Team:Toulouse/Modelling

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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<p style="color:#E7E7E7"> <a href="http://2014.igem.org/wiki/index.php?title=Team:Toulouse/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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      <h2>Modeling</h2>
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<a href="http://2014.igem.org/Team:Toulouse"style="color:#000000">Home </a> </td>
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  <p style="margin:0 auto; color:#696969; width:960px; padding-top:20px; font-size:16px;"> Project&nbsp;&nbsp;&nbsp;>&nbsp;&nbsp;&nbsp;Spreading</p>  
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<a href="http://2014.igem.org/Team:Toulouse/Team"style="color:#000000"> Team </a> </td>
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<div class="Title">Spreading</div> <br/>
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<a href="http://igem.org/Team.cgi?year=2014&team_name=Toulouse"style="color:#000000"> Official Team Profile </a></td>
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How can SubtiTree respect the environment ? How do we keep control on Subtitree?
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Our engineered bacterium has been designed to be inoculated in a tree and to cure fungal diseases. Understanding the environmental issues resulting from the use of a modified organism in the nature, our team worked on different aspects in order to ensure a safe use of SubtiTree.
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The first objective is to avoid the spreading of our smart bacterium outside the tree. In other words, the purpose is to ensure that once SubtiTree is in the tree, it is unable to live anywhere else. Another issue concerns the horizontal transfers of the genetic material between different bacteria.
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Taking into account these issues, we thought about three modules.
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<div class="Sub_title"><div id="Auxotrophy">Auxotrophy</div></div>
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<a href="http://2014.igem.org/Team:Toulouse/Project"style="color:#000000"> Project</a></td>
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To make the bacterium dependant on the tree and to avoid its spreading in the environment, it should be preferable to use a strain of B.subtilis which is auxotroph to a particular amino acid. The bacterium should be unable to synthesize one essential amino acid, and should find it in its environment. The glutamine could be a good example since it is wide-spread in the phloem sap. It is the amino acid which is present in highest concentration in the phloem sap. If our bacterium is unable to synthesize the glutamine, it will be obliged to take it in its close environment, that is to say the phloem sap.
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Thus, if the bacterium is in the sap, it can grow normally without any deficiency since it uses the glutamine present in the sap ; but if it escapes from the tree and a fortiori from the sap, it will not be able to survive for a long time. Indeed, glutamine is found in very low quantities in the ground. This system should guarantee that the bacterium develops only in the tree and not elsewhere in the surroundings of the tree.<br/>  
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Auxotroph B.sutbilis strains already exist and are indexed in databases as BGSC (Bacillus Genetic Stock Center), so it is easy to find. 
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<div class="Sub_title"><div id="NonSporing">Non-sporing </div></div>
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In order to limit the spreading of our bacterium, we decided to limit its lifespan to only one season. The bacteria should be injected in spring, grow during the summer and finally should be inactivated in fall.<br\>
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Bacillus subtilis is a sporing bacterium : sporulation enable the microorganism to handle very harsh conditions and to spread tree to tree. Indeed, a spore is a very resistant form that is adapted for unfavourable conditions and for dispersal.<br/>  
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To keep the control on the development of SubtiTree, our strain should therefore be non-sporing. Thus, after a season of treatment, the sape become less nutritious, the temperature is low and the engineered bacterium cannot survive the following winter.<br/>
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In addition, deleting all the engineered bacterial community every year puts a brake on the evolution due to random mutation = to keep control on the genetic constructions
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<a href="http://2014.igem.org/Team:Toulouse/Modeling"style="color:#000000"> Modeling</a></td>
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<div class="Sub_title"><div id="Toxin">Toxin-antitoxin system</div></div>
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The goal of this module is to prevent horizontal transfer between bacteria. Indeed, it is necessary to avoid any exchange of genetic material between wild type organisms and optimized organisms : it could be dangerous because of mutations, and considering ethics, it seems to be essential to avoid the spreading of synthetic genes.<br/>
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Considering this issue, we thought about a system to avoid such transfers : a toxin-antitoxin module. It involves the addition of two genes to the bacterium : a gene encoding for a toxin (for example tse2) and a gene encoding for the antitoxin (tsi1), placing them in an opposite way on the genome. The large space between them will permit to avoid simultaneous transfers : if the optimised bacterium transfers the gene encoding for the toxin, the probability that the gene encoding for the antitoxin may be transferred simultaneously is really low since they are located far away from each other.<br/>
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Therefore, if the host bacterium receives the gene encoding for the toxin, it will be unable to survive since it will not have the antitoxin. If it receives the antitoxin only, it will not be useful for the bacterium, and will not affect it.<br/>
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To sum up, since a simultaneous transfer is dimly probable, the bacterium will either die because of the toxin or live while expressing the antitoxin (useless).
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<a href="http://2014.igem.org/Team:Toulouse/Notebook"style="color:#000000"> Notebook</a></td>
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<div class="Sub_title">Integrative plasmid ?</div>
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All our constructions should be carried by integrative plasmids (pS.., pS.., pS..). Consequently, our different genetic modules would be integrated in the bacterium genome. The integration in the genome is more stable as the constructions are less likely to be transferred to other microorganisms. In addition to that, the expression of our genetic modules would not be dependant on a selective pressure based on an antibiotic resistance (as we can not inject antibiotics in the tree), allowing a high level of transcription in planta.
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<a href="http://2014.igem.org/Team:Toulouse/Safety"style=" color:#000000"> Safety </a></td>
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<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
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Revision as of 16:18, 28 September 2014