redefinition of individuality in bacteria. Given the many applications of known communication systems (e.g., quorum sensing, conjugation) in synthetic biology, harnessing the capacity of the nanotubes will open endless possibilities for new applications as amorph computing....
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<p>Our goal this summer was to see how the synthetic biology community could harness the power of <a href="https://2011.igem.org/Team:Paris_Bettencourt/Potential_Application">amorphous computation</a> and <a href="https://2011.igem.org/Team:Paris_Bettencourt/Potential_Application">metabolic engineering</a> of this nanotube network. Each cell is potentially a tiny individual computer linked directly and only to its closest neighbours. The existence of the so-called nanotubes is however still debated.</p>
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<p><span style="font-size:16px;color:#0009FF;"><i>The challenge:</i></span> Using synthetic biology to characterize the nanotubes: the structure, composition and control of which are still unknown. We decided to work on this challenging problem by providing other proofs to support this discovery.</p>
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<p>We decided therefore to <em>investigate</em> this phenomenon and <em>characterize</em> it using the tools synthetic biology provides. We created <em>new <i>B.subtilis</i> BioBricks</em>, filling a surprising hole in the part registry since very few iGEM teams worked on this organism in the past. Those BioBricks were used to provide <em>new evidence</em> supporting the existence of a nanotube network.</p>
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<h3>See our work!</h3>
<h3>See our work!</h3>
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     <td style="width:200px;"><center><a href=https://2011.igem.org/Team:Paris_Bettencourt/Project><img src="https://static.igem.org/mediawiki/2011/8/86/Logo_projet.png" alt="our logo" width="170px"></a></center></td>
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     <td style="width:200px;"><center><a href="https://2011.igem.org/Team:Paris_Bettencourt/Project"><img src="https://static.igem.org/mediawiki/2011/8/86/Logo_projet.png" alt="our logo" width="150px"></a></center></td>
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   <p><b>The project:</b></p><p>In February, a team lead by Dubey and Ben-Yehuda discovered an extraordinary new form of communication for bacteria: nanotubes between individual cells! This type of link is well known between eukaryotic cells, but here it was observed between cells widely used by synthetic biologists (<i>Bacillus subtilis</i>). We decided to investigate this new communication way in details using the tools synthetic biology can design. You can find out more about our project in the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Project">Project</a> section.</p>
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   <p><b><p>The project:<p></b> We bet-hedged our chances using different reporter systems by creating <a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs">several devices</a> relying on protein or RNA diffusion. Our devices rely on an emitter cell and a receiver cell that amplifies the signal. We chose to work with signaling molecules of different sizes and natures to test thoroughly the diffusion possibilities. Experiments were coupled with a <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling">thorough modeling</a> approach tackling both the detection devices as well as diffusion, <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Assisted_diffusion">assisted transfer</a> within the tubes and the membrane fusion within.</b></p>
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    <td style="width:200px;"><center><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/List"><img src="https://static.igem.org/mediawiki/2011/c/c1/Results_button.png" alt="our logo" width="150px"></a></center></td>
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  <img src="https://static.igem.org/mediawiki/2011/2/28/Paris_Bettencourt_team.png" alt="our team" width="150px"></center>
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     <b>The Team:</b>
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     <b>Our lab achievements</b>
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     <p>We are fifteen parisian students coming from many different disciplines who came together to participate to the iGEM competition. Come and meet the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Team">Team</a>.</p>
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     <p>We worked very hard to test the presence of nanotubes and characterize them. Come and find out more about the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/List">results</a> of this scientific summer.</p>
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    <b>The Tool:</b>
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    <p>We are developping new tools to help the biologis to develop his own genetic circuits. With <a href="https://2011.igem.org/Team:Paris_Bettencourt/RISC">BioHave</a>, you can browse a biologic part database by systhematic method. You programm the behavior you want and <a href="https://2011.igem.org/Team:Paris_Bettencourt/RISC">BioHave</a> gives you the bests combination of parts to build it!</p>
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  <td style="width:200px;"><center><a href="https://2011.igem.org/Team:Paris_Bettencourt/Safety"><img src="https://static.igem.org/mediawiki/2011/4/47/World_button.png" alt="our logo" width="150px"></a></center></td>
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     <b>The values:</b>  
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<a href="https://2011.igem.org/Team:Paris_Bettencourt/Safety"><img src="http://www.formation-reani-plus.com/resources/premier-secours.jpg" alt="Safety" width="150px"></a></center></p>
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     <p>Ethics and safety are two main concerns when building genetically engineered organisms.</p>  
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     <p>You can visit our <a href="https://2011.igem.org/Team:Paris_Bettencourt/HumanPractice">Human practice</a> page and our <a href="https://2011.igem.org/Team:Paris_Bettencourt/Safety">safety</a> page.</p>
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     <b>Ethic and Safety:</b>  
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     <p>Ethic and safety are two main concern when building genetically engineered organism.</p>  
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     <p>You can visit our <a href="https://2011.igem.org/Team:Paris_Bettencourt/HumanPractice">Human practice</a> work and our <a href="https://2011.igem.org/Team:Paris_Bettencourt/Safety">safety</a> page.</p>
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<h2>New Achievements since Regional Jamboree</h2>
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<p>We have:</p>
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<li>Characterized a fully functioning <b>T7 autoloop (emitter and receiver) </b>  device in <i>B. subtilis</i>.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/T7_diffusion">(15)</a></li>
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<li>Characterized a fully functioning <b>sporulation device (KinA emitter and Sin operon receiver) </b>  device in <i>B. subtilis</i>.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/SinOp">(16)</a></li>
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<li><b>Integrated in the chromosome</b> of <i>B. subtilis</i> the T7 polymerase diffusion entire system (emitter and receiver) and the YFP:tetR emitter system</li>
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<li><b>Integrated in an episomal </b>plasmid in <i>B. subtilis</i> the TetO Array and the c1 system</li>
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<li><b>Tested nanotubes formation</b> between species (<i>B. subtilis</i> and <i>E. coli</i>) with the system: TetR-YFP emitter in <i>E. coli</i> and TetO array receiver in <i>B. subtilis</i>. No evidence of nanotubes was found so far.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/YFP_TetR_diffusion_experiments">(17)</a></li>
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<li><b>Tested nanotubes formation</b> between species (<i>B. subtilis</i> and <i>E. coli</i>) with the system T7 autoloop. No evidence of nanotubes was found so far.  <a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/T7_diffusion_experiments">(18)</a></li>
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<li>Created a new <b>biobricked integrative plasmid pDCPKO</b> for <i>B. subtilis</i><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/Methodologies/Integration">(19)</a>
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<li>Created and analyzed the<b> collaboration map</b> between iGEM teams throughout the years as a part of our Human Practice project <a href="https://2011.igem.org/Team:Paris_Bettencourt/HumanPractice/collaborationMap">(20)</a>
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<li>A bonus track: <b>Protocol - The song</b> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Protocol_the_song">(21)</a></li>
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<li>Survived a second wiki freeze night.
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<h2>Achievements</h2>
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<p>We have:</p>
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<li>Used <em>rational design</em> in combination with <em>modeling</em> to create <b>6</b> new couples of emitter/receiver constructs <a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs">(1)</a> that could help characterize nanotubes' properties, using <b>synthetic biology</b> approach.</li>
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<li>Proofs of principle of <b>5</b> working <em>emitter</em> and <em>receiver</em> devices.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/T7_diffusion">(2)</a> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/tRNA_diffusion">(3)</a> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/YFP_TetR_diffusion">(4)</a></li>
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<li>Successfully reproduced the <em>GFP experiment</em> of the founding paper <a href="https://2011.igem.org/Team:Paris_Bettencourt/GFP_diff">(5)</a>, indirectly proving <em>the existence of the nanotubes</em> under our microscopes.</li>
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<li>Developed <b>two</b> original <em>models</em> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Diffusion">(6)</a> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Assisted_diffusion">(7)</a> that could explain the observed transport parameters through the nanotubes.</li>
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<li>Built a <em>microfluidic chemostat chip</em>, to monitor single bacterial layers under controlled conditions.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/Methodologies/Microchemostat_HastyJ">(8)</a></li>
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<li>Reproduced the original <em>antibiotic experiment</em> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Atb_exp">(9)</a>, design complementary controls and proposed alternative explanations for the results observed.</li>
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<li>Created 38 new biobricks, based on new charachterized parts, all are now at the registry <a href="https://2011.igem.org/Team:Paris_Bettencourt/Parts">(10)</a> and devices for B. <i>subtilis</i>.</li>
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<li>Specifically, created and characterized an <em>efficient amplifier</em> with positive feedback loop of T7 RNA polymerase on T7 promoter.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/T7_diffusion">(11)</a></li>
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<li>Created devices aiming at hijacking <b>two</b> endogenic <em>bistable switches</em> in B. <i>subtilis.</i> <a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs">(12)</a></li>
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<li>Created and characterized a fully functioning <b>fluorescent concentrator</b>  device.<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/YFP_TetR_diffusion">(13)</a></li>
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<li><em>Collaborated</em> with the Grenoble iGEM team for the <em>human practice</em><a href="https://2011.igem.org/Team:Paris_Bettencourt/HumanPractice">(14)</a>, building a <b>scientific and citizen proposal on synthetic biology</b>.</li>
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<li>Most importantly, we have learned a lot during this <em>iGEM</em> phase of the competition. We were selected as <b>one of the three finalists of the European Jamboree</b> and advanced to the World Championship in Boston.</li>
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<p id="references">References</p>
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<li><i>Intercellular Nanotubes Mediate Bacterial Communication</i>, Dubey and Ben-Yehuda, Cell, 2011, available <a href="http://bms.ucsf.edu/sites/ucsf-bms.ixm.ca/files/marjordan_06022011.pdf">here</a></li>
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Latest revision as of 02:24, 29 October 2011

Team IGEM Paris 2011

Towards harnessing bacterial nanotubes by and for synthetic biology

iGEM Logo

The interest: A recent ground-breaking paper [1] described a new cell-to-cell bacterial communication system: nanotubes. Through excellent electronic microscopy images, antibiotic resistance transfer, faint fluorescence transfer, and cross-antibiotic resistance, previously unknown exchange channels were revealed between B.subtilis cells and even between completely different species. Results suggest that protein and/or RNA can travel through these tubes. This discovery may lead to a redefinition of individuality in bacteria. Given the many applications of known communication systems (e.g., quorum sensing, conjugation) in synthetic biology, harnessing the capacity of the nanotubes will open endless possibilities for new applications as amorph computing....


The challenge: Using synthetic biology to characterize the nanotubes: the structure, composition and control of which are still unknown. We decided to work on this challenging problem by providing other proofs to support this discovery.



See our work!


our logo

The project:

We bet-hedged our chances using different reporter systems by creating several devices relying on protein or RNA diffusion. Our devices rely on an emitter cell and a receiver cell that amplifies the signal. We chose to work with signaling molecules of different sizes and natures to test thoroughly the diffusion possibilities. Experiments were coupled with a thorough modeling approach tackling both the detection devices as well as diffusion, assisted transfer within the tubes and the membrane fusion within.


our logo
Our lab achievements

We worked very hard to test the presence of nanotubes and characterize them. Come and find out more about the results of this scientific summer.

our logo
The values:

Ethics and safety are two main concerns when building genetically engineered organisms.

You can visit our Human practice page and our safety page.


New Achievements since Regional Jamboree

We have:

  • Characterized a fully functioning T7 autoloop (emitter and receiver) device in B. subtilis.(15)
  • Characterized a fully functioning sporulation device (KinA emitter and Sin operon receiver) device in B. subtilis.(16)
  • Integrated in the chromosome of B. subtilis the T7 polymerase diffusion entire system (emitter and receiver) and the YFP:tetR emitter system
  • Integrated in an episomal plasmid in B. subtilis the TetO Array and the c1 system
  • Tested nanotubes formation between species (B. subtilis and E. coli) with the system: TetR-YFP emitter in E. coli and TetO array receiver in B. subtilis. No evidence of nanotubes was found so far.(17)
  • Tested nanotubes formation between species (B. subtilis and E. coli) with the system T7 autoloop. No evidence of nanotubes was found so far. (18)
  • Created a new biobricked integrative plasmid pDCPKO for B. subtilis(19)
  • Created and analyzed the collaboration map between iGEM teams throughout the years as a part of our Human Practice project (20)
  • A bonus track: Protocol - The song (21)
  • Survived a second wiki freeze night.

Achievements

We have:

  • Used rational design in combination with modeling to create 6 new couples of emitter/receiver constructs (1) that could help characterize nanotubes' properties, using synthetic biology approach.
  • Proofs of principle of 5 working emitter and receiver devices.(2) (3) (4)
  • Successfully reproduced the GFP experiment of the founding paper (5), indirectly proving the existence of the nanotubes under our microscopes.
  • Developed two original models (6) (7) that could explain the observed transport parameters through the nanotubes.
  • Built a microfluidic chemostat chip, to monitor single bacterial layers under controlled conditions.(8)
  • Reproduced the original antibiotic experiment (9), design complementary controls and proposed alternative explanations for the results observed.
  • Created 38 new biobricks, based on new charachterized parts, all are now at the registry (10) and devices for B. subtilis.
  • Specifically, created and characterized an efficient amplifier with positive feedback loop of T7 RNA polymerase on T7 promoter.(11)
  • Created devices aiming at hijacking two endogenic bistable switches in B. subtilis. (12)
  • Created and characterized a fully functioning fluorescent concentrator device.(13)
  • Collaborated with the Grenoble iGEM team for the human practice(14), building a scientific and citizen proposal on synthetic biology.
  • Most importantly, we have learned a lot during this iGEM phase of the competition. We were selected as one of the three finalists of the European Jamboree and advanced to the World Championship in Boston.

References

  1. Intercellular Nanotubes Mediate Bacterial Communication, Dubey and Ben-Yehuda, Cell, 2011, available here