Team:Grenoble/Projet/Design

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Si vous éditez la page commencez par décommenter ces lignes, publier, PUIS commencer à faire ce que vous avez à faire et quand vous avez fini de publier remettez en commentaire.
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<h1>Design and principle</h1>
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Ne laissez pas le carré trop longtemps si vous n'éditez pas, chaque fois reprenez ce qui est sur internet plutôt que ce que vous avez sur votre PC
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<h2><a href="#toggle">Toggle Switch</a></h2>
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ps: dans Geany selectionner une ou plusieurs lignes et appuyer sur "Ctrl + E" pour commenter ou décommenter
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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 <u><b>it corresponds to an irreversible choice between two pathways depending on the environment.</b></u> 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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  <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="" width="400"></a></td>
 
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  <td><p>Suppose that initially the genes in the Toggle Switch are both expressed.</p></td>
 
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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" alt="" title="" width="400"></a></td>
 
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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
 
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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="" width="400"></a></td>
 
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  <td><p>The bacteria toggle to one side and totally block the expression of lacI.</p></td>
 
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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="" width="400"></a></td>
 
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  <td><p>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.</p></td>
 
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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="" width="400"></a></td>
 
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  <td><p>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.</p></td>
 
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<h3>Importance of Toggle Switch for 'Le Projet'  ? </h3>
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<h2>Table of content</h2>
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Importance of Toggle Switch for Le Projet  ?
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Our Toggle switch is composed by the two repressors (LacI and TetR), also the ways express ether a Quorum Sensing receptor (CinR) or the Quorum Sensing synthesise enzyme (CinI). By this ways the bacterium will engage itself in secretion path or receptor path.
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(missing picture)
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That’s why we use Toggle Switch to have two different behaviours in one cell type, and simplify the immobilisation on plate. We use cell’s communication to finalise our biosensor so we need a homogeneous repartition of ‘sender cell’ and ‘receptor cell’ to have a good communication and response. So locate specifically (homogeneously) two type of cell, will be very hard work contrary to one ‘differentiable type cell’ that we can locate uniformly on the plate.
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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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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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<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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<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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<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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<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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</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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<h2 id="qs">Quorum sensing explanation</h2>
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<h2>References :</h2>
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<h3>In a few words</h3>
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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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Quorum sensing is an important phase of physiological development of the bacteria. It’s the communication signal between bacteria carried by a signalling molecule. All bacteria can produce or detect the quorum sensing molecule. Quorum sensing involves a secreted molecule which allows the number of bacteria to be known and give a logical response to a high level of population. Frequently the Quorum sensing is the signal to stop the growth, activate the virulence state, or activate luminescence.
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The quorum sensing (QS) detection is links to his concentration in the medium, so when the bacteria are in low numbers the QS molecule is at a low concentration and does not activate the response. But when the bacteria become too abundant the QS concentration is higher and activates the response.
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  <td><p>Beginning of growth phase, cells are few, so the production of QS is very low, no response activity.
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  <td><p>Middle Growth phase bacteria are many but not enough for activate QS response, the concentration in QS is not high enough.</p></td>
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  <td><p>In Stationary phase, bacteria are very concentrated so the production of QS is maximal and the lack of space up the concentration of QS. Both phenomena are sufficient to activate a response.</p></td>
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<h3>Biologically, what is happening ?</h3>
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The Quorum sensing system is composed of three elements: an enzyme, a secreted molecule and a receptor.
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A bacterium synthesises this Quorum sensing enzyme which in turn synthesizes the quorum sensing molecule. This molecule diffuses within and outside the cell (around 1mm/h), and can enter inside the issuing bacterium or any other bacteria in its neighbourhood. The QS molecule interacts with its receptor protein. The complex binds to DNA and activates or represses genes generating the appropriate response.
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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


Contact Us:

Clic here !

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