Team:Evry/Overview/Project

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      <h1>The Sponge Patrol Project</h1>
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For our third participation to the iGEM competition, we decided to introduce a new chassis to the competition, Pseudovibrio denitrificans.
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<h1> The Sponge Patrol Project</h1>
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Water is the most precious and fragile resource on Earth. However <b><FONT COLOR=#0099CC>seas and oceans</FONT></b> are polluted by a wide range of compounds stemming from human activities.
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Faced with this issue, our team wants to heighten awareness about environmental pollution and particularly its devastating consequences on the aquatic life.
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In this line of thinking we are driven to design a bioremediation tool based on the considerable filtration capacity of <b><FONT COLOR=#FFCC33>sponges</font></b> to decrease the marine pollution and protect aquatic ecosystems.
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Our project is based on the engineering of this bacterium in the <b><FONT COLOR=#996666>microbiome </FONT></b>in order to develop a filtrating system allowing to sense and even degrade pollutants in water
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<img src="https://static.igem.org/mediawiki/2014/a/aa/Schema_HOME_Basse_Definition_%281%29_%282%29.png" style="width:30%;height:30%;">
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<br>blabla bla
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Sum up of overview parts
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<br>un cadre ou une liste d'items
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                      <FONT color="white"> <h5>Chassis</h5></font>
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                        <a href="#chassis"><img class="img-circle" src="https://static.igem.org/mediawiki/2014/7/7e/Chassis_EVRY.png" height="128" width="128" alt="Conference" border="30px" style="box-shadow: 0 0 8px rgba(0, 0, 0, .8); "/></a>
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                        <font colors ="white"><h5>Transposons</h5></font>
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                        <a href="#transposons"><img class="img-circle" src="https://static.igem.org/mediawiki/2014/b/bf/Transpo3.png" height="128" width="128" alt="Workshops" style="box-shadow: 0 0 8px rgba(0, 0, 0, .8); "></a>
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                        <FONT color="white"><h5>Target</h5></font>
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                        <a href="#target"><img class="img-circle" src="https://static.igem.org/mediawiki/2014/f/f1/Image1.jpg" height="128" width="128" alt="Hackathons" style="box-shadow: 0 0 8px rgba(0, 0, 0, .8)"></a>
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<br>Le détail des 3 soius-unités avec une image sympa pour chacun, on clique dessus pour avoir la suite
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<h4 id="chassis"> Chassis </h4> </font>
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For our third participation in the iGEM competition, we decided to use <b><FONT COLOR=#666699>a new chassis </FONT></b> which is able to work in the depth of oceans through a forceful duo: <b>sponge and bacterium</b>.
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Sponge can filtrate up to 20m<sup>3</sup> of water/day/kg thus being one of the most powerful existing filtrating  system.
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We focused on the sponge <b><FONT COLOR=#FFCC33>Spongia Officinalis</FONT></b>, which lives in episymbiosis with the bacterium: <i><FONT COLOR=#006633>Pseudovibrio denitrificans</font></i>.
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Pseudovibrio denitrificans is a marine bacterium which as been not yet characterized and also never been used in iGEM.
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<br>
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Likewise, we bring in the iGEM competition Spongia Officinalis, a sponge with impressive features and capacities.
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<br>
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This is why we dedicate a part to introducing them.
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Chassis : draw a bacteria in water the same as the one in the logo
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<a href="https://2014.igem.org/Team:Evry/Biology/Chassis" ><img src="https://static.igem.org/mediawiki/2014/d/db/Chassis_seemore_EVRY.png" style="width:15%;height:15%"/></a>
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<h4 id="transposons"> Transposons </h4></font>
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Our synthetic system is based on the bacterium Pseudovibrio denitrificans, which is yet arduous to transform due to its marin origin.
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In order to be able to transform our bacterium with genes of interest, we have created a new backbone enabling us to use <FONT COLOR=#CC6699> <b>the transposon system</b></font> in our bacterium.
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This tool allows to insert genes easily into unknown bacteria.
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<a href="https://2014.igem.org/Team:Evry/Biology/Transposons" ><img src="https://static.igem.org/mediawiki/2014/6/62/Tranposeemore.png" style="width:10%;height:10%"/></a>
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<h4 id="target"> Target </h4></font>
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<p>
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This year, our team objective is to develop a filtrating system allowing the sensing and eventually degradation of <b><FONT COLOR=#333300>pollutants</font></b>.
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To achieve that goal, we have chosen to work on the most important classes of marine pollutants: phenols, PCBs, nitrites and heavy metals.
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<br><br>
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<a href="https://2014.igem.org/Team:Evry/Biology/ToxicCompounds" ><img src="https://static.igem.org/mediawiki/2014/3/31/Targetseemore.png" style="width:5%;height:5%"/></a>
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<h4 id="target"> Philosophy </h4></FONT>
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This year, we decided to include in our project a philosophical reflexion on the methods used in iGEM and in synthetic biology. We observed that there was an important contrast between what synthetic biologists ambition to do — a rational, rigorous design with controlled and predicted results — and how they actually design their biological systems — by trial and error, and tinkering. As students engaged in the practice of synthetic biology, we thought that it was very important to take a critical look at the field, and to question whether design in synthetic biology can truly be compared to engineering, or if it is instead the result of inelegant but efficient kludges.
 +
Since our project means to use sponges as part of our biosensing agent, we also discussed the ethical issues raised by the modification of an animal's microbiome, and by the use of an animal as a bioremediation tool in potentially toxic areas.
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We also had an important reflexion about the risks inherent to the release of genetically modified organisms in seawater, and tried to assert whether a symbiosis between the bacteria and the sponge could be a safe and efficient biological containment of the engineered micro-organisms.
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<h2> A specific chassis for a specific environnement: Seas & Oceans</h2>
 
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As seen in the <a href="https://2014.igem.org/Team:Evry/Overview" <b><big> overview</big></b></a> our biosensors should work optimaly in native marine conditions, a conditions for which <b><font color= "red"> no current chassis</font></b> in iGEM is ready for.
 
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Moreover it has to attach to sponges and stick with them without disturbing the microbiome for as long as possible.
 
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Therefore came up the necessity to use a bacterium naturally present on the sponges, may it be an epibiont or a symbiont.
 
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To be up to the task the bacterium should have the following properties:
 
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    <li> be massively present on the sponge surface / avoiding being in an unfavorable position for food competition.</li>
 
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    <li> be found mainly in sponges / avoid spreading to species in contact with sponges.</li>
 
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    <li> be the phenotypically closest possible  to a known bacterium. / avoid cell cultures difficulties.</li>
 
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To be up to the task the sponge should have the following properties:
 
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    <li> be numerously present in the ocean / avoiding putting species in danger.</li>
 
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    <li> be a natural host of the bacterium / avoid adapting its microbiom to the new epibiont.</li>
 
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    <li> be easily culturable in a laboratoty / avoid sopnge culture difficulties.</li>
 
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The closest combination sponge/bacterium that could fit the requirement is <i><big>Spongia Officinalis / Pseudovibrio denitrificans </big></i>
 
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<a href="https://2014.igem.org/Team:Evry/Biology/CellCharacterization">To learn more ...</a>
 
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<br>    <a id="igem-link" target="_blank" href="https://2014.igem.org/Team:Evry/Biology/CellCharacterization" title="Go to iGEM site"><img src="https://static.igem.org/mediawiki/2014/c/c8/Mus%C3%A9um.jpg" width="10%"/></a>
 
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<a href="https://2014.igem.org/Team:Evry/Policy_and_Practices/Philosophy" ><img src="https://static.igem.org/mediawiki/2014/f/f5/Livre_see_more.jpg"/></a>
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<br> Transposons: a transposons
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<br><a href="https://2014.igem.org/Team:Evry/Biology/Transposons">To learn more ...</a>
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<br> Compounds/target : some usine in the background I think the title need to be change and as to be rename target
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<h4 id="target"> Model </h4></FONT>
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<br> <a href="https://2014.igem.org/Team:Evry/Biology/Sensors">To learn more ...</a>
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<a href="https://2014.igem.org/Team:Evry/Biology/Sensors"><img src="https://static.igem.org/mediawiki/2014/c/cb/Warning.png" width="10%"/></a>
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This year we provided two models of the sponge, and also two sensors models. Concernerning the sponge sponge modethe first model was a flux model of the sponges in one dimension. The second model is a 2D diffusion model. It t  ake into accoun the number and the size of the sponge spore. We also model  two sensor  model. The first one about the PCB and the second one for the phenol. The phonol model acess the biological results
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<a href="https://2014.igem.org/Team:Evry/Model/Sponge" ><img src="https://static.igem.org/mediawiki/2014/b/b7/Model_see_more.jpg"/></a>  
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Latest revision as of 03:59, 18 October 2014

IGEM Evry 2014

Overview - Project

The Sponge Patrol Project



Water is the most precious and fragile resource on Earth. However seas and oceans are polluted by a wide range of compounds stemming from human activities. Faced with this issue, our team wants to heighten awareness about environmental pollution and particularly its devastating consequences on the aquatic life. In this line of thinking we are driven to design a bioremediation tool based on the considerable filtration capacity of sponges to decrease the marine pollution and protect aquatic ecosystems. Our project is based on the engineering of this bacterium in the microbiome in order to develop a filtrating system allowing to sense and even degrade pollutants in water


Chassis
Conference
Transposons
Workshops
Target
Hackathons


Chassis


For our third participation in the iGEM competition, we decided to use a new chassis which is able to work in the depth of oceans through a forceful duo: sponge and bacterium. Sponge can filtrate up to 20m3 of water/day/kg thus being one of the most powerful existing filtrating system. We focused on the sponge Spongia Officinalis, which lives in episymbiosis with the bacterium: Pseudovibrio denitrificans.
Pseudovibrio denitrificans is a marine bacterium which as been not yet characterized and also never been used in iGEM.
Likewise, we bring in the iGEM competition Spongia Officinalis, a sponge with impressive features and capacities.
This is why we dedicate a part to introducing them.




Transposons


Our synthetic system is based on the bacterium Pseudovibrio denitrificans, which is yet arduous to transform due to its marin origin. In order to be able to transform our bacterium with genes of interest, we have created a new backbone enabling us to use the transposon system in our bacterium. This tool allows to insert genes easily into unknown bacteria.




Target


This year, our team objective is to develop a filtrating system allowing the sensing and eventually degradation of pollutants. To achieve that goal, we have chosen to work on the most important classes of marine pollutants: phenols, PCBs, nitrites and heavy metals.

Philosophy


This year, we decided to include in our project a philosophical reflexion on the methods used in iGEM and in synthetic biology. We observed that there was an important contrast between what synthetic biologists ambition to do — a rational, rigorous design with controlled and predicted results — and how they actually design their biological systems — by trial and error, and tinkering. As students engaged in the practice of synthetic biology, we thought that it was very important to take a critical look at the field, and to question whether design in synthetic biology can truly be compared to engineering, or if it is instead the result of inelegant but efficient kludges. Since our project means to use sponges as part of our biosensing agent, we also discussed the ethical issues raised by the modification of an animal's microbiome, and by the use of an animal as a bioremediation tool in potentially toxic areas. We also had an important reflexion about the risks inherent to the release of genetically modified organisms in seawater, and tried to assert whether a symbiosis between the bacteria and the sponge could be a safe and efficient biological containment of the engineered micro-organisms.

Model


This year we provided two models of the sponge, and also two sensors models. Concernerning the sponge sponge modethe first model was a flux model of the sponges in one dimension. The second model is a 2D diffusion model. It t ake into accoun the number and the size of the sponge spore. We also model two sensor model. The first one about the PCB and the second one for the phenol. The phonol model acess the biological results