Team:Evry/Project

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<h1>Project overview</h1>
<h1>Project overview</h1>
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For our first participation in iGEM, we have decided to introduce a new organism to the competition: <i>Xenopus tropicalis</i>. Its common name is the Western clawed frog, a diploid cousin of the model organism <i>Xenopus laevis</i>. Aside for the soft spot French have for frogs, we also believe <i>Xenopus</i> could be a great multicellular chassis for synthetic biology. We are therefore bringing this organism to iGEM for the first time, along with the tools we need to bring Synthetic biology to the multicellular era.
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<p>For our first participation in iGEM, we have decided to introduce a new organism to the competition: <i>Xenopus tropicalis</i>. Its common name is the Western clawed frog, a diploid cousin of the model organism <i>Xenopus laevis</i>. Aside for the soft spot us Frenchmen have for frogs, we also believe <i>Xenopus</i> could be a great multicellular chassis for synthetic biology. We are therefore bringing this organism to iGEM for the first time, along with the tools we need to bring Synthetic biology to the multicellular era.
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<p>
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The laboratory part of our work can be divided into two categories: the creation of synthetic biology tools for <i>Xenopus</i> and the creation of a synthetic hormonal system. We created a multi-level model of this inter-tissue communication system, concurrently laying the groundwork for modeling of synthetic genetic systems in multicellular organisms. Finally, using vertebrates in synthetic biology poses deep ethical problems, which come alongside those of animal experimentation. iGEM aims to be cool and fun, but can we or should we keep the same attitude when working with vertebrate embryos ? Should we reduce animals to objects or tools by using words such as chassis when working with these multicellular organisms? Our resident philosopher lead our team’s reflection on these issues, proposing a guide for future synthetic biologists who wish to work with <i>Xenopus</i>.  
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</p> <p>
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The laboratory part of our work can be divided into two categories: The creation of synthetic biology tools for <i>Xenopus</i>, and the creation of a synthetic hormonal system. We created a multi-level model of this inter-tissue communication system, concurrently laying the groundwork for modelling of synthetic genetic systems in multicellular organisms. Finally, using vertebrates in synthetic biology poses deep ethical problems, which come alongside those of animal experimentation. iGEM aims to be cool and fun, but can we or should be keep the same attitude when working with vertebrate embryos ? Should we reduce animals to objects or tools by using words such as chassis when working with these multicellular organisms? Our resident philosopher lead our team’s reflection on these issues, proposing a guide for future synthetic biologists who wish to work with <i>Xenopus</i>.  
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<div id="contourmenu" style="position: relative; margin-left: auto; margin-right: auto; width: 700px; text-align: left; background-color: #cee9f4; border-radius: 7px; align: left">
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<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br>
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<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br>
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<div id="item" style="margin-left:20px;">
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<ul>
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<a href="#frog">A new multicellular chassis for synthetic biology: <i>Xenopus tropicalis</i></a>
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<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a>
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</br>
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<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a>
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<a href="#model" style="text-decoration:none;"><li>Engineering a synthetic, orthogonal hormone as a communication device</li></a><br>
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<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a>
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<a href="#game" style="text-decoration:none;"><li>Goldenbrick: A new Biobrick standard for one-shot assembly of multiple parts</li></a><br>
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<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a>
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<a href="#human" style="text-decoration:none;"><li>Modelling: A multi-level approach to model synthetic systems in multicellular organisms</li></a><br>
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<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a>
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<a href="#dummies" style="text-decoration:none;"><li>Xenopus for dummies: an iGEMer guidebook</a><br><br>
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<a href="#human" style="text-decoration:none;"><li>We collaborated with La Paillasse community lab to create an augmented reality interface for interacting with tadpoles </li></a><br>
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</ul>
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<a href="#human" style="text-decoration:none;"><li> Collaborating with <i>Xenopus</i> made us investigate on the specific relationships that are created through the development of animal biotechnlogies </li></a><br>
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A quick summary of each project is proposed in this page. Please go on the specific page of each project for more details!
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<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center>
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<img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 />
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<!-- #Bannière Grenouille -->
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<h2 id="frog"> <b> <i>Xenopus</i>: A new chassis for multicellular synthetic biology </b> </h2>
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<!-- Xenopus Tropicalis -->
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<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2>
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<p>While iGEM has so far been mostly focused on en engineering unicellular organisms and bacteria in particular, we have decided work on the next step for synthetic biology: Multicellular engineering. Using our new biobrick tools, the road towards synthetic circuits in <i>Xenopus</i> is open, multiplying the number of potential applications in terms of synthetic biology. </p>
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<p>
 +
While iGEM has so far been mostly focused on en engineering unicellular organisms and bacteria in particular, we have decided work on the next step for synthetic biology: Multicellular engineering. Using our new biobrick tools, the road towards synthetic circuits in <i>Xenopus</i> is open, multiplying the number of potential applications in terms of synthetic biology.
 +
</p>
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<p><i>Xenopus</i> is a model organism for developmental biology. Rapid development, easy handling and direct injection of plasmids into the fertilized egg allow testing of constructs in less than two weeks. We provide frog compatible plasmids for using this system in biobrick standard format. We have submitted two complementary systems: The first allows rapid testing of the system, but in a transient way. It also includes tools for debugging of the system. Once a working system is in place, it can be reassembled and integrated on the chromosome for longer-term use. </p>
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<p>
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<i>Xenopus</i> is a model organism for developmental biology. Rapid development, easy handling and direct injection of plasmids into the fertilized egg allow testing of constructs in less than two weeks. We provide frog compatible plasmids for using this system in biobrick standard format. We have submitted two complementary systems: The first allows rapid testing of the system, but in a transient way. It also includes tools for debugging of the system. Once a working system is in place, it can be reassembled and integrated on the chromosome for longer-term use.
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</p>
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<br>
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<div id="contourmenu" class="moredetails">
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<table style="background:transparent";>
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<tr><td><img style="padding-top:10px;padding-left:10px;" src="http://2012.igem.org/wiki/images/b/bd/Xenope.png" width=80px></td>
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<h3 style="text-align:center; padding-left:20px;"></u>
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<a href="http://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a>
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<a href="http://2012.igem.org/Team:Evry/FrenchFrog">Visit the project page ></a>
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<h2><b></b>A synthetic, orthogonal hormonal system </h2>
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<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2>
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<p>
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In order to be able to bring synthetic biology to multicellular organisms, it is essential that we have a communication device enabling cell-to-cell or tissue-to-tissue communication. We have advanced towards the implementation of the first synthetic hormone, which would allow communication between cells in an orthogonal manner. We have submitted an auxin receiver device to the registry, for use in combination with an auxin production system that we have adapted for eukaryotic chassis.
 +
</p>
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<p><i>In order to be able to bring synthetic biology to multicellular organisms, it is essential that we have a communication device enabling cell-to-cell or tissue-to-tissue communication. We have advanced towards the implementation of the first synthetic hormone, which would allow communication between cells in an orthogonal manner. We have submitted an auxin receiver device to the registry, for use in combination with an auxin production system that we have adapted for eukaryotic chassis. </p>
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<br>
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<div id="contourmenu" class="moredetails" style="align:center">
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<table style="background:transparent";>
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<tr><td><img style="padding-top:10px;padding-left:10px;" src="http://2012.igem.org/wiki/images/e/e2/Hormone.png" width=80px></td>
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<h3 style="text-align:center; padding-left:20px;"></u>
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<a href="http://2012.igem.org/Team:Evry/AIDSystem"><center>More details here...</center></a>
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<a href="http://2012.igem.org/Team:Evry/AIDSystem">Visit the project page ></a>
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<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2>
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<p>
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Merging the power of the Golden Gate multi-fragment cloning technique with the standardization of the Biobrick format. As a result, our team is developing this year a new parts format: the GoldenBricks. This is a new ultrafast cloning technique designed to assemble entire cassette in one shot. Ultimately, the GoldenBricks method is paving the way for future PartsRegistry formats!
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</p>
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<div id="contourmenu" class="moredetails">
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<table style="background:transparent";>
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<tr><td><img style="padding-top:10px;padding-left:10px;" src="http://2012.igem.org/wiki/images/a/a4/GoldeN.png" width=80px></td>
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<h3 style="text-align:center; padding-left:20px;"></u>
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<a href="http://2012.igem.org/Team:Evry/GB"><center>More details here...</center></a>
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</u></h3></td>
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<h2><b>Modeling a tadpole:</b> a multi-level approach</h2>
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<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2>
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<p>
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Modeling a synthetic system at the whole organism scale is a challenge in itself. Using differential equations and agent based simulation, we aimed at modeling our entire synthetic hormonal system, as well as providing a new set of mathematical tool for iGEM in order to model complete organisms.
 +
</p>
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<p>Modeling a synthetic system at the whole organism scale is a challenge in itself. Using differential equations and agent based simulation, we aimed at modeling our entire synthetic hormonal system, as well as providing a new set of mathematical tool for iGEM in order to model complete organisms.
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<br>
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<div id="contourmenu" class="moredetails">
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<table style="background:transparent";>
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<tr><td><img style="padding-top:10px;padding-left:10px;" src="http://2012.igem.org/wiki/images/5/5b/ModelingDHIUHEIUHD.png" width=80px></td>
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<h3 style="text-align:center; padding-left:20px;"></u>
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<a href="http://2012.igem.org/Team:Evry/Modeling"><center>More details here...</center></a>
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<p><a href="http://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p>
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<h2 id="human">Human practice: What does it mean to be a chassis?</h2>
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Working with vertebrate embryos raised many questions among the team. We decided to track the changes in our attitude to animal experimentation during our project. Before starting our experiments, we answered a list of questions concerning animal experimentation and synthetic biology. Our reflection progressively lead us to realize that considering animals as mere chassis waiting to be engineered was quite a problematic conception that we had to question.
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</p>
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<!--<h2><a name="game" style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2>
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<p><a href="http://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p>
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<h2><b>Cloning:</b> a new biobrick cloning format</h2>
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<h3 style="text-align:center; padding-left:20px;"></u>
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<p>We have started the development ou a new biobrick format that may revolutionize the future of iGEM cloning by enabling the assembly of a complete expression cassette in one shot, in a cheaper and most reliable way than all the current cloning method. We are the initiator of that project and we are going to develop it in partneship with the iGEM Paris Bettencourt and the CINVESTAV-IPN-UNAM_MX team in Mexico.
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<a href="http://2012.igem.org/Team:Evry/HumanPractice"><center>More details here...</center></a>
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<p><a href="http://2012.igem.org/Team:Evry/GB">Visit the project page ></a></p>
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<!-- Frog for dummies -->
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<h2 id="dummies">Xenopus for dummies: a guidebook for iGEMers</h2>
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<p>
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Xenopus is a quite complex organism we were the first team to work with it in iGEM. This is why we wrote a guidebook to help future teams find information and brainstorm for project with this organism, in the dummies format!
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</p>
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<h2><b>Human practice:</b> What does it mean to be a chassis</h2>
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<br>
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<div id="contourmenu" class="moredetails">
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<p>Working with vertebrate embryos raised many questions among the team. We decided to track the changes in our attitude to animal experimentation during our project. Before starting our experiments, we answered a list of questions concerning animal experimentations and synthetic biology. Our reflection progressively lead us to realize that considering animals as mere chassis waiting to be engineered was quite a problematic conception that we had to question. </p>
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<table style="background:transparent";>
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<tr><td><img style="padding-top:10px;padding-left:10px;" src="http://2012.igem.org/wiki/images/b/b9/FrogForDummies.png" width=80px></td>
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<h3 style="text-align:center; padding-left:20px;"></u>
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<a href="http://2012.igem.org/Team:Evry/FrogForDummies"><center>More details here...</center></a>
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<div id="contourmenu" style="position: relative; margin-left: auto; margin-right: auto; width: 300px; height: 50px; text-align: center; background-color: #cee9f4; border-radius: 7px; align: left">
<div id="contourmenu" style="position: relative; margin-left: auto; margin-right: auto; width: 300px; height: 50px; text-align: center; background-color: #cee9f4; border-radius: 7px; align: left">
<br />
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<p><a href="http://2012.igem.org/Team:Evry/HumanPractice">Visit the project page ></a></p>
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<p><a href="http://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p>
<br />
<br />
</font>
</font>
</div>
</div>
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<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2>
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<p><a href="http://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p>
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Latest revision as of 23:51, 26 October 2012


Project overview

For our first participation in iGEM, we have decided to introduce a new organism to the competition: Xenopus tropicalis. Its common name is the Western clawed frog, a diploid cousin of the model organism Xenopus laevis. Aside for the soft spot French have for frogs, we also believe Xenopus could be a great multicellular chassis for synthetic biology. We are therefore bringing this organism to iGEM for the first time, along with the tools we need to bring Synthetic biology to the multicellular era.

The laboratory part of our work can be divided into two categories: the creation of synthetic biology tools for Xenopus and the creation of a synthetic hormonal system. We created a multi-level model of this inter-tissue communication system, concurrently laying the groundwork for modeling of synthetic genetic systems in multicellular organisms. Finally, using vertebrates in synthetic biology poses deep ethical problems, which come alongside those of animal experimentation. iGEM aims to be cool and fun, but can we or should we keep the same attitude when working with vertebrate embryos ? Should we reduce animals to objects or tools by using words such as chassis when working with these multicellular organisms? Our resident philosopher lead our team’s reflection on these issues, proposing a guide for future synthetic biologists who wish to work with Xenopus.






Xenopus: A new multicellular chassis

While iGEM has so far been mostly focused on en engineering unicellular organisms and bacteria in particular, we have decided work on the next step for synthetic biology: Multicellular engineering. Using our new biobrick tools, the road towards synthetic circuits in Xenopus is open, multiplying the number of potential applications in terms of synthetic biology.

Xenopus is a model organism for developmental biology. Rapid development, easy handling and direct injection of plasmids into the fertilized egg allow testing of constructs in less than two weeks. We provide frog compatible plasmids for using this system in biobrick standard format. We have submitted two complementary systems: The first allows rapid testing of the system, but in a transient way. It also includes tools for debugging of the system. Once a working system is in place, it can be reassembled and integrated on the chromosome for longer-term use.


Intertissue communication: An orthogonal hormonal system

In order to be able to bring synthetic biology to multicellular organisms, it is essential that we have a communication device enabling cell-to-cell or tissue-to-tissue communication. We have advanced towards the implementation of the first synthetic hormone, which would allow communication between cells in an orthogonal manner. We have submitted an auxin receiver device to the registry, for use in combination with an auxin production system that we have adapted for eukaryotic chassis.


GoldenBrick: A new biobrick cloning format

Merging the power of the Golden Gate multi-fragment cloning technique with the standardization of the Biobrick format. As a result, our team is developing this year a new parts format: the GoldenBricks. This is a new ultrafast cloning technique designed to assemble entire cassette in one shot. Ultimately, the GoldenBricks method is paving the way for future PartsRegistry formats!


Modeling a tadpole: A multi-level approach

Modeling a synthetic system at the whole organism scale is a challenge in itself. Using differential equations and agent based simulation, we aimed at modeling our entire synthetic hormonal system, as well as providing a new set of mathematical tool for iGEM in order to model complete organisms.


Human practice: What does it mean to be a chassis?

Working with vertebrate embryos raised many questions among the team. We decided to track the changes in our attitude to animal experimentation during our project. Before starting our experiments, we answered a list of questions concerning animal experimentation and synthetic biology. Our reflection progressively lead us to realize that considering animals as mere chassis waiting to be engineered was quite a problematic conception that we had to question.




Xenopus for dummies: a guidebook for iGEMers

Xenopus is a quite complex organism we were the first team to work with it in iGEM. This is why we wrote a guidebook to help future teams find information and brainstorm for project with this organism, in the dummies format!




Retrieved from "http://2012.igem.org/Team:Evry/Project"