Team:Grenoble/Projet/Design

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<h1>Design and principle</h1>
 
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<h2><a href="#toggle">Toggle Switch</a></h2>
 
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<h2><a href="#qs">Quorum Sensing</a></h2>
 
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<h2 id="toggle">Toggle switch explanation</h2>
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<h3>In a few words</h3>
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<h1>Genetic Network</h1>
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Our project is based on a toggle switch system. So we have to explain how it works. Basically it corresponds to an irreversible choice between two pathways depending on the environment. In reality, the reversibility is possible but very difficult to obtain because of the strength of the interactions and the stability of the system (defined by hysteresis * insérer un lien ici*).  
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we design the following circuit, based on Gardner and al. Gardner's <a href="#1">[1]</a> work and balagadd and al. on Predator–Prey ecosystem <a href="#2">[2]</a>.
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<a href="https://static.igem.org/mediawiki/2011/b/b6/Toggle1.png"><img src="https://static.igem.org/mediawiki/2011/b/b6/Toggle1.png" alt="2 pathways toggle switch" title="Choose one way, no turning back !"></a>  
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<center><a href="https://static.igem.org/mediawiki/2011/8/80/Reseau_regulation_compl2_%281%29.png"><img height="400" src="https://static.igem.org/mediawiki/2011/8/80/Reseau_regulation_compl2_%281%29.png"></a></center>
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<h3>Genetically, what is happening ?</h3>
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Contrary to us, bacteria can’t think or make voluntary choices. So how can they choose a pathway? Through our project, we are creating a genetic system which helps bacteria to take such a decision. For that, we exploit chemical components of the environment which influence the bacterial behaviour. By taking into account two proteins repressing each other’s expression (LacI and XR), we create the fundaments of a toggle system that can switch when using two inducers (IPTG and X) in the medium. 
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It can be divided into four parts: the Toggle Switch, the Quorum Sensing, the Coloration and the post-transcriptional regulation. (Coloration is included in Quorum Sensing page) </p>
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<a href="https://static.igem.org/mediawiki/2011/7/7c/Toggle2.png"><img src="https://static.igem.org/mediawiki/2011/7/7c/Toggle2.png" alt="" title=""></a>
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<h2>Table of content</h2>
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  <td><a href="https://static.igem.org/mediawiki/2011/8/8d/Toggle3.png"><img src="https://static.igem.org/mediawiki/2011/8/8d/Toggle3.png" alt="" title=""></a></td>
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  <td>Suppose that initially the genes in the Toggle Switch are both expressed.</td>
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In the following pages, you can find the explanation about the differents sub-parts of our genetic network. Moreover we explane to you the importance of both to our project.
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  <td><a href="https://static.igem.org/mediawiki/2011/0/0a/Toggle4.png"><img src="https://static.igem.org/mediawiki/2011/0/0a/Toggle4.png.png" alt="" title=""></a></td>
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  <td>If the effect of LacI is dominant through the presence of a high level of IPTG, the bacteria will synthesise more XR and switch off the expression of lacI</td>
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For an introduction to the genetic circuit, see our tutorials in the human practice
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section or download them here :
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  <td><a href="https://static.igem.org/mediawiki/2011/d/d5/Toggle5.png.png"><img src="https://static.igem.org/mediawiki/2011/d/d5/Toggle5.png" alt="" title=""></a></td>
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  <td>The bacteria toggle to one side and totally block the expression of lacI.</td>
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<a href="https://static.igem.org/mediawiki/2011/9/91/M_for_B.png">
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Modelling for biologist</a>
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  <td><a href="https://static.igem.org/mediawiki/2011/1/15/Toggle6.png"><img src="https://static.igem.org/mediawiki/2011/1/15/Toggle6.png" alt="" title=""></a></td>
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  <td>We need to use very high level of the second inducer X to try to switch the toggle back because the active pathway creates an excess of XR, inhibiting lacI expression. </td>
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<a href="https://static.igem.org/mediawiki/2011/5/54/B_for_M.png">
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Synthetic Biology for modellers</a>
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  <td><a href="https://static.igem.org/mediawiki/2011/9/97/Toggle7.png"><img src="https://static.igem.org/mediawiki/2011/9/97/Toggle7.png" alt="" title=""></a></td>
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  <td>The amount of X would have to be so high as to relieve the inhibition of lacI expression and consequently turn off the other pathway</td>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Design/toggle"><img class="icon" src="https://static.igem.org/mediawiki/2011/2/20/Bouton_toggle.png"/></a>
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<big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/Design/toggle" class="menu">Toggle Switch:</a></big></big><br/>
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The toggle switch offers the bacteria the capacity to choose between two pathways in function of their environment. Thanks to that our E.coli can activate one of two Quorum Sensing (*insérer un lien ici*) ways.
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum" class="menu"><img class="icon" src="https://static.igem.org/mediawiki/2011/f/f8/Bouton_QS_color.png"/></a>
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<big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum" class="menu">Quorum Sensing :</a></big></big><br/>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum" class="menu">The Quorum Sensing</a><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum#coloration" class="menu">Coloration</a><br/>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/regulation" ><img class="icon" src="https://static.igem.org/mediawiki/2011/9/97/Bouton_regulation.png"/></a>
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<big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/regulation" class="menu">Post-transcriptional regulation :</a></big></big><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/regulation" class="menu">A post-transcriptional regulation system</a><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/regulation#rsma" class="menu">The RsmA translational regulation system</a><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/regulation#rpos" class="menu">The rpoS regulation system</a><br/>
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<br/><br/><br/>
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</p>
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<p>
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You can find the results of our biological experiments in the
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Results">results page
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</a>.
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        </p>
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<h2 id="qs">Quorum Sensing</h2>
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<h2>References :</h2>
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GARDNER'S WORK: "Construction of a genetic toggle switch in Escherichia coli", Timothy S. Gardner, Charles R. Cantor and James J. Collins, Nature, 2000, Vol.403, p339-42.
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PREY AND PREDATOR: "A synthetic Escherichia coli predator–prey ecosystem", Frederick K Balagadd, Hao Song, Jun Ozaki, Cynthia H Collins, Matthew Barnet, Frances H Arnold, Stephen R Quake and Lingchong You, Molecular Systems Biology, 2008;4:187.
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There is a risk for the eyes and the skin, but the UV lamp is only used to take a picture of our gel after electrophoresis, so we are never directly exposed because there is a protective cover and we wear a mask that shields from UV.
 
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<dt>Centrifuge:</dt>
 
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The centrifuges have to be perfectly balanced. All the centrifuges in our lab have detectors that warn the operator in case of imbalance.
 
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The operation of the autoclave require a specific training and has only be performed by trained people.
 
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    <optgroup label="Genetic network Homepage">
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    <option value="#Content" selected="selected">General network</option>
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    <optgroup label="Toggle Switch" >
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                                    <option value="/Design/toggle" >The Toggle Switch</option>
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                            <optgroup label="Quorum Sensing">
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                                    <option value="/Design/quorum">The Quorum Sensing</option>
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                                    <option value="/Design/quorum#coloration">The Coloration</option>
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                            </optgroup>
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                            <optgroup label="Post Transcriptional Regulation">
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    <option value="/regulation">A Post-Transcriptional Regulation System</option>
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    <option value="/regulation#rsma">The RsmA Translational Regulation System</option>
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    <option value="/regulation#rpos">The rpoS regulation system</option>
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Latest revision as of 18:24, 31 January 2012

Grenoble 2011, Mercuro-Coli iGEM


Genetic Network

we design the following circuit, based on Gardner and al. Gardner's [1] work and balagadd and al. on Predator–Prey ecosystem [2].



It can be divided into four parts: the Toggle Switch, the Quorum Sensing, the Coloration and the post-transcriptional regulation. (Coloration is included in Quorum Sensing page)



Table of content

In the following pages, you can find the explanation about the differents sub-parts of our genetic network. Moreover we explane to you the importance of both to our project.

For an introduction to the genetic circuit, see our tutorials in the human practice section or download them here :

Toggle Switch:




Quorum Sensing :
The Quorum Sensing
Coloration


Post-transcriptional regulation :
A post-transcriptional regulation system
The RsmA translational regulation system
The rpoS regulation system



You can find the results of our biological experiments in the results page .

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iGEM 2011 Main Page


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