Team:Paris Bettencourt/Experiments

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<h1>Demonstrative experiments</h1>
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<h1>Experiments</h1>
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<p>In the Dubey and Ben-Yehuda paper <a href="http://bms.ucsf.edu/sites/ucsf-bms.ixm.ca/files/marjordan_06022011.pdf">[1]</a> a set of simple experiments are made to prove the existence of the nanotubes. We tryied to reproduce some of them in order to demonstrate again the existence of these entities as a medium of communication between bacteria, and to be sure we are in the good experimental conditions to produce them and that we can go on with our designs.</p>
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<p>You can find here all the experiments we did in the lab! The data is organized by design and you will be able to find both the characterization steps and our diffusion experiments.</p>
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<h2>Preliminaries experiments</h2>
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<p>We tryied to reproduce the two keystone experiments of the paper: the GFP diffusion, and the antibiotic resistance exchange, with less sucess for the latter.</p>
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   <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/GFP_diff"><img style="width:150px" src="https://static.igem.org/mediawiki/2011/8/80/GFP-diff-button.png"></a>
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   <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Preliminaries"><img style="width:150px" src="https://static.igem.org/mediawiki/2011/8/80/GFP-diff-button.png"></a>
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   <td><b>The <a href="https://2011.igem.org/Team:Paris_Bettencourt/GFP_diff">GFP diffusion experiment</a></b> is the simplest experiment possible. One Bacillus Subtlis strain that produce GFP is mixed with a wild type strain. If some nanotubes are formed, the GFP will diffuse through the tubes and color the non fluorescent strain. We invite you to <a href="https://2011.igem.org/Team:Paris_Bettencourt/GFP_diff">visit corresponding the page</a> to learn more about what we did and the results we had.
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   <td><b><a href="https://2011.igem.org/Team:Paris_Bettencourt/Preliminaries">Preliminaries experiments</a></b>: go back and see how we re-did the experiment of the original nanotubes paper.
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<h2>New devices</h2>
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<p>We designed entirely these new devices. They are usually composed of an emitter, a receptor and an amplifier sub-unit.</p>
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   <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Atb_exp"><img style="width:150px" src="https://static.igem.org/mediawiki/2011/2/2b/Question_mark_button.png"></a>
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   <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/YFP_TetR_diffusion"><img style="width:150px" src="https://static.igem.org/mediawiki/2011/d/d0/YFP_concentration_button.png"></a>
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   <td><p><b>The <a href="https://2011.igem.org/Team:Paris_Bettencourt/Atb_exp">antibiotic resistance exchange</a></b> is a more tricky experiment in which bacteria are shown to exchange resistance enzyme through nanotube and allow the population to survive even though all the cells does not carry the resistence.We invite you to <a href="https://2011.igem.org/Team:Paris_Bettencourt/Atb_exp">visit corresponding the page</a> to learn more about what we did and the results we had.</p>
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   <td><b><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/YFP_TetR_diffusion">YFP concentrator</a></b> This design relies on a TetO-array which allow us to concentrate YFP-TetR fusion proteins.
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  <td style="width:200px; text-align:center;"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/T7_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/e/e4/T7_button.png"></a>
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  <td><b><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/T7_diffusion">T7 RNA polymerase diffusion</a></b> In this design, we introduce the use of the T7 polymerase both as the transfer molecule and as the auto-amplification system.
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  <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/tRNA_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/5/53/TRNAamber-button.png"></a>
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  <td><b><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/tRNA_diffusion">tRNA amber diffusion</a></b> The tRNA amber is the smallest molecule we are trying to get pass the nanotubes.
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<h2>Using bistable switches</h2>
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<p>During our brainstormings, we noticed several natural or artificial bistable switches that could serve both as a receptor and an auto-amplifier. One molecule carefully chosen could toggle the switch in another position. All we have to do is see if it diffuses through the nanotubes.
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  <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/ComS_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/2/21/ComS-button.png"></a>
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  <td><b>"<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/ComS_diffusion">ComS diffusion</a></b> We took advantage of a switch already existing in <i>B.Subtilis</i> (the ComK/ComS switch) and tried to see if we could toggle it from one state to the other using molecules diffusing through the nanotubes.
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  <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/SinOp"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/2/21/ComS-button.png"></a>
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  <td><b><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/SinOp">Sin Operon</a></b>
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  <td style="width:200px; text-align:center">Lambda switch<a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/Lambda_switch"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/2/21/ComS-button.png"></a>
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  <td><b><a href="https://2011.igem.org/Team:Paris_Bettencourt/Experiments/Lambda_switch">Lambda switch</a></b>
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<div id="scroll_left"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs"><img src="https://static.igem.org/mediawiki/2011/0/0a/Arrow-left-big.png" style="width:100%;"></a><a href="https://2011.igem.org/Team:Paris_Bettencourt/Designs">Go back to the designs!</a></div>
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<div id="scroll_left"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling"><img src="https://static.igem.org/mediawiki/2011/0/0a/Arrow-left-big.png" style="width:100%;"></a><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling">Modeling overview</a></div>
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Latest revision as of 18:58, 27 October 2011

Team IGEM Paris 2011

Experiments

You can find here all the experiments we did in the lab! The data is organized by design and you will be able to find both the characterization steps and our diffusion experiments.

Preliminaries experiments

Preliminaries experiments: go back and see how we re-did the experiment of the original nanotubes paper.

New devices

We designed entirely these new devices. They are usually composed of an emitter, a receptor and an amplifier sub-unit.

YFP concentrator This design relies on a TetO-array which allow us to concentrate YFP-TetR fusion proteins.
T7 RNA polymerase diffusion In this design, we introduce the use of the T7 polymerase both as the transfer molecule and as the auto-amplification system.
tRNA amber diffusion The tRNA amber is the smallest molecule we are trying to get pass the nanotubes.

Using bistable switches

During our brainstormings, we noticed several natural or artificial bistable switches that could serve both as a receptor and an auto-amplifier. One molecule carefully chosen could toggle the switch in another position. All we have to do is see if it diffuses through the nanotubes.

"ComS diffusion We took advantage of a switch already existing in B.Subtilis (the ComK/ComS switch) and tried to see if we could toggle it from one state to the other using molecules diffusing through the nanotubes.
Sin Operon
Lambda switch Lambda switch

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