http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Tiff&year=&month=2012.igem.org - User contributions [en]2024-03-28T17:15:15ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Evry/AttributionsTeam:Evry/Attributions2012-10-27T03:11:26Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<ul><br />
<h1>Attributions</h1><br />
<br />
<h2>Many thanks to all those who helped us, advised us and encouraged us over the summer !</h2><br />
<br />
<br />
<h3>The team</h3><br />
<br />
The team is composed of a mix of students, from L2 (2nd year after baccalaureate) to M2 (5th year after baccalaureate). We worked together from mid june to the end of september, some full time, some part time. More details can be found on the team page.<br />
<br />
<h3>Funding and administrative management</h3><br />
<br />
The team did most of the fundraising work, creating a sponsoring file, contacting potential sponsors and presenting the project. We managed the money ourselves, through Genopole and through a "1901 law" association. Genopole supported our project, paying inscription and jamboree participation fees, as well as donating 5000 euros towards the project. Evry university contributed 7200 euros. Sanofi donated 15 000 euros, and the French embassy in the United States donated 1500 euros. Our other sponsors helped us by providing discounts or free samples. <br />
<br />
<p>Many people at iSSB helped us securing funding and manage the team, notably Jean-Loup Faulon with the Sanofi funding, Dominique Zeliszewski with the sponsoring file preparation and team organisation, Joan Hérisson with setting up the lab, Maelle Cochennec who managed the money we kept at Genopole. Our work would also not have been possible without the help of Sylvie Bobelet and Bernadette Lauret, who solved so many problems the team encountered over the summer. Our supervisor Thomas Landrain was very important to the success of the team, as he brought several important members to the team, he advised us with Nicolas Pollet a lot on the strategic design of our scientific project and helped organizing the human practices in coordination with La Paillasse. Our supervisor Alfonso Jaramillo encouraged us to launch the team and opened his lab to the team.</p><br />
<br />
<br />
<h3>Cloning</h3><br />
<br />
All cloning work was done by the team in <a href="http://www.issb.genopole.fr/">Institute of Systems & Synthetic Biology</a>, Evry. Supervisors Thomas Landrain and Andrew Tolonen gave advice on cloning strategy throughout the project. <br />
<br />
<h3>Animal work</h3><br />
<br />
Adult frogs are kept in the animal house shared between the Metamorphosys team of iSSB and Watchfrog (a company). The adult frogs were handled by Aurore Thelie from Nicolas Pollet's team (for HCG injection, egg and sperm recovery). <br />
For the auxin toxicity tests, auxin penetration experiments and the <i>E. coli </i> to <i> Xenopus </i> communication devices, the fertilised eggs were provided by the <a href="http://indigene.issb.genopole.fr/">Metamophosys</a> team of the iSSB. <br />
<br />
For all tests of biobricks in <i>Xenopus </i>, the team was provided with unfertilised eggs and sperm, and <i>in vitro </i> fertilisation and DNA injection were done by team members under the supervision of Nicolas Pollet. Eggs were sorted and kept and analysed by the team, in the Metamorphosys labs.<br />
<br />
<h3>Microscopy</h3><br />
<br />
Most microscopy photos were taken in the Metamorphosys labs by the team, with the help and supervision of Nicolas Pollet, Aurore Thélie and Léna Vouillot (Postdoc and PhD student in Metamorphosys team).<br />
<br />
We would like to thank Dr. Daniel Stockholm and <a href="http://www.genethon.fr/en/">Genethon</a> for letting us use LSM 510 META Laser Scanning Microscope from Zeiss, which was used with his help and that of Nicolas Pollet and Aurore Thélie for high definition fluorescence images. <br />
<br />
<h3>HPLC</h3><br />
<br />
Many thanks to Damien Baud (Genoscope, Evry), who run our samples on HPLC, and to our advisor Anna who helped us analyse the spectra. <br />
<br />
<h3>Mass spectrometry</h3><br />
<br />
Our beautiful advisor Anna Mlynarczyk ran our samples on LTQ-Orbitrap-XL Mass spectrometer in the LAMBE laboratory (Evry University). Thank you to Veronique Legros for advising and help using it. <br />
<br />
<br />
<br />
<br />
</ul><br />
<script type="text/javascript">writeFooter()</script><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T03:44:38Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<br />
<br />
<br><br />
<div id="contourmenu" class="moredetails" style="align:center"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/e/e2/Hormone.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/a/a4/GoldeN.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a href="https://2012.igem.org/Team:Evry/GB"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/5/5b/ModelingDHIUHEIUHD.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a href="https://2012.igem.org/Team:Evry/Modeling"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/ba/HumanPractice.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a href="https://2012.igem.org/Team:Evry/HumanPractice"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/FrenchFrogTeam:Evry/FrenchFrog2012-09-27T01:22:11Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<br />
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center><br />
<br />
<h2>Establishment of a new chassis</b></h2><br/><br />
<br />
<p>So far, synthetic biology has mostly focused on bacteria, since they are simple to engineer. iGEM teams and laboratories have met synthetic biology laboratories on unicellular organisms in order to understand the underlying biology and have developed an impressive database of molecular parts. Some work has also been done on engineering mammalian cells and a few iGEM teams have followed this trend. Synthetic biologists are now imagining the rational design of multicellular organisms with numerous applications ranging from gene therapy or drug production to environmental monitoring. This year, our team would like to be part of that challenge.</p><br />
<br />
<p>The arrival of <i>Xenopus</i> as a chassis in synthetic biology requires the creation of new standards and protocols that the community will be able to build on. We provided the registry with such tools that allow rapid construction and characterization of devices in vivo, and include debugging tools. We think they will be very useful for later iGEM teams and synthetic biologists who wish to work with <i>Xenopus</i> for building multicellular systems.</p><br />
<br />
<p>A multi-tissular systems allows testing protein effect into an animal. The expression/degradation of a protein (a protein fused to GFP in example) can be followed in the organism. <i>Xenopus</i> can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of <a href="http://www.oecd.org/chemicalsafety/testingofchemicals/41620749.pdf">detecting thyroid disruptor using <i>Xenopus</i></a>. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis <i>xenopus</i> because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.<br />
<br />
<!-- <p>You want to make the move from bacteria to multicellular synthetic biology ? Make sure you check out our Introduction to <i>Xenopus</i> page, and our Frogs for dummies page to make sure you are aware of all the differences between genetic engineering in eukaryotes.</p> --><br />
<br />
<p>This year, the Evry iGEM team is going to be the one of the first iGEM team to work on a vertebrate. Our work is focused both on developing a system for intercellular and intertissue communication, and creating the tools for the iGEM community to easily express genes in specific tissues. We believe the tadpole is a chassis of choice for iGEM on multicellular organisms, as experiments can be conducted in one week using microinjection methods. We hope to demonstrate the feasibility of engineering <i> Xenopus </i> in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: <br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.<br />
</p><br/><br />
<br />
<br />
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a><br />
<p><br />
<br/><i>Xenopus tropicalis</i> represents a challenge as it is a vertebrate but also because it's a new chassis in the iGEM competition. To make sure we meet iGEM’s expectations on time, we have had to develop a new biobrick plasmid backbone compatible with<i> Xenopus tropicalis</i> (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into <i>Xenopus</i>'s eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in <i>Xenopus</i>, the plasmid does not replicate. Therefore, it is only active in the first two or three weeks of development, as the injected plasmid is passed on randomly to daughter cells. After that, it becomes too diluted. <br />
<br/><br/></p><br />
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank"><br />
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/><br />
<br />
<ul><br />
<li><b>Kozac</b> : The Kozak consensus sequence is essential for the initiation of the translation process in eukaryotes. The sequence is the following (gcc)gccRccAUGG, where upper case letters are highly-conserved bases, and lower case letter can vary</li><br/><br />
<li><b>Promoter </b>: The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites <b>SalI</b> and <b>HindIII</b> in order to be able to switch more easily to other promoters</li><br/><br />
<li><b>5'UTR and 3’UTR</b> : UTRs are Untranslated Region. The B-globin 5' UTR is located upstream of the coding sequence and is involved in 5'RNA capping. The 3'UTR is located downstream of the coding sequence and may contain sequences for the regulation of translation efficiency, mRNA stability, and polyadenylation signals</li><br/><br />
<li><b>SV40 PolyA signal</b> : The simian virus 40 polyadenylation signal is involved in the maturation of the mRNA for translation and is composed of a succession of adenine bases </li><br/><br />
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/><br />
<li><b>Biobrick prefix and suffix</b></li><br/><br />
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/><br />
By putting all the parts necessary for expression in eukaryotes, we have made plasmids where any coding biobrick (containing Kozak sequence) can be cloned in directly without having to transfer each parts individually. These plasmids can be used to rapidly test genetic constructions in<i> Xenopus tropicalis</i> after a single cloning.<br/> It is possible to easily change promoter with the restriction sites SalI and HindIII. <br/><br />
The plasmid also contains tools to calibrate the system in combination with a model. For instance, it contains sites for in vitro transcription (sp6 sites) of genes to make RNA that can then be injected directly in the embryo, allowing a much finer control of the ratio between levels of different genes during construct testing. <br/><br />
<br/><br />
To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the <a href="https://2012.igem.org/Team:Evry/InjectionTuto" target="_blank">injecting tutorial</a>.For a plasmid of 4kb it represents approximately 45 million of plasmids per injection. As the cell divides, plasmids are shared between cells but not replicated so a high concentration of DNA is necessary to ensure there will be DNA in most of the organism. Once the transcription machinery turns on during the development, plasmids are transcribed and translated. Since the tadpole stage starts after a few days, we can work on a whole vertebrate with most organs formed within a week. With different tissues it is possible to diversify the type of expression with different promoters.<br />
<br/><br />
<br/><br />
So far we have made 3 new plasmid backbones with different promoters :<br />
<br/><br/><br />
<li>With a <b>CMV promoter</b> for an ubiquitous expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>), <br />
<li>With a <b>Hsp70 promoter</b> for an inducible expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),<br />
<li>With a <b>Elastase promoter</b> for a tissue specific expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li><br />
<br/><br />
<br />
Our goal was to provide tools which would allow to rapidly build and characterize constructs in the embryos (along with a synthetic hormone to make them communicate), with tools for debugging (by injecting mRNA) and with ubiquitous, inducible and tissue specific promoters.<br />
</ul><br />
<br />
<br />
<br/><br/><br/><br />
<br />
<br />
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/><br />
<br />
<p>The <a href="https://2012.igem.org/Team:Evry/InjectionTuto">injection tutorial</a> explains very simply with diagram how we did injection and how take care about your embryos and tadpole. The experiment carries on 5 days, from the unfertilized egg to a swimming tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).<br />
<br />
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/><br />
<br />
<p>pCS2+ GFP-aid: this plasmid contains the constitutive and ubiquitous promoter CMV and the aid sequenced of the aid system fusionned to GFP (Green Fluorescent Protein)(Nishimura et al., 2009), this Biobrick created by our team is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812010">BBa_K812010</a>, and it was integrated into our Eucaryotic plasmid <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812000">BBa_K812000</a>.We injected about 3.78E+7 plasmids.</p><br/><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" /> <br />
</b></b><br />
<p><br />
GFP-aid expression from the embryo at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 20 (one day after injection )to a tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> ~46 (four days after injection). For this tadpole the expression is localized in the skin.</b></b></b><br />
</p><br />
<br />
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.<br />
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<br><br><br />
<h4><b>The characterization of all reporter and promoters is <u><a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a></u>.</b></h4><br><br />
<br />
<h2>Conclusion</h2><br/><br />
<br />
<p>This new BioBricked plasmid is ready to use in <i>Xenopus tropicalis</i>. As you can see above the plasmid pCS2+ with the CMV pomoter express the fluorescent protein GFP-aid, but this plasmid carry on important things to express a gene into eukaryotic calls. The 5'UTR region and the 3' UTR region was needed for gene expression in euklaryotic organism. The simplest way to do that was to use a plasmid already used in eukaryotic cells, vertebrate and especially <i>Xenopus tropicalis</i> as pCS2+. This pCS2+ was Biobricked to be compatible with the registry. <br><br />
<br />
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: <a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a>.<br><br />
<br />
<p><br />
Nevertheless we expected a more uniform expression of the reporters with the CMV promoter. Within tadpole, fluorescent proteins were observed in one to four different tissues, and tissues were different between tadpoles.<br />
</p><br />
<br />
<p><br />
Explanation: The plasmid DNA does not diffuse in the egg and stay in the same area around the injection site. This means that depending on the injection site, the plasmid will be inherited by a given set of cells within the tadpole. This question was raised in our <a href="https://2012.igem.org/Team:Evry/plasmid_splitting">model</a>. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.<br />
</p><br />
<br />
<p><br />
Our experiment showed us that plasmids injected do not diffuse in the whole organism. To express a protein with a promoter tissue specific it is a problem, because of the very low the probability to have the plasmid into the expected tissue. To solve the problem it is possible to easily integrate promoters and genes into the <i>Xenopus</i>'s chromosome with the REMI technic [3]. A new plasmid pCS2+ with I-SceI sites upstream the promoter and downstream of the reporter could allow the integration of the sequence between this two I-SceI restriction sites. This plasmid could be useful for the eukaryotic community, they could change promoters easily with SalI and HindIII and the reporter is compatible with the registry (with BB prefix and suffix), and they would have the choice to test a construction by plasmid injection or DNA chromosome integration.<br />
</p><br />
<br />
<p><br />
Moreover, the expression of reporters decreases during time, because plasmid DNA is subjected to a catabolic activity during development but also plasmid DNA gets diluted as cells proliferate and the quantity of plasmid DNA decreases for each cell. Integration into the chromosome could prevent it. <br />
</p><br />
<br />
<p><br />
Our project raised important ethics question because the team use tadpole, an animal. We reflect that working with tadpole involved new questions about the animal pain but also about using animals in iGEM and in Synthetic Biology. It made us think about these questions, our reflection is in <a href="https://2012.igem.org/Team:Evry/HumanPractice">Human Practice</a>.</p><br><br />
<br />
<div id="citation_box"><br />
<p id="references">References:</p><br />
<ol><br />
<li><i>Inducible control of tissue-specific transgene expression in <i>Xenopus</i> tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li><br />
<br />
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li><br />
<br />
<li><i>REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants</li> Kahmann R., Basse C., European Journal of Plant Pathology</li><br />
</ol><br />
</div><br />
<br><br />
<br />
<script type="text/javascript">writeFooter()</script> <br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/FrenchFrogTeam:Evry/FrenchFrog2012-09-27T01:21:55Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<br />
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center><br />
<center><img src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" alt="Image unavailable" width="100px" /></center><br />
<br />
<h2>Establishment of a new chassis</b></h2><br/><br />
<br />
<p>So far, synthetic biology has mostly focused on bacteria, since they are simple to engineer. iGEM teams and laboratories have met synthetic biology laboratories on unicellular organisms in order to understand the underlying biology and have developed an impressive database of molecular parts. Some work has also been done on engineering mammalian cells and a few iGEM teams have followed this trend. Synthetic biologists are now imagining the rational design of multicellular organisms with numerous applications ranging from gene therapy or drug production to environmental monitoring. This year, our team would like to be part of that challenge.</p><br />
<br />
<p>The arrival of <i>Xenopus</i> as a chassis in synthetic biology requires the creation of new standards and protocols that the community will be able to build on. We provided the registry with such tools that allow rapid construction and characterization of devices in vivo, and include debugging tools. We think they will be very useful for later iGEM teams and synthetic biologists who wish to work with <i>Xenopus</i> for building multicellular systems.</p><br />
<br />
<p>A multi-tissular systems allows testing protein effect into an animal. The expression/degradation of a protein (a protein fused to GFP in example) can be followed in the organism. <i>Xenopus</i> can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of <a href="http://www.oecd.org/chemicalsafety/testingofchemicals/41620749.pdf">detecting thyroid disruptor using <i>Xenopus</i></a>. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis <i>xenopus</i> because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.<br />
<br />
<!-- <p>You want to make the move from bacteria to multicellular synthetic biology ? Make sure you check out our Introduction to <i>Xenopus</i> page, and our Frogs for dummies page to make sure you are aware of all the differences between genetic engineering in eukaryotes.</p> --><br />
<br />
<p>This year, the Evry iGEM team is going to be the one of the first iGEM team to work on a vertebrate. Our work is focused both on developing a system for intercellular and intertissue communication, and creating the tools for the iGEM community to easily express genes in specific tissues. We believe the tadpole is a chassis of choice for iGEM on multicellular organisms, as experiments can be conducted in one week using microinjection methods. We hope to demonstrate the feasibility of engineering <i> Xenopus </i> in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: <br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.<br />
</p><br/><br />
<br />
<br />
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a><br />
<p><br />
<br/><i>Xenopus tropicalis</i> represents a challenge as it is a vertebrate but also because it's a new chassis in the iGEM competition. To make sure we meet iGEM’s expectations on time, we have had to develop a new biobrick plasmid backbone compatible with<i> Xenopus tropicalis</i> (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into <i>Xenopus</i>'s eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in <i>Xenopus</i>, the plasmid does not replicate. Therefore, it is only active in the first two or three weeks of development, as the injected plasmid is passed on randomly to daughter cells. After that, it becomes too diluted. <br />
<br/><br/></p><br />
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank"><br />
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/><br />
<br />
<ul><br />
<li><b>Kozac</b> : The Kozak consensus sequence is essential for the initiation of the translation process in eukaryotes. The sequence is the following (gcc)gccRccAUGG, where upper case letters are highly-conserved bases, and lower case letter can vary</li><br/><br />
<li><b>Promoter </b>: The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites <b>SalI</b> and <b>HindIII</b> in order to be able to switch more easily to other promoters</li><br/><br />
<li><b>5'UTR and 3’UTR</b> : UTRs are Untranslated Region. The B-globin 5' UTR is located upstream of the coding sequence and is involved in 5'RNA capping. The 3'UTR is located downstream of the coding sequence and may contain sequences for the regulation of translation efficiency, mRNA stability, and polyadenylation signals</li><br/><br />
<li><b>SV40 PolyA signal</b> : The simian virus 40 polyadenylation signal is involved in the maturation of the mRNA for translation and is composed of a succession of adenine bases </li><br/><br />
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/><br />
<li><b>Biobrick prefix and suffix</b></li><br/><br />
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/><br />
By putting all the parts necessary for expression in eukaryotes, we have made plasmids where any coding biobrick (containing Kozak sequence) can be cloned in directly without having to transfer each parts individually. These plasmids can be used to rapidly test genetic constructions in<i> Xenopus tropicalis</i> after a single cloning.<br/> It is possible to easily change promoter with the restriction sites SalI and HindIII. <br/><br />
The plasmid also contains tools to calibrate the system in combination with a model. For instance, it contains sites for in vitro transcription (sp6 sites) of genes to make RNA that can then be injected directly in the embryo, allowing a much finer control of the ratio between levels of different genes during construct testing. <br/><br />
<br/><br />
To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the <a href="https://2012.igem.org/Team:Evry/InjectionTuto" target="_blank">injecting tutorial</a>.For a plasmid of 4kb it represents approximately 45 million of plasmids per injection. As the cell divides, plasmids are shared between cells but not replicated so a high concentration of DNA is necessary to ensure there will be DNA in most of the organism. Once the transcription machinery turns on during the development, plasmids are transcribed and translated. Since the tadpole stage starts after a few days, we can work on a whole vertebrate with most organs formed within a week. With different tissues it is possible to diversify the type of expression with different promoters.<br />
<br/><br />
<br/><br />
So far we have made 3 new plasmid backbones with different promoters :<br />
<br/><br/><br />
<li>With a <b>CMV promoter</b> for an ubiquitous expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>), <br />
<li>With a <b>Hsp70 promoter</b> for an inducible expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),<br />
<li>With a <b>Elastase promoter</b> for a tissue specific expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li><br />
<br/><br />
<br />
Our goal was to provide tools which would allow to rapidly build and characterize constructs in the embryos (along with a synthetic hormone to make them communicate), with tools for debugging (by injecting mRNA) and with ubiquitous, inducible and tissue specific promoters.<br />
</ul><br />
<br />
<br />
<br/><br/><br/><br />
<br />
<br />
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/><br />
<br />
<p>The <a href="https://2012.igem.org/Team:Evry/InjectionTuto">injection tutorial</a> explains very simply with diagram how we did injection and how take care about your embryos and tadpole. The experiment carries on 5 days, from the unfertilized egg to a swimming tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).<br />
<br />
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/><br />
<br />
<p>pCS2+ GFP-aid: this plasmid contains the constitutive and ubiquitous promoter CMV and the aid sequenced of the aid system fusionned to GFP (Green Fluorescent Protein)(Nishimura et al., 2009), this Biobrick created by our team is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812010">BBa_K812010</a>, and it was integrated into our Eucaryotic plasmid <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812000">BBa_K812000</a>.We injected about 3.78E+7 plasmids.</p><br/><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" /> <br />
</b></b><br />
<p><br />
GFP-aid expression from the embryo at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 20 (one day after injection )to a tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> ~46 (four days after injection). For this tadpole the expression is localized in the skin.</b></b></b><br />
</p><br />
<br />
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.<br />
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<br><br><br />
<h4><b>The characterization of all reporter and promoters is <u><a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a></u>.</b></h4><br><br />
<br />
<h2>Conclusion</h2><br/><br />
<br />
<p>This new BioBricked plasmid is ready to use in <i>Xenopus tropicalis</i>. As you can see above the plasmid pCS2+ with the CMV pomoter express the fluorescent protein GFP-aid, but this plasmid carry on important things to express a gene into eukaryotic calls. The 5'UTR region and the 3' UTR region was needed for gene expression in euklaryotic organism. The simplest way to do that was to use a plasmid already used in eukaryotic cells, vertebrate and especially <i>Xenopus tropicalis</i> as pCS2+. This pCS2+ was Biobricked to be compatible with the registry. <br><br />
<br />
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: <a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a>.<br><br />
<br />
<p><br />
Nevertheless we expected a more uniform expression of the reporters with the CMV promoter. Within tadpole, fluorescent proteins were observed in one to four different tissues, and tissues were different between tadpoles.<br />
</p><br />
<br />
<p><br />
Explanation: The plasmid DNA does not diffuse in the egg and stay in the same area around the injection site. This means that depending on the injection site, the plasmid will be inherited by a given set of cells within the tadpole. This question was raised in our <a href="https://2012.igem.org/Team:Evry/plasmid_splitting">model</a>. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.<br />
</p><br />
<br />
<p><br />
Our experiment showed us that plasmids injected do not diffuse in the whole organism. To express a protein with a promoter tissue specific it is a problem, because of the very low the probability to have the plasmid into the expected tissue. To solve the problem it is possible to easily integrate promoters and genes into the <i>Xenopus</i>'s chromosome with the REMI technic [3]. A new plasmid pCS2+ with I-SceI sites upstream the promoter and downstream of the reporter could allow the integration of the sequence between this two I-SceI restriction sites. This plasmid could be useful for the eukaryotic community, they could change promoters easily with SalI and HindIII and the reporter is compatible with the registry (with BB prefix and suffix), and they would have the choice to test a construction by plasmid injection or DNA chromosome integration.<br />
</p><br />
<br />
<p><br />
Moreover, the expression of reporters decreases during time, because plasmid DNA is subjected to a catabolic activity during development but also plasmid DNA gets diluted as cells proliferate and the quantity of plasmid DNA decreases for each cell. Integration into the chromosome could prevent it. <br />
</p><br />
<br />
<p><br />
Our project raised important ethics question because the team use tadpole, an animal. We reflect that working with tadpole involved new questions about the animal pain but also about using animals in iGEM and in Synthetic Biology. It made us think about these questions, our reflection is in <a href="https://2012.igem.org/Team:Evry/HumanPractice">Human Practice</a>.</p><br><br />
<br />
<div id="citation_box"><br />
<p id="references">References:</p><br />
<ol><br />
<li><i>Inducible control of tissue-specific transgene expression in <i>Xenopus</i> tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li><br />
<br />
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li><br />
<br />
<li><i>REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants</li> Kahmann R., Basse C., European Journal of Plant Pathology</li><br />
</ol><br />
</div><br />
<br><br />
<br />
<script type="text/javascript">writeFooter()</script> <br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/FrenchFrogTeam:Evry/FrenchFrog2012-09-27T01:21:16Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<center><img src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" alt="Image unavailable" width="100px" /></center><br />
<br />
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center><br />
<br />
<h2>Establishment of a new chassis</b></h2><br/><br />
<br />
<p>So far, synthetic biology has mostly focused on bacteria, since they are simple to engineer. iGEM teams and laboratories have met synthetic biology laboratories on unicellular organisms in order to understand the underlying biology and have developed an impressive database of molecular parts. Some work has also been done on engineering mammalian cells and a few iGEM teams have followed this trend. Synthetic biologists are now imagining the rational design of multicellular organisms with numerous applications ranging from gene therapy or drug production to environmental monitoring. This year, our team would like to be part of that challenge.</p><br />
<br />
<p>The arrival of <i>Xenopus</i> as a chassis in synthetic biology requires the creation of new standards and protocols that the community will be able to build on. We provided the registry with such tools that allow rapid construction and characterization of devices in vivo, and include debugging tools. We think they will be very useful for later iGEM teams and synthetic biologists who wish to work with <i>Xenopus</i> for building multicellular systems.</p><br />
<br />
<p>A multi-tissular systems allows testing protein effect into an animal. The expression/degradation of a protein (a protein fused to GFP in example) can be followed in the organism. <i>Xenopus</i> can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of <a href="http://www.oecd.org/chemicalsafety/testingofchemicals/41620749.pdf">detecting thyroid disruptor using <i>Xenopus</i></a>. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis <i>xenopus</i> because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.<br />
<br />
<!-- <p>You want to make the move from bacteria to multicellular synthetic biology ? Make sure you check out our Introduction to <i>Xenopus</i> page, and our Frogs for dummies page to make sure you are aware of all the differences between genetic engineering in eukaryotes.</p> --><br />
<br />
<p>This year, the Evry iGEM team is going to be the one of the first iGEM team to work on a vertebrate. Our work is focused both on developing a system for intercellular and intertissue communication, and creating the tools for the iGEM community to easily express genes in specific tissues. We believe the tadpole is a chassis of choice for iGEM on multicellular organisms, as experiments can be conducted in one week using microinjection methods. We hope to demonstrate the feasibility of engineering <i> Xenopus </i> in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: <br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.<br />
</p><br/><br />
<br />
<br />
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a><br />
<p><br />
<br/><i>Xenopus tropicalis</i> represents a challenge as it is a vertebrate but also because it's a new chassis in the iGEM competition. To make sure we meet iGEM’s expectations on time, we have had to develop a new biobrick plasmid backbone compatible with<i> Xenopus tropicalis</i> (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into <i>Xenopus</i>'s eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in <i>Xenopus</i>, the plasmid does not replicate. Therefore, it is only active in the first two or three weeks of development, as the injected plasmid is passed on randomly to daughter cells. After that, it becomes too diluted. <br />
<br/><br/></p><br />
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank"><br />
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/><br />
<br />
<ul><br />
<li><b>Kozac</b> : The Kozak consensus sequence is essential for the initiation of the translation process in eukaryotes. The sequence is the following (gcc)gccRccAUGG, where upper case letters are highly-conserved bases, and lower case letter can vary</li><br/><br />
<li><b>Promoter </b>: The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites <b>SalI</b> and <b>HindIII</b> in order to be able to switch more easily to other promoters</li><br/><br />
<li><b>5'UTR and 3’UTR</b> : UTRs are Untranslated Region. The B-globin 5' UTR is located upstream of the coding sequence and is involved in 5'RNA capping. The 3'UTR is located downstream of the coding sequence and may contain sequences for the regulation of translation efficiency, mRNA stability, and polyadenylation signals</li><br/><br />
<li><b>SV40 PolyA signal</b> : The simian virus 40 polyadenylation signal is involved in the maturation of the mRNA for translation and is composed of a succession of adenine bases </li><br/><br />
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/><br />
<li><b>Biobrick prefix and suffix</b></li><br/><br />
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/><br />
By putting all the parts necessary for expression in eukaryotes, we have made plasmids where any coding biobrick (containing Kozak sequence) can be cloned in directly without having to transfer each parts individually. These plasmids can be used to rapidly test genetic constructions in<i> Xenopus tropicalis</i> after a single cloning.<br/> It is possible to easily change promoter with the restriction sites SalI and HindIII. <br/><br />
The plasmid also contains tools to calibrate the system in combination with a model. For instance, it contains sites for in vitro transcription (sp6 sites) of genes to make RNA that can then be injected directly in the embryo, allowing a much finer control of the ratio between levels of different genes during construct testing. <br/><br />
<br/><br />
To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the <a href="https://2012.igem.org/Team:Evry/InjectionTuto" target="_blank">injecting tutorial</a>.For a plasmid of 4kb it represents approximately 45 million of plasmids per injection. As the cell divides, plasmids are shared between cells but not replicated so a high concentration of DNA is necessary to ensure there will be DNA in most of the organism. Once the transcription machinery turns on during the development, plasmids are transcribed and translated. Since the tadpole stage starts after a few days, we can work on a whole vertebrate with most organs formed within a week. With different tissues it is possible to diversify the type of expression with different promoters.<br />
<br/><br />
<br/><br />
So far we have made 3 new plasmid backbones with different promoters :<br />
<br/><br/><br />
<li>With a <b>CMV promoter</b> for an ubiquitous expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>), <br />
<li>With a <b>Hsp70 promoter</b> for an inducible expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),<br />
<li>With a <b>Elastase promoter</b> for a tissue specific expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li><br />
<br/><br />
<br />
Our goal was to provide tools which would allow to rapidly build and characterize constructs in the embryos (along with a synthetic hormone to make them communicate), with tools for debugging (by injecting mRNA) and with ubiquitous, inducible and tissue specific promoters.<br />
</ul><br />
<br />
<br />
<br/><br/><br/><br />
<br />
<br />
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/><br />
<br />
<p>The <a href="https://2012.igem.org/Team:Evry/InjectionTuto">injection tutorial</a> explains very simply with diagram how we did injection and how take care about your embryos and tadpole. The experiment carries on 5 days, from the unfertilized egg to a swimming tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).<br />
<br />
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/><br />
<br />
<p>pCS2+ GFP-aid: this plasmid contains the constitutive and ubiquitous promoter CMV and the aid sequenced of the aid system fusionned to GFP (Green Fluorescent Protein)(Nishimura et al., 2009), this Biobrick created by our team is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812010">BBa_K812010</a>, and it was integrated into our Eucaryotic plasmid <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812000">BBa_K812000</a>.We injected about 3.78E+7 plasmids.</p><br/><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" /> <br />
</b></b><br />
<p><br />
GFP-aid expression from the embryo at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 20 (one day after injection )to a tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> ~46 (four days after injection). For this tadpole the expression is localized in the skin.</b></b></b><br />
</p><br />
<br />
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.<br />
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<br><br><br />
<h4><b>The characterization of all reporter and promoters is <u><a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a></u>.</b></h4><br><br />
<br />
<h2>Conclusion</h2><br/><br />
<br />
<p>This new BioBricked plasmid is ready to use in <i>Xenopus tropicalis</i>. As you can see above the plasmid pCS2+ with the CMV pomoter express the fluorescent protein GFP-aid, but this plasmid carry on important things to express a gene into eukaryotic calls. The 5'UTR region and the 3' UTR region was needed for gene expression in euklaryotic organism. The simplest way to do that was to use a plasmid already used in eukaryotic cells, vertebrate and especially <i>Xenopus tropicalis</i> as pCS2+. This pCS2+ was Biobricked to be compatible with the registry. <br><br />
<br />
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: <a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a>.<br><br />
<br />
<p><br />
Nevertheless we expected a more uniform expression of the reporters with the CMV promoter. Within tadpole, fluorescent proteins were observed in one to four different tissues, and tissues were different between tadpoles.<br />
</p><br />
<br />
<p><br />
Explanation: The plasmid DNA does not diffuse in the egg and stay in the same area around the injection site. This means that depending on the injection site, the plasmid will be inherited by a given set of cells within the tadpole. This question was raised in our <a href="https://2012.igem.org/Team:Evry/plasmid_splitting">model</a>. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.<br />
</p><br />
<br />
<p><br />
Our experiment showed us that plasmids injected do not diffuse in the whole organism. To express a protein with a promoter tissue specific it is a problem, because of the very low the probability to have the plasmid into the expected tissue. To solve the problem it is possible to easily integrate promoters and genes into the <i>Xenopus</i>'s chromosome with the REMI technic [3]. A new plasmid pCS2+ with I-SceI sites upstream the promoter and downstream of the reporter could allow the integration of the sequence between this two I-SceI restriction sites. This plasmid could be useful for the eukaryotic community, they could change promoters easily with SalI and HindIII and the reporter is compatible with the registry (with BB prefix and suffix), and they would have the choice to test a construction by plasmid injection or DNA chromosome integration.<br />
</p><br />
<br />
<p><br />
Moreover, the expression of reporters decreases during time, because plasmid DNA is subjected to a catabolic activity during development but also plasmid DNA gets diluted as cells proliferate and the quantity of plasmid DNA decreases for each cell. Integration into the chromosome could prevent it. <br />
</p><br />
<br />
<p><br />
Our project raised important ethics question because the team use tadpole, an animal. We reflect that working with tadpole involved new questions about the animal pain but also about using animals in iGEM and in Synthetic Biology. It made us think about these questions, our reflection is in <a href="https://2012.igem.org/Team:Evry/HumanPractice">Human Practice</a>.</p><br><br />
<br />
<div id="citation_box"><br />
<p id="references">References:</p><br />
<ol><br />
<li><i>Inducible control of tissue-specific transgene expression in <i>Xenopus</i> tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li><br />
<br />
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li><br />
<br />
<li><i>REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants</li> Kahmann R., Basse C., European Journal of Plant Pathology</li><br />
</ol><br />
</div><br />
<br><br />
<br />
<script type="text/javascript">writeFooter()</script> <br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/FrenchFrogTeam:Evry/FrenchFrog2012-09-27T01:21:01Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<center><img src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" alt="Image unavailable" width="50px" /></center><br />
<br />
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center><br />
<br />
<h2>Establishment of a new chassis</b></h2><br/><br />
<br />
<p>So far, synthetic biology has mostly focused on bacteria, since they are simple to engineer. iGEM teams and laboratories have met synthetic biology laboratories on unicellular organisms in order to understand the underlying biology and have developed an impressive database of molecular parts. Some work has also been done on engineering mammalian cells and a few iGEM teams have followed this trend. Synthetic biologists are now imagining the rational design of multicellular organisms with numerous applications ranging from gene therapy or drug production to environmental monitoring. This year, our team would like to be part of that challenge.</p><br />
<br />
<p>The arrival of <i>Xenopus</i> as a chassis in synthetic biology requires the creation of new standards and protocols that the community will be able to build on. We provided the registry with such tools that allow rapid construction and characterization of devices in vivo, and include debugging tools. We think they will be very useful for later iGEM teams and synthetic biologists who wish to work with <i>Xenopus</i> for building multicellular systems.</p><br />
<br />
<p>A multi-tissular systems allows testing protein effect into an animal. The expression/degradation of a protein (a protein fused to GFP in example) can be followed in the organism. <i>Xenopus</i> can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of <a href="http://www.oecd.org/chemicalsafety/testingofchemicals/41620749.pdf">detecting thyroid disruptor using <i>Xenopus</i></a>. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis <i>xenopus</i> because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.<br />
<br />
<!-- <p>You want to make the move from bacteria to multicellular synthetic biology ? Make sure you check out our Introduction to <i>Xenopus</i> page, and our Frogs for dummies page to make sure you are aware of all the differences between genetic engineering in eukaryotes.</p> --><br />
<br />
<p>This year, the Evry iGEM team is going to be the one of the first iGEM team to work on a vertebrate. Our work is focused both on developing a system for intercellular and intertissue communication, and creating the tools for the iGEM community to easily express genes in specific tissues. We believe the tadpole is a chassis of choice for iGEM on multicellular organisms, as experiments can be conducted in one week using microinjection methods. We hope to demonstrate the feasibility of engineering <i> Xenopus </i> in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: <br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.<br />
</p><br/><br />
<br />
<br />
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a><br />
<p><br />
<br/><i>Xenopus tropicalis</i> represents a challenge as it is a vertebrate but also because it's a new chassis in the iGEM competition. To make sure we meet iGEM’s expectations on time, we have had to develop a new biobrick plasmid backbone compatible with<i> Xenopus tropicalis</i> (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into <i>Xenopus</i>'s eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in <i>Xenopus</i>, the plasmid does not replicate. Therefore, it is only active in the first two or three weeks of development, as the injected plasmid is passed on randomly to daughter cells. After that, it becomes too diluted. <br />
<br/><br/></p><br />
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank"><br />
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/><br />
<br />
<ul><br />
<li><b>Kozac</b> : The Kozak consensus sequence is essential for the initiation of the translation process in eukaryotes. The sequence is the following (gcc)gccRccAUGG, where upper case letters are highly-conserved bases, and lower case letter can vary</li><br/><br />
<li><b>Promoter </b>: The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites <b>SalI</b> and <b>HindIII</b> in order to be able to switch more easily to other promoters</li><br/><br />
<li><b>5'UTR and 3’UTR</b> : UTRs are Untranslated Region. The B-globin 5' UTR is located upstream of the coding sequence and is involved in 5'RNA capping. The 3'UTR is located downstream of the coding sequence and may contain sequences for the regulation of translation efficiency, mRNA stability, and polyadenylation signals</li><br/><br />
<li><b>SV40 PolyA signal</b> : The simian virus 40 polyadenylation signal is involved in the maturation of the mRNA for translation and is composed of a succession of adenine bases </li><br/><br />
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/><br />
<li><b>Biobrick prefix and suffix</b></li><br/><br />
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/><br />
By putting all the parts necessary for expression in eukaryotes, we have made plasmids where any coding biobrick (containing Kozak sequence) can be cloned in directly without having to transfer each parts individually. These plasmids can be used to rapidly test genetic constructions in<i> Xenopus tropicalis</i> after a single cloning.<br/> It is possible to easily change promoter with the restriction sites SalI and HindIII. <br/><br />
The plasmid also contains tools to calibrate the system in combination with a model. For instance, it contains sites for in vitro transcription (sp6 sites) of genes to make RNA that can then be injected directly in the embryo, allowing a much finer control of the ratio between levels of different genes during construct testing. <br/><br />
<br/><br />
To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the <a href="https://2012.igem.org/Team:Evry/InjectionTuto" target="_blank">injecting tutorial</a>.For a plasmid of 4kb it represents approximately 45 million of plasmids per injection. As the cell divides, plasmids are shared between cells but not replicated so a high concentration of DNA is necessary to ensure there will be DNA in most of the organism. Once the transcription machinery turns on during the development, plasmids are transcribed and translated. Since the tadpole stage starts after a few days, we can work on a whole vertebrate with most organs formed within a week. With different tissues it is possible to diversify the type of expression with different promoters.<br />
<br/><br />
<br/><br />
So far we have made 3 new plasmid backbones with different promoters :<br />
<br/><br/><br />
<li>With a <b>CMV promoter</b> for an ubiquitous expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>), <br />
<li>With a <b>Hsp70 promoter</b> for an inducible expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),<br />
<li>With a <b>Elastase promoter</b> for a tissue specific expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li><br />
<br/><br />
<br />
Our goal was to provide tools which would allow to rapidly build and characterize constructs in the embryos (along with a synthetic hormone to make them communicate), with tools for debugging (by injecting mRNA) and with ubiquitous, inducible and tissue specific promoters.<br />
</ul><br />
<br />
<br />
<br/><br/><br/><br />
<br />
<br />
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/><br />
<br />
<p>The <a href="https://2012.igem.org/Team:Evry/InjectionTuto">injection tutorial</a> explains very simply with diagram how we did injection and how take care about your embryos and tadpole. The experiment carries on 5 days, from the unfertilized egg to a swimming tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).<br />
<br />
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/><br />
<br />
<p>pCS2+ GFP-aid: this plasmid contains the constitutive and ubiquitous promoter CMV and the aid sequenced of the aid system fusionned to GFP (Green Fluorescent Protein)(Nishimura et al., 2009), this Biobrick created by our team is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812010">BBa_K812010</a>, and it was integrated into our Eucaryotic plasmid <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812000">BBa_K812000</a>.We injected about 3.78E+7 plasmids.</p><br/><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" /> <br />
</b></b><br />
<p><br />
GFP-aid expression from the embryo at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 20 (one day after injection )to a tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> ~46 (four days after injection). For this tadpole the expression is localized in the skin.</b></b></b><br />
</p><br />
<br />
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.<br />
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<br><br><br />
<h4><b>The characterization of all reporter and promoters is <u><a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a></u>.</b></h4><br><br />
<br />
<h2>Conclusion</h2><br/><br />
<br />
<p>This new BioBricked plasmid is ready to use in <i>Xenopus tropicalis</i>. As you can see above the plasmid pCS2+ with the CMV pomoter express the fluorescent protein GFP-aid, but this plasmid carry on important things to express a gene into eukaryotic calls. The 5'UTR region and the 3' UTR region was needed for gene expression in euklaryotic organism. The simplest way to do that was to use a plasmid already used in eukaryotic cells, vertebrate and especially <i>Xenopus tropicalis</i> as pCS2+. This pCS2+ was Biobricked to be compatible with the registry. <br><br />
<br />
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: <a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a>.<br><br />
<br />
<p><br />
Nevertheless we expected a more uniform expression of the reporters with the CMV promoter. Within tadpole, fluorescent proteins were observed in one to four different tissues, and tissues were different between tadpoles.<br />
</p><br />
<br />
<p><br />
Explanation: The plasmid DNA does not diffuse in the egg and stay in the same area around the injection site. This means that depending on the injection site, the plasmid will be inherited by a given set of cells within the tadpole. This question was raised in our <a href="https://2012.igem.org/Team:Evry/plasmid_splitting">model</a>. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.<br />
</p><br />
<br />
<p><br />
Our experiment showed us that plasmids injected do not diffuse in the whole organism. To express a protein with a promoter tissue specific it is a problem, because of the very low the probability to have the plasmid into the expected tissue. To solve the problem it is possible to easily integrate promoters and genes into the <i>Xenopus</i>'s chromosome with the REMI technic [3]. A new plasmid pCS2+ with I-SceI sites upstream the promoter and downstream of the reporter could allow the integration of the sequence between this two I-SceI restriction sites. This plasmid could be useful for the eukaryotic community, they could change promoters easily with SalI and HindIII and the reporter is compatible with the registry (with BB prefix and suffix), and they would have the choice to test a construction by plasmid injection or DNA chromosome integration.<br />
</p><br />
<br />
<p><br />
Moreover, the expression of reporters decreases during time, because plasmid DNA is subjected to a catabolic activity during development but also plasmid DNA gets diluted as cells proliferate and the quantity of plasmid DNA decreases for each cell. Integration into the chromosome could prevent it. <br />
</p><br />
<br />
<p><br />
Our project raised important ethics question because the team use tadpole, an animal. We reflect that working with tadpole involved new questions about the animal pain but also about using animals in iGEM and in Synthetic Biology. It made us think about these questions, our reflection is in <a href="https://2012.igem.org/Team:Evry/HumanPractice">Human Practice</a>.</p><br><br />
<br />
<div id="citation_box"><br />
<p id="references">References:</p><br />
<ol><br />
<li><i>Inducible control of tissue-specific transgene expression in <i>Xenopus</i> tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li><br />
<br />
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li><br />
<br />
<li><i>REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants</li> Kahmann R., Basse C., European Journal of Plant Pathology</li><br />
</ol><br />
</div><br />
<br><br />
<br />
<script type="text/javascript">writeFooter()</script> <br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/FrenchFrogTeam:Evry/FrenchFrog2012-09-27T01:20:46Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<center><img src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" alt="Image unavailable" width="950px" /></center><br />
<br />
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center><br />
<br />
<h2>Establishment of a new chassis</b></h2><br/><br />
<br />
<p>So far, synthetic biology has mostly focused on bacteria, since they are simple to engineer. iGEM teams and laboratories have met synthetic biology laboratories on unicellular organisms in order to understand the underlying biology and have developed an impressive database of molecular parts. Some work has also been done on engineering mammalian cells and a few iGEM teams have followed this trend. Synthetic biologists are now imagining the rational design of multicellular organisms with numerous applications ranging from gene therapy or drug production to environmental monitoring. This year, our team would like to be part of that challenge.</p><br />
<br />
<p>The arrival of <i>Xenopus</i> as a chassis in synthetic biology requires the creation of new standards and protocols that the community will be able to build on. We provided the registry with such tools that allow rapid construction and characterization of devices in vivo, and include debugging tools. We think they will be very useful for later iGEM teams and synthetic biologists who wish to work with <i>Xenopus</i> for building multicellular systems.</p><br />
<br />
<p>A multi-tissular systems allows testing protein effect into an animal. The expression/degradation of a protein (a protein fused to GFP in example) can be followed in the organism. <i>Xenopus</i> can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of <a href="http://www.oecd.org/chemicalsafety/testingofchemicals/41620749.pdf">detecting thyroid disruptor using <i>Xenopus</i></a>. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis <i>xenopus</i> because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.<br />
<br />
<!-- <p>You want to make the move from bacteria to multicellular synthetic biology ? Make sure you check out our Introduction to <i>Xenopus</i> page, and our Frogs for dummies page to make sure you are aware of all the differences between genetic engineering in eukaryotes.</p> --><br />
<br />
<p>This year, the Evry iGEM team is going to be the one of the first iGEM team to work on a vertebrate. Our work is focused both on developing a system for intercellular and intertissue communication, and creating the tools for the iGEM community to easily express genes in specific tissues. We believe the tadpole is a chassis of choice for iGEM on multicellular organisms, as experiments can be conducted in one week using microinjection methods. We hope to demonstrate the feasibility of engineering <i> Xenopus </i> in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: <br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.<br />
</p><br/><br />
<br />
<br />
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a><br />
<p><br />
<br/><i>Xenopus tropicalis</i> represents a challenge as it is a vertebrate but also because it's a new chassis in the iGEM competition. To make sure we meet iGEM’s expectations on time, we have had to develop a new biobrick plasmid backbone compatible with<i> Xenopus tropicalis</i> (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into <i>Xenopus</i>'s eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in <i>Xenopus</i>, the plasmid does not replicate. Therefore, it is only active in the first two or three weeks of development, as the injected plasmid is passed on randomly to daughter cells. After that, it becomes too diluted. <br />
<br/><br/></p><br />
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank"><br />
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/><br />
<br />
<ul><br />
<li><b>Kozac</b> : The Kozak consensus sequence is essential for the initiation of the translation process in eukaryotes. The sequence is the following (gcc)gccRccAUGG, where upper case letters are highly-conserved bases, and lower case letter can vary</li><br/><br />
<li><b>Promoter </b>: The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites <b>SalI</b> and <b>HindIII</b> in order to be able to switch more easily to other promoters</li><br/><br />
<li><b>5'UTR and 3’UTR</b> : UTRs are Untranslated Region. The B-globin 5' UTR is located upstream of the coding sequence and is involved in 5'RNA capping. The 3'UTR is located downstream of the coding sequence and may contain sequences for the regulation of translation efficiency, mRNA stability, and polyadenylation signals</li><br/><br />
<li><b>SV40 PolyA signal</b> : The simian virus 40 polyadenylation signal is involved in the maturation of the mRNA for translation and is composed of a succession of adenine bases </li><br/><br />
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/><br />
<li><b>Biobrick prefix and suffix</b></li><br/><br />
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/><br />
By putting all the parts necessary for expression in eukaryotes, we have made plasmids where any coding biobrick (containing Kozak sequence) can be cloned in directly without having to transfer each parts individually. These plasmids can be used to rapidly test genetic constructions in<i> Xenopus tropicalis</i> after a single cloning.<br/> It is possible to easily change promoter with the restriction sites SalI and HindIII. <br/><br />
The plasmid also contains tools to calibrate the system in combination with a model. For instance, it contains sites for in vitro transcription (sp6 sites) of genes to make RNA that can then be injected directly in the embryo, allowing a much finer control of the ratio between levels of different genes during construct testing. <br/><br />
<br/><br />
To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the <a href="https://2012.igem.org/Team:Evry/InjectionTuto" target="_blank">injecting tutorial</a>.For a plasmid of 4kb it represents approximately 45 million of plasmids per injection. As the cell divides, plasmids are shared between cells but not replicated so a high concentration of DNA is necessary to ensure there will be DNA in most of the organism. Once the transcription machinery turns on during the development, plasmids are transcribed and translated. Since the tadpole stage starts after a few days, we can work on a whole vertebrate with most organs formed within a week. With different tissues it is possible to diversify the type of expression with different promoters.<br />
<br/><br />
<br/><br />
So far we have made 3 new plasmid backbones with different promoters :<br />
<br/><br/><br />
<li>With a <b>CMV promoter</b> for an ubiquitous expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>), <br />
<li>With a <b>Hsp70 promoter</b> for an inducible expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),<br />
<li>With a <b>Elastase promoter</b> for a tissue specific expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li><br />
<br/><br />
<br />
Our goal was to provide tools which would allow to rapidly build and characterize constructs in the embryos (along with a synthetic hormone to make them communicate), with tools for debugging (by injecting mRNA) and with ubiquitous, inducible and tissue specific promoters.<br />
</ul><br />
<br />
<br />
<br/><br/><br/><br />
<br />
<br />
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/><br />
<br />
<p>The <a href="https://2012.igem.org/Team:Evry/InjectionTuto">injection tutorial</a> explains very simply with diagram how we did injection and how take care about your embryos and tadpole. The experiment carries on 5 days, from the unfertilized egg to a swimming tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).<br />
<br />
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/><br />
<br />
<p>pCS2+ GFP-aid: this plasmid contains the constitutive and ubiquitous promoter CMV and the aid sequenced of the aid system fusionned to GFP (Green Fluorescent Protein)(Nishimura et al., 2009), this Biobrick created by our team is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812010">BBa_K812010</a>, and it was integrated into our Eucaryotic plasmid <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812000">BBa_K812000</a>.We injected about 3.78E+7 plasmids.</p><br/><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" /> <br />
</b></b><br />
<p><br />
GFP-aid expression from the embryo at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 20 (one day after injection )to a tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> ~46 (four days after injection). For this tadpole the expression is localized in the skin.</b></b></b><br />
</p><br />
<br />
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.<br />
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<br><br><br />
<h4><b>The characterization of all reporter and promoters is <u><a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a></u>.</b></h4><br><br />
<br />
<h2>Conclusion</h2><br/><br />
<br />
<p>This new BioBricked plasmid is ready to use in <i>Xenopus tropicalis</i>. As you can see above the plasmid pCS2+ with the CMV pomoter express the fluorescent protein GFP-aid, but this plasmid carry on important things to express a gene into eukaryotic calls. The 5'UTR region and the 3' UTR region was needed for gene expression in euklaryotic organism. The simplest way to do that was to use a plasmid already used in eukaryotic cells, vertebrate and especially <i>Xenopus tropicalis</i> as pCS2+. This pCS2+ was Biobricked to be compatible with the registry. <br><br />
<br />
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: <a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a>.<br><br />
<br />
<p><br />
Nevertheless we expected a more uniform expression of the reporters with the CMV promoter. Within tadpole, fluorescent proteins were observed in one to four different tissues, and tissues were different between tadpoles.<br />
</p><br />
<br />
<p><br />
Explanation: The plasmid DNA does not diffuse in the egg and stay in the same area around the injection site. This means that depending on the injection site, the plasmid will be inherited by a given set of cells within the tadpole. This question was raised in our <a href="https://2012.igem.org/Team:Evry/plasmid_splitting">model</a>. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.<br />
</p><br />
<br />
<p><br />
Our experiment showed us that plasmids injected do not diffuse in the whole organism. To express a protein with a promoter tissue specific it is a problem, because of the very low the probability to have the plasmid into the expected tissue. To solve the problem it is possible to easily integrate promoters and genes into the <i>Xenopus</i>'s chromosome with the REMI technic [3]. A new plasmid pCS2+ with I-SceI sites upstream the promoter and downstream of the reporter could allow the integration of the sequence between this two I-SceI restriction sites. This plasmid could be useful for the eukaryotic community, they could change promoters easily with SalI and HindIII and the reporter is compatible with the registry (with BB prefix and suffix), and they would have the choice to test a construction by plasmid injection or DNA chromosome integration.<br />
</p><br />
<br />
<p><br />
Moreover, the expression of reporters decreases during time, because plasmid DNA is subjected to a catabolic activity during development but also plasmid DNA gets diluted as cells proliferate and the quantity of plasmid DNA decreases for each cell. Integration into the chromosome could prevent it. <br />
</p><br />
<br />
<p><br />
Our project raised important ethics question because the team use tadpole, an animal. We reflect that working with tadpole involved new questions about the animal pain but also about using animals in iGEM and in Synthetic Biology. It made us think about these questions, our reflection is in <a href="https://2012.igem.org/Team:Evry/HumanPractice">Human Practice</a>.</p><br><br />
<br />
<div id="citation_box"><br />
<p id="references">References:</p><br />
<ol><br />
<li><i>Inducible control of tissue-specific transgene expression in <i>Xenopus</i> tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li><br />
<br />
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li><br />
<br />
<li><i>REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants</li> Kahmann R., Basse C., European Journal of Plant Pathology</li><br />
</ol><br />
</div><br />
<br><br />
<br />
<script type="text/javascript">writeFooter()</script> <br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T01:03:26Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/e/e2/Hormone.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/a/a4/GoldeN.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/GB"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/5/5b/ModelingDHIUHEIUHD.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/Modeling"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/ba/HumanPractice.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T00:55:13Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/e/e2/Hormone.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://static.igem.org/mediawiki/2012/a/a4/GoldeN.png"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://static.igem.org/mediawiki/2012/5/5b/ModelingDHIUHEIUHD.png"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://static.igem.org/mediawiki/2012/b/ba/HumanPractice.png"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T00:53:05Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/e/e2/Hormone.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T00:51:57Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/b/bd/Xenope.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem">More details here...</a><br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/main-img.jsTeam:Evry/main-img.js2012-09-27T00:27:33Z<p>Tiff: </p>
<hr />
<div>(function($){<br />
<br />
var Renderer = function(elt){<br />
var dom = $(elt)<br />
var canvas = dom.get(0)<br />
var ctx = canvas.getContext("2d");<br />
var gfx = arbor.Graphics(canvas)<br />
var sys = null<br />
<br />
var _vignette = null<br />
var selected = null,<br />
nearest = null,<br />
_mouseP = null;<br />
<br />
<br />
var that = {<br />
init:function(pSystem){<br />
sys = pSystem<br />
sys.screen({size:{width:dom.width(), height:dom.height()},padding:[36,60,36,60]})<br />
<br />
$(window).resize(that.resize)<br />
that.resize()<br />
that._initMouseHandling()<br />
<br />
if (document.referrer.match(/GoldenBricksxxxxxxxx|Plasmids|AIDSystem/)){<br />
// if we got here by hitting the back button in one of the Benchwork, <br />
// start with the Benchwork section pre-selected<br />
that.switchSection('Benchwork')<br />
}<br />
},<br />
resize:function(){<br />
// canvas.width = .5* $(window).width()<br />
// canvas.height = .5* $(window).height()<br />
sys.screen({size:{width:canvas.width, height:canvas.height}})<br />
_vignette = null<br />
that.redraw()<br />
},<br />
redraw:function(){<br />
gfx.clear()<br />
sys.eachEdge(function(edge, p1, p2){<br />
if (edge.source.data.alpha * edge.target.data.alpha == 0) return<br />
gfx.line(p1, p2, {stroke:"#b2b19d", width:3, alpha:edge.target.data.alpha})<br />
})<br />
sys.eachNode(function(node, pt){<br />
var w = Math.max(20, 20+gfx.textWidth(node.name) )<br />
if (node.data.alpha===0) return<br />
<br />
if (node.data.shape=='img'){<br />
var img_elem = new Image();<br />
img_elem.src = node.data.url;<br />
ctx.drawImage(img_elem, pt.x-w/2, pt.y-w/2, w, w); // Redimensionnement de l'image prévue comme tu le souhaitais !<br />
gfx.oval(pt.x-w/2, pt.y-w/2, w, w, {fill:node.data.color, alpha:0})<br />
}<br />
<br />
else if (node.data.shape=='dot'){<br />
gfx.oval(pt.x-w/2, pt.y-w/2, w, w, {fill:node.data.color, alpha:node.data.alpha})<br />
gfx.text(node.name, pt.x, pt.y+7, {color:"white", align:"center", font:"Arial", weight:"bold", size:12}) <br />
}<br />
<br />
else{<br />
gfx.rect(pt.x-w/2, pt.y-8, w, 20, 4, {fill:node.data.color, alpha:node.data.alpha})<br />
gfx.text(node.name, pt.x, pt.y+9, {color:"white", align:"center", font:"Arial", size:12})<br />
gfx.text(node.name, pt.x, pt.y+9, {color:"white", align:"center", font:"Arial", size:12})<br />
}<br />
})<br />
that._drawVignette()<br />
},<br />
<br />
_drawVignette:function(){<br />
var w = canvas.width<br />
var h = canvas.height<br />
var r = 20<br />
<br />
if (!_vignette){<br />
var top = ctx.createLinearGradient(0,0,0,r)<br />
top.addColorStop(0, "#e0e0e0")<br />
top.addColorStop(.7, "rgba(255,255,255,0)")<br />
<br />
var bot = ctx.createLinearGradient(0,h-r,0,h)<br />
bot.addColorStop(0, "rgba(255,255,255,0)")<br />
bot.addColorStop(1, "white")<br />
<br />
_vignette = {bot:bot}<br />
}<br />
<br />
// top<br />
ctx.fillStyle = _vignette.top<br />
ctx.fillRect(0,0, w,r)<br />
<br />
// bot<br />
ctx.fillStyle = _vignette.bot<br />
ctx.fillRect(0,h-r, w,r)<br />
},<br />
<br />
switchMode:function(e){<br />
if (e.mode=='hidden'){<br />
dom.stop(true).fadeTo(e.dt,0, function(){<br />
if (sys) sys.stop()<br />
$(this).hide()<br />
})<br />
}else if (e.mode=='visible'){<br />
dom.stop(true).css('opacity',0).show().fadeTo(e.dt,1,function(){<br />
that.resize()<br />
})<br />
if (sys) sys.start()<br />
}<br />
},<br />
<br />
switchSection:function(newSection){<br />
var parent = sys.getEdgesFrom(newSection)[0].source<br />
var children = $.map(sys.getEdgesFrom(newSection), function(edge){<br />
return edge.target<br />
})<br />
<br />
sys.eachNode(function(node){<br />
if (node.data.shape=='dot') return // skip all but leafnodes<br />
if (node.data.shape=='img') return // skip all but leafnodes<br />
var nowVisible = ($.inArray(node, children)>=0)<br />
var newAlpha = (nowVisible) ? 1 : 0<br />
var dt = (nowVisible) ? .5 : .5<br />
sys.tweenNode(node, dt, {alpha:newAlpha})<br />
<br />
if (newAlpha==1){<br />
node.p.x = parent.p.x + .05*Math.random() - .025<br />
node.p.y = parent.p.y + .05*Math.random() - .025<br />
node.tempMass = .001<br />
}<br />
})<br />
},<br />
<br />
<br />
_initMouseHandling:function(){<br />
// no-nonsense drag and drop (thanks springy.js)<br />
selected = null;<br />
nearest = null;<br />
var dragged = null;<br />
var oldmass = 1<br />
<br />
var _section = null<br />
<br />
var handler = {<br />
moved:function(e){<br />
var pos = $(canvas).offset();<br />
_mouseP = arbor.Point(e.pageX-pos.left, e.pageY-pos.top)<br />
nearest = sys.nearest(_mouseP);<br />
<br />
if (!nearest.node) return false<br />
<br />
// if (nearest.node.data.shape!='dot'){<br />
selected = (nearest.distance < 50) ? nearest : null<br />
if (selected){<br />
dom.addClass('linkable')<br />
window.status = selected.node.data.link//.replace(/^\//,"http://"+window.location.host+"/")//.replace(/^#/,'')<br />
}<br />
else{<br />
dom.removeClass('linkable')<br />
window.status = ''<br />
}<br />
// }else <br />
if ($.inArray(nearest.node.name, ['The French Froggies Project!','Xenopus as a chassis','Hormonal Communicati','Modelingxxxxxxxxxxxx','GoldenBricksxxxxxxxx', 'Human Practicexxxxxx', 'The Teamxxxxxxxxxxxx']) >=0 ){<br />
if (nearest.node.name!=_section){<br />
_section = nearest.node.name<br />
that.switchSection(_section)<br />
}<br />
dom.removeClass('linkable')<br />
window.status = ''<br />
}<br />
<br />
return false<br />
},<br />
clicked:function(e){<br />
var pos = $(canvas).offset();<br />
_mouseP = arbor.Point(e.pageX-pos.left, e.pageY-pos.top)<br />
nearest = dragged = sys.nearest(_mouseP);<br />
<br />
if (nearest && selected && nearest.node===selected.node){<br />
var link = selected.node.data.link<br />
if (link.match(/^#/)){<br />
$(that).trigger({type:"navigate", path:link.substr(1)})<br />
}else{<br />
window.location = link<br />
}<br />
return false<br />
}<br />
<br />
<br />
if (dragged && dragged.node !== null) dragged.node.fixed = true<br />
<br />
$(canvas).unbind('mousemove', handler.moved);<br />
$(canvas).bind('mousemove', handler.dragged)<br />
$(window).bind('mouseup', handler.dropped)<br />
<br />
return false<br />
},<br />
dragged:function(e){<br />
var old_nearest = nearest && nearest.node._id<br />
var pos = $(canvas).offset();<br />
var s = arbor.Point(e.pageX-pos.left, e.pageY-pos.top)<br />
<br />
if (!nearest) return<br />
if (dragged !== null && dragged.node !== null){<br />
var p = sys.fromScreen(s)<br />
dragged.node.p = p<br />
}<br />
<br />
return false<br />
},<br />
<br />
dropped:function(e){<br />
if (dragged===null || dragged.node===undefined) return<br />
if (dragged.node !== null) dragged.node.fixed = false<br />
dragged.node.tempMass = 1000<br />
dragged = null;<br />
// selected = null<br />
$(canvas).unbind('mousemove', handler.dragged)<br />
$(window).unbind('mouseup', handler.dropped)<br />
$(canvas).bind('mousemove', handler.moved);<br />
_mouseP = null<br />
return false<br />
}<br />
<br />
<br />
}<br />
<br />
$(canvas).mousedown(handler.clicked);<br />
$(canvas).mousemove(handler.moved);<br />
<br />
}<br />
}<br />
<br />
return that<br />
}<br />
<br />
<br />
var Nav = function(elt){<br />
var dom = $(elt)<br />
<br />
var _path = null<br />
<br />
var that = {<br />
init:function(){<br />
$(window).bind('popstate',that.navigate)<br />
dom.find('> a').click(that.back)<br />
$('.more').one('click',that.more)<br />
<br />
$('#Model dl:not(.datastructure) dt').click(that.reveal)<br />
that.update()<br />
return that<br />
},<br />
more:function(e){<br />
$(this).removeAttr('href').addClass('less').html('&nbsp;').siblings().fadeIn()<br />
$(this).next('h2').find('a').one('click', that.less)<br />
<br />
return false<br />
},<br />
less:function(e){<br />
var more = $(this).closest('h2').prev('a')<br />
$(this).closest('h2').prev('a')<br />
.nextAll().fadeOut(function(){<br />
$(more).text('creation & use').removeClass('less').attr('href','#')<br />
})<br />
$(this).closest('h2').prev('a').one('click',that.more)<br />
<br />
return false<br />
},<br />
reveal:function(e){<br />
$(this).next('dd').fadeToggle('fast')<br />
return false<br />
},<br />
back:function(){<br />
_path = "/"<br />
if (window.history && window.history.pushState){<br />
window.history.pushState({path:_path}, "", _path);<br />
}<br />
that.update()<br />
return false<br />
},<br />
navigate:function(e){<br />
var oldpath = _path<br />
if (e.type=='navigate'){<br />
_path = e.path<br />
if (window.history && window.history.pushState){<br />
window.history.pushState({path:_path}, "", _path);<br />
}else{<br />
that.update()<br />
}<br />
}else if (e.type=='popstate'){<br />
var state = e.originalEvent.state || {}<br />
_path = state.path || window.location.pathname.replace(/^\//,'')<br />
}<br />
if (_path != oldpath) that.update()<br />
},<br />
update:function(){<br />
var dt = 'slow'<br />
if (_path===null){<br />
// this is the original page load. don't animate anything just jump<br />
// to the proper state<br />
_path = window.location.pathname.replace(/^\//,'')<br />
dt = 0<br />
dom.find('p').css('opacity',0).show().fadeTo('slow',1)<br />
}<br />
<br />
switch (_path){<br />
case '':<br />
case '/':<br />
// dom.find('p').text('a graph visualization library using web workers and jQuery')<br />
dom.find('> a').removeClass('active').attr('href','#')<br />
<br />
$('#Model').fadeTo('fast',0, function(){<br />
$(this).hide()<br />
$(that).trigger({type:'mode', mode:'visible', dt:dt})<br />
})<br />
document.title = "The French Froggies Project!"<br />
break<br />
<br />
}<br />
<br />
}<br />
}<br />
return that<br />
}<br />
<br />
$(document).ready(function(){<br />
var CLR = {<br />
branch:"#b2b19d",<br />
level3benchwork:"#FFBF3E",<br />
level3model:"#4B86C7"<br />
}<br />
/*Thibault BEGIN*/<br />
var theUI = {<br />
<br />
// ['The French Froggies Project!','Xenopus as a chassis','Hormonal Communicati','Modelingxxxxxxxxxxxx','GoldenBricksxxxxxxxx', 'Human Practicexxxxxx', 'The Teamxxxxxxxxxxxx']<br />
<br />
nodes:{"The French Froggies Project!":{color:"#51C215", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/Project', url:'https://static.igem.org/mediawiki/2012/c/cf/French.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
<br />
"Xenopus as a chassis":{color:"#63a358", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/FrenchFrog', url:'https://static.igem.org/mediawiki/2012/b/bd/Xenope.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"New Xenopus plasmids":{color:"#63a358", alpha:0, link:'FrenchFrog#plasmid'},<br />
"Injection in Xenopus":{color:"#63a358", alpha:0, link:'InjectionTuto'},<br />
"Development stages":{color:"#63a358", alpha:0, link:'Stages'},<br />
"Characterization":{color:"#63a358", alpha:0, link:'Tadpole_injection1'},<br />
<br />
"Hormonal Communicati":{color:"#852c2b", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/AIDSystem', url:'https://static.igem.org/mediawiki/2012/e/e2/Hormone.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"Auxin emitter":{color:"#852c2b", alpha:0, link:'AIDSystem#auxin'},<br />
"Auxin receiver":{color:"#852c2b", alpha:0, link:'AIDSystem#AID'},<br />
"Auxin toxicity":{color:"#852c2b", alpha:0, link:'AuxinTOX'},<br />
"Auxin uptake":{color:"#852c2b", alpha:0, link:'auxin_uptake'},<br />
<br />
"Modelingxxxxxxxxxxxx":{color:"#1A5291", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/Modeling', url:'https://static.igem.org/mediawiki/2012/5/5b/ModelingDHIUHEIUHD.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"General Model":{color:CLR.level3model, alpha:0, link:'ODE_model'},<br />
"ODEs derivations":{color:CLR.level3model, alpha:0, link:'auxin_pde'},<br />
"Diffusion":{color:CLR.level3model, alpha:0, link:'Auxin_diffusion'},<br />
"Auxin production":{color:CLR.level3model, alpha:0, link:'auxin_production'},<br />
"Auxin reception":{color:CLR.level3model, alpha:0, link:'auxin_detection'},<br />
"Plasmid diffusion":{color:CLR.level3model, alpha:0, link:'plasmid_splitting'},<br />
"Model integration":{color:CLR.level3model, alpha:0, link:'model_integration'},<br />
<br />
"GoldenBricksxxxxxxxx":{color:"#1A5291", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/GB', url:'https://static.igem.org/mediawiki/2012/a/a4/GoldeN.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
<br />
"Human Practicexxxxxx":{color:"#a6953f", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/HumanPractice', url:'https://static.igem.org/mediawiki/2012/b/ba/HumanPractice.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"Hi Xenope!":{color:"#a6953f", alpha:0, link:'Team:Evry/HumanPractice/Introduction'},<br />
"Be a chassis?":{color:"#a6953f", alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/modelorganism'},<br />
"Free the frogs!":{color:"#a6953f", alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/freedthefrogs'},<br />
"Chassis, really?":{color:"#a6953f", alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/chassis'},<br />
"Working with Xenopus?":{color:"#a6953f", alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/future'},<br />
"Legislation":{color:"#a6953f", alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/others'},<br />
<br />
"The Teamxxxxxxxxxxxx":{color:"#632e8c", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/Team', url:'https://static.igem.org/mediawiki/2012/9/93/TeamEVRY.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"Our Team":{color:"#632e8c", alpha:0, link:'Team'},<br />
"Our Sponsors":{color:"#632e8c", alpha:0, link:'Sponsors'},<br />
"Attributions":{color:"#632e8c", alpha:0, link:'Attributions'},<br />
"Official profile":{color:"#632e8c", alpha:0, link:'https://igem.org/Team.cgi?year=2012'},<br />
"Collaborations":{color:"#632e8c", alpha:0, link:'Collaboration'}<br />
},<br />
<br />
edges:{<br />
<br />
<br />
"The French Froggies Project!":{<br />
"Xenopus as a chassis":{"length":0.8,"weight":2},<br />
"Hormonal Communicati":{"length":0.8,"weight":2},<br />
"Modelingxxxxxxxxxxxx":{"length":0.8,"weight":2},<br />
"GoldenBricksxxxxxxxx":{"length":1.5,"weight":2},<br />
"Human Practicexxxxxx":{"length":0.75,"weight":2},<br />
"The Teamxxxxxxxxxxxx":{"length":0.5,"weight":2}<br />
},<br />
<br />
<br />
"Xenopus as a chassis":{<br />
"Creation of new Xenopus plasmids":{"length":0.75,"weight":1},<br />
"How to micro inject in Xenopus eggs":{"length":0.75,"weight":2},<br />
"Development stages":{"length":0.75,"weight":2},<br />
"Characterization of plasmids and reporters":{"length":0.75,"weight":2}<br />
},<br />
"Hormonal Communicati":{<br />
"The auxin emitter":{"length":1,"weight":2},<br />
"The auxin receiver":{"length":1,"weight":2},<br />
"Auxin toxicity":{"length":1,"weight":2},<br />
"Auxin Uptake":{"length":1,"weight":2}<br />
<br />
},<br />
<br />
"Modelingxxxxxxxxxxxx":{<br />
"General Model":{"length":0.5,"weight":2},<br />
"Rigorous derivations of ODEs":{"length":0.5,"weight":2},<br />
"Diffusion in a realistic geometry":{"length":0.75,"weight":2},<br />
"Auxin production":{"length":0.5,"weight":2},<br />
"Auxin reception":{"length":0.5,"weight":2},<br />
"Plasmid diffusion":{"length":0.5,"weight":2},<br />
"Model integration":{"length":0.5,"weight":2}<br />
<br />
},<br />
<br />
"GoldenBricksxxxxxxxx":{},<br />
<br />
<br />
"Human Practicexxxxxx":{<br />
"Hi Xenope!":{"length":0.5,"weight":2},<br />
"Would you be my chassis?":{"length":0.5,"weight":2},<br />
"Free the frogs!":{"length":0.5,"weight":2},<br />
"I'm a chassis, really?":{"length":0.5,"weight":2},<br />
"Should we work with Xenopus again?":{"length":0.5,"weight":2},<br />
"What the laws says...":{"length":0.5,"weight":2}<br />
},<br />
<br />
"The Teamxxxxxxxxxxxx":{<br />
"Our Team":{"length":0.5,"weight":2},<br />
"Our Sponsors":{"length":0.5,"weight":2},<br />
"Attributions":{"length":0.5,"weight":2},<br />
"Official profile":{"length":0.5,"weight":2},<br />
"Collaborations":{"length":0.5,"weight":2}<br />
}<br />
}<br />
}<br />
/*Thibault END*/<br />
<br />
var sys = arbor.ParticleSystem()<br />
sys.parameters({stiffness:900, repulsion:50, gravity:true, dt:0.015})<br />
sys.renderer = Renderer("#sitemap")<br />
sys.graft(theUI)<br />
<br />
var nav = Nav("#nav")<br />
$(sys.renderer).bind('navigate', nav.navigate)<br />
$(nav).bind('mode', sys.renderer.switchMode)<br />
nav.init()<br />
})<br />
})(this.jQuery)</div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T00:18:39Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/0/0f/French_frog.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem">More details here...</a><br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/css_v1Team:Evry/css v12012-09-27T00:18:20Z<p>Tiff: </p>
<hr />
<div>body<br />
{<br />
width: auto;<br />
color: #333333;<br />
/*background:#e9e4de;*/<br />
background-image:url(https://static.igem.org/mediawiki/2012/0/06/Embryos.png);<br />
background-repeat:no-repeat<br />
margin:0px 0px 0px 0px;<br />
}<br />
<br />
/* la barre titre (baniere igem+ menu haut)*/<br />
#top-section<br />
{<br />
height: auto;<br />
margin-top: 0 px;<br />
margin-left: auto;<br />
margin-right: auto;<br />
margin-bottom: 0 !important;<br />
padding:0;<br />
border: none;<br />
display: display;<br />
}<br />
<br />
/*le conteneur de la banière igem avec un lien vers igem*/<br />
#p-logo<br />
{<br />
display:none;<br />
border:none;<br />
margin:none;<br />
}<br />
<br />
/* la barre de menu du haut */<br />
#menubar<br />
{<br />
color:#000000;<br />
}<br />
<br />
/*les lien de la barre de menu du haut */<br />
#menubar a<br />
{<br />
text-decoration:none;<br />
color:#000000;<br />
}<br />
<br />
/* le menu de haut gauche */<br />
.left-menu<br />
{<br />
background-color:transparent;<br />
/*display:none;*/<br />
}<br />
<br />
/* le menu de login haut droite*/<br />
.right-menu<br />
{<br />
color:transparent;<br />
text-decoration:none;<br />
background-color:none;<br />
right: 15px;<br />
}<br />
<br />
/* les lien du login */<br />
.right-menu a<br />
{<br />
color:transparent;<br />
text-decoration:transparent;<br />
background-color:none;<br />
}<br />
<br />
/* la barre de recherche*/<br />
#search-controls<br />
{<br />
display:none;<br />
}<br />
<br />
/* le body de la page*/<br />
#content<br />
{<br />
background-color: transparent;<br />
border:none;<br />
padding:none;<br />
margin:none;<br />
line-height:1em;<br />
}<br />
<br />
/*titre de page */<br />
.firstHeading<br />
{<br />
display:none;<br />
border: none;<br />
}<br />
<br />
/* contenu de page*/<br />
#bodyContent<br />
{<br />
}<br />
<br />
#footer-wrapper<br />
{<br />
position: absolute;<br />
width: 941px;<br />
left: -1px;<br />
margin-top:25px;<br />
margin-bottom:30px;<br />
padding: 7px 15px 7px 15px;<br />
background-color:#ffffff;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
/*border: 1px solid black;*/<br />
}<br />
<br />
/* la boite en bas de page*/<br />
#footer-box<br />
{<br />
display: none;<br />
margin-bottom: 10px;<br />
}<br />
<br />
/* le cadre sous le body useless */<br />
#catlinks<br />
{<br />
display: none;<br />
}<br />
<br />
/* ----------------End of the wiki hack -------------------------------------*/<br />
<br />
/* position of the logo */<br />
#evry_logo <br />
{<br />
position:absolute;<br />
top:25px;<br />
left: 35px;<br />
width:200px;<br />
/*background-color:#FFA500;*/<br />
}<br />
<br />
/* Position of the banner */ <br />
#evry_banner{ <br />
position:absolute;<br />
top:16px;<br />
width:720px;<br />
left:230px;<br />
/*background-color:#800080;*/<br />
}<br />
<br />
<br />
/*white font over the grey one on the top*/<br />
#white_thingy<br />
{<br />
position:relative;<br />
top:-20px;<br />
height:200px;<br />
background-color:#ffffff;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
}<br />
<br />
#back_image<br />
{<br />
position:absolute;<br />
top:147px;<br />
left:-155px;<br />
height:900px;<br />
width:1280px;<br />
background-color:transparent;<br />
/*background-image:url(http://files.myopera.com/gokuss1234/albums/8827422/Opera-Background-Blue-Bubbles.png);*/<br />
background-position:center;<br />
background-repeat:no-repeat;<br />
}<br />
<br />
/* notre page !*/<br />
#main_evry2012<br />
{<br />
position:absolute;<br />
top:0px;<br />
left:50%;<br />
margin-left:-486px;<br />
margin-bottom: 10px;<br />
width: 972px;<br />
height: 100%;<br />
text-align: center;<br />
}<br />
<br />
/* conteneur du texte wiki*/<br />
#maincontainer_evry2012<br />
{<br />
padding:15px 15px 15px 15px;<br />
background:#ffffff;<br />
margin-bottom: 10px;<br />
<br />
/*border:1px solid black;*/<br />
position:absolute;<br />
text-align:justify;<br />
top:210px;/*178px*/<br />
width:940px;<br />
heigth:auto;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
}<br />
<br />
/* conteneur du texte wiki pour la page d'acueil*/<br />
#maincontainer_evry2012bis<br />
{<br />
padding:15px 15px 15px 15px;<br />
background:transparent;<br />
margin-bottom: 10px;<br />
color:white;<br />
<br />
<br />
/*border:1px solid black;*/<br />
position:absolute;<br />
text-align:justify;<br />
top:210px;/*178px*/<br />
width:940px;<br />
heigth:auto;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
}<br />
<br />
/* ------- Menu -----------*/<br />
<br />
/* Frame containg the entire menu (transparent) */<br />
#menu_evry2012<br />
{<br />
text-align:center;<br />
position:absolute;<br />
z-index:10;<br />
left:220px; <br />
top:163px;<br />
float:center;<br />
font-weight:bold;<br />
}<br />
<br />
#menu_evry2012 a<br />
{<br />
color:#505050;<br />
text-decoration:none;<br />
display:block;<br />
padding:8px;<br />
margin: 0px 0px 0px 0px;<br />
/*height:18px;*/<br />
width:auto;<br />
background-color:#ffffff;<br />
font-size:11px;<br />
}<br />
<br />
#menu_evry2012 .menu_list_item_evry2012 ul a<br />
{<br />
color:#696969;<br />
font-size:11px;<br />
width:120px; /* Size of the scroling menu*/<br />
border: 1px solid #e6e1db;<br />
}<br />
<br />
#menu_evry2012 a:hover<br />
{<br />
background-color:#e6e1db;<br />
display:block;<br />
width:auto; /* size of the hover block */<br />
position:relative;<br />
}<br />
<br />
#menu_evry2012 a:active<br />
{<br />
background-color:#e6e1db;<br />
display:block;<br />
}<br />
<br />
<br />
<br />
<br />
/* Style of the menu level1 */<br />
#menu_list_evry2012<br />
{<br />
list-style:none; <br />
text-align:center;<br />
margin-left:0px;<br />
margin-top:0px;<br />
padding:0px;<br />
border:none;<br />
position:relative;<br />
}<br />
<br />
.menu_list_item_evry2012<br />
{<br />
float: left;<br />
width: 80px;<br />
padding: 0;<br />
border:0;<br />
}<br />
<br />
/*Second level menu*/<br />
.menu_list_item_evry2012 ul<br />
{<br />
display:none; /* initially hide the entire list hierarchy */<br />
padding:2px; /* this is our box border width */<br />
list-style: none;<br />
width:110px;<br />
}<br />
<br />
/* 2nd level drop-down box */<br />
.menu_list_item_evry2012:hover ul,<br />
.menu_list_item_evry2012 a:hover ul<br />
{<br />
display:block;<br />
position:relative;<br />
margin:0;<br />
top:0px; /* place us just up underneath the top-level images */<br />
left:-2px; /* left-align our drop-down to the previous button border */<br />
height:auto; /* the drop-down height will be determiend by line count */<br />
width:110px;<br />
background-color:transparent; /* this sets our menu's effective "border" color */<br />
font-size:12px; /* this (and also below) sets the menu's font size */<br />
list-style: none;<br />
}<br />
<br />
/*Third level menu*/<br />
<br />
/* hide inactive 3rd-level menus */<br />
.menu_list_item_evry2012:hover ul li ul,<br />
.menu_list_item_evry2012 a:hover ul li a ul<br />
{<br />
display:none;<br />
}<br />
<br />
.menu_list_item_evry2012:hover ul li:hover ul,<br />
/* 3rd level drop-down box */<br />
.menu_list_item_evry2012 a:hover ul li a:hover ul<br />
{<br />
display:block;<br />
position:absolute;<br />
top:0px;<br />
left:140px;<br />
}<br />
<br />
<br />
/* End of the menu */<br />
<br />
<br />
/* scroling buttons */<br />
<br />
#scroll_left<br />
{<br />
display:block;<br />
height:350px;<br />
width:140px;<br />
background-color:transparent;<br />
z-index:400;<br />
position:fixed;<br />
top:400px;<br />
left:5px;<br />
}<br />
<br />
#scroll_left a<br />
{<br />
font-size:11px;<br />
color:#273572;<br />
font-weight:bold;<br />
}<br />
<br />
#scroll_right<br />
{<br />
display:block;<br />
height:350px;<br />
width:100px;<br />
background-color:transparent;<br />
z-index:400;<br />
position:fixed;<br />
top:400px;<br />
right:5px;<br />
}<br />
<br />
#scroll_right a<br />
{<br />
font-size:11px;<br />
color:#273572;<br />
font-weight:bold;<br />
}<br />
<br />
<br />
<br />
/*TEXT formating*/<br />
.legende_schema<br />
{<br />
font-style:italic;<br />
text-align: center;<br />
}<br />
<br />
a<br />
{<br />
text-decoration:none;<br />
}<br />
<br />
#title<br />
{<br />
display:block;<br />
top:-400px;<br />
left:60px;<br />
}<br />
<br />
h1<br />
{<br />
font-style: normal;<br />
text-decoration: none;<br />
border: none;<br />
line-height:1em;<br />
padding:15px 0px 15px 0px;<br />
font-weight:bold;<br />
font-size: 30px;<br />
color:#cb6228;<br />
}<br />
<br />
h2<br />
{<br />
font-style: normal;<br />
font-weight:bold;<br />
font-style:italic;<br />
font-size: 22px;<br />
line-height:1em;<br />
text-decoration:none;<br />
border:none;<br />
padding:0px 0px 10px 0px;<br />
color:#364d01;<br />
margin-top:25px;<br />
}<br />
<br />
h3<br />
{<br />
padding-left:25px;<br />
font-style:bold;<br />
font-size: 18px;<br />
text-decoration:none;<br />
border:none;<br />
line-height:1em;<br />
padding:0px 0px 5px 5px;<br />
margin-top:20px;<br />
}<br />
<br />
h4<br />
{<br />
font-style:italic;<br />
}<br />
<br />
/*block for paper citations*/<br />
#citation_box<br />
{<br />
margin-top:30px;<br />
padding:10px;<br />
border-style:none;<br />
border-width:2px;<br />
border-color:#BDFEBC;<br />
background-color:#ECECEC;<br />
text-align:left;<br />
}<br />
<br />
#citation_box ol,li<br />
{<br />
text-style:italic;<br />
}<br />
<br />
#references<br />
{<br />
text-style:bold;<br />
text-size:14px;<br />
}<br />
<br />
table.parameter<br />
{<br />
width:100%; <br />
display: block; <br />
margin-left: auto; <br />
margin-right: auto; <br />
cellpadding:0px; <br />
cellspacing:0px;Experimentals_Parameters <br />
align:middle; <br />
}<br />
<br />
table.parameter td<br />
{<br />
padding:5px;<br />
}<br />
<br />
#table-fixed-size<br />
{<br />
table-layout:fixed;<br />
word-wrap: break-word;<br />
width:100px;<br />
}<br />
<br />
em {<br />
color: #cb6228;<br />
font-style: normal;<br />
font-weight:bold;<br />
}<br />
<br />
strong {<br />
color: #364d01;<br />
}<br />
<br />
.orange, a.orange:visited<br />
{<br />
color:#cb6228;<br />
}<br />
<br />
.green, a.green:visited<br />
{<br />
color:#364d01;<br />
}<br />
<br />
#param<br />
{<br />
border-collapse:collapse;<br />
text-align:center;<br />
}<br />
<br />
#param td, #param th<br />
{<br />
border: 1px solid black;<br />
padding:10px;<br />
}<br />
<br />
#team<br />
{<br />
padding:5px;<br />
}<br />
<br />
#team td<br />
{<br />
align:left;<br />
vertical-align:top;<br />
}<br />
<br />
.moredetails<br />
{<br />
width: 300px;<br />
text-align: left;<br />
background-color: #CEE9F4;<br />
border-radius: 7px;<br />
margin-left: 625px;<br />
}<br />
<br />
.moredetails a<br />
{<br />
font-style: italic;<br />
font-weight: bold;<br />
}<br />
<br />
.moredetails a:hover<br />
{<br />
text-decoration:underline<br />
}<br />
<br />
.ania<br />
{<br />
color:#cb6228;<br />
}</div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-27T00:11:51Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/0/0f/French_frog.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem">More details here...</a><br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/css_v1Team:Evry/css v12012-09-27T00:10:03Z<p>Tiff: </p>
<hr />
<div>body<br />
{<br />
width: auto;<br />
color: #333333;<br />
/*background:#e9e4de;*/<br />
background-image:url(https://static.igem.org/mediawiki/2012/0/06/Embryos.png);<br />
background-repeat:no-repeat<br />
margin:0px 0px 0px 0px;<br />
}<br />
<br />
/* la barre titre (baniere igem+ menu haut)*/<br />
#top-section<br />
{<br />
height: auto;<br />
margin-top: 0 px;<br />
margin-left: auto;<br />
margin-right: auto;<br />
margin-bottom: 0 !important;<br />
padding:0;<br />
border: none;<br />
display: display;<br />
}<br />
<br />
/*le conteneur de la banière igem avec un lien vers igem*/<br />
#p-logo<br />
{<br />
display:none;<br />
border:none;<br />
margin:none;<br />
}<br />
<br />
/* la barre de menu du haut */<br />
#menubar<br />
{<br />
color:#000000;<br />
}<br />
<br />
/*les lien de la barre de menu du haut */<br />
#menubar a<br />
{<br />
text-decoration:none;<br />
color:#000000;<br />
}<br />
<br />
/* le menu de haut gauche */<br />
.left-menu<br />
{<br />
background-color:transparent;<br />
/*display:none;*/<br />
}<br />
<br />
/* le menu de login haut droite*/<br />
.right-menu<br />
{<br />
color:transparent;<br />
text-decoration:none;<br />
background-color:none;<br />
right: 15px;<br />
}<br />
<br />
/* les lien du login */<br />
.right-menu a<br />
{<br />
color:transparent;<br />
text-decoration:transparent;<br />
background-color:none;<br />
}<br />
<br />
/* la barre de recherche*/<br />
#search-controls<br />
{<br />
display:none;<br />
}<br />
<br />
/* le body de la page*/<br />
#content<br />
{<br />
background-color: transparent;<br />
border:none;<br />
padding:none;<br />
margin:none;<br />
line-height:1em;<br />
}<br />
<br />
/*titre de page */<br />
.firstHeading<br />
{<br />
display:none;<br />
border: none;<br />
}<br />
<br />
/* contenu de page*/<br />
#bodyContent<br />
{<br />
}<br />
<br />
#footer-wrapper<br />
{<br />
position: absolute;<br />
width: 941px;<br />
left: -1px;<br />
margin-top:25px;<br />
margin-bottom:30px;<br />
padding: 7px 15px 7px 15px;<br />
background-color:#ffffff;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
/*border: 1px solid black;*/<br />
}<br />
<br />
/* la boite en bas de page*/<br />
#footer-box<br />
{<br />
display: none;<br />
margin-bottom: 10px;<br />
}<br />
<br />
/* le cadre sous le body useless */<br />
#catlinks<br />
{<br />
display: none;<br />
}<br />
<br />
/* ----------------End of the wiki hack -------------------------------------*/<br />
<br />
/* position of the logo */<br />
#evry_logo <br />
{<br />
position:absolute;<br />
top:25px;<br />
left: 35px;<br />
width:200px;<br />
/*background-color:#FFA500;*/<br />
}<br />
<br />
/* Position of the banner */ <br />
#evry_banner{ <br />
position:absolute;<br />
top:16px;<br />
width:720px;<br />
left:230px;<br />
/*background-color:#800080;*/<br />
}<br />
<br />
<br />
/*white font over the grey one on the top*/<br />
#white_thingy<br />
{<br />
position:relative;<br />
top:-20px;<br />
height:200px;<br />
background-color:#ffffff;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
}<br />
<br />
#back_image<br />
{<br />
position:absolute;<br />
top:147px;<br />
left:-155px;<br />
height:900px;<br />
width:1280px;<br />
background-color:transparent;<br />
/*background-image:url(http://files.myopera.com/gokuss1234/albums/8827422/Opera-Background-Blue-Bubbles.png);*/<br />
background-position:center;<br />
background-repeat:no-repeat;<br />
}<br />
<br />
/* notre page !*/<br />
#main_evry2012<br />
{<br />
position:absolute;<br />
top:0px;<br />
left:50%;<br />
margin-left:-486px;<br />
margin-bottom: 10px;<br />
width: 972px;<br />
height: 100%;<br />
text-align: center;<br />
}<br />
<br />
/* conteneur du texte wiki*/<br />
#maincontainer_evry2012<br />
{<br />
padding:15px 15px 15px 15px;<br />
background:#ffffff;<br />
margin-bottom: 10px;<br />
<br />
/*border:1px solid black;*/<br />
position:absolute;<br />
text-align:justify;<br />
top:210px;/*178px*/<br />
width:940px;<br />
heigth:auto;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
}<br />
<br />
/* conteneur du texte wiki pour la page d'acueil*/<br />
#maincontainer_evry2012bis<br />
{<br />
padding:15px 15px 15px 15px;<br />
background:transparent;<br />
margin-bottom: 10px;<br />
color:white;<br />
<br />
<br />
/*border:1px solid black;*/<br />
position:absolute;<br />
text-align:justify;<br />
top:210px;/*178px*/<br />
width:940px;<br />
heigth:auto;<br />
-moz-border-radius-topright:15px;<br />
-moz-border-radius-bottomright:15px;<br />
-webkit-border-top-right-radius:15px;<br />
-webkit-border-bottom-right-radius:15px;<br />
border-top-right-radius:15px;<br />
border-bottom-right-radius:15px;<br />
border-radius: 15px;<br />
}<br />
<br />
/* ------- Menu -----------*/<br />
<br />
/* Frame containg the entire menu (transparent) */<br />
#menu_evry2012<br />
{<br />
text-align:center;<br />
position:absolute;<br />
z-index:10;<br />
left:220px; <br />
top:163px;<br />
float:center;<br />
font-weight:bold;<br />
}<br />
<br />
#menu_evry2012 a<br />
{<br />
color:#505050;<br />
text-decoration:none;<br />
display:block;<br />
padding:8px;<br />
margin: 0px 0px 0px 0px;<br />
/*height:18px;*/<br />
width:auto;<br />
background-color:#ffffff;<br />
font-size:11px;<br />
}<br />
<br />
#menu_evry2012 .menu_list_item_evry2012 ul a<br />
{<br />
color:#696969;<br />
font-size:11px;<br />
width:120px; /* Size of the scroling menu*/<br />
border: 1px solid #e6e1db;<br />
}<br />
<br />
#menu_evry2012 a:hover<br />
{<br />
background-color:#e6e1db;<br />
display:block;<br />
width:auto; /* size of the hover block */<br />
position:relative;<br />
}<br />
<br />
#menu_evry2012 a:active<br />
{<br />
background-color:#e6e1db;<br />
display:block;<br />
}<br />
<br />
<br />
<br />
<br />
/* Style of the menu level1 */<br />
#menu_list_evry2012<br />
{<br />
list-style:none; <br />
text-align:center;<br />
margin-left:0px;<br />
margin-top:0px;<br />
padding:0px;<br />
border:none;<br />
position:relative;<br />
}<br />
<br />
.menu_list_item_evry2012<br />
{<br />
float: left;<br />
width: 80px;<br />
padding: 0;<br />
border:0;<br />
}<br />
<br />
/*Second level menu*/<br />
.menu_list_item_evry2012 ul<br />
{<br />
display:none; /* initially hide the entire list hierarchy */<br />
padding:2px; /* this is our box border width */<br />
list-style: none;<br />
width:110px;<br />
}<br />
<br />
/* 2nd level drop-down box */<br />
.menu_list_item_evry2012:hover ul,<br />
.menu_list_item_evry2012 a:hover ul<br />
{<br />
display:block;<br />
position:relative;<br />
margin:0;<br />
top:0px; /* place us just up underneath the top-level images */<br />
left:-2px; /* left-align our drop-down to the previous button border */<br />
height:auto; /* the drop-down height will be determiend by line count */<br />
width:110px;<br />
background-color:transparent; /* this sets our menu's effective "border" color */<br />
font-size:12px; /* this (and also below) sets the menu's font size */<br />
list-style: none;<br />
}<br />
<br />
/*Third level menu*/<br />
<br />
/* hide inactive 3rd-level menus */<br />
.menu_list_item_evry2012:hover ul li ul,<br />
.menu_list_item_evry2012 a:hover ul li a ul<br />
{<br />
display:none;<br />
}<br />
<br />
.menu_list_item_evry2012:hover ul li:hover ul,<br />
/* 3rd level drop-down box */<br />
.menu_list_item_evry2012 a:hover ul li a:hover ul<br />
{<br />
display:block;<br />
position:absolute;<br />
top:0px;<br />
left:140px;<br />
}<br />
<br />
<br />
/* End of the menu */<br />
<br />
<br />
/* scroling buttons */<br />
<br />
#scroll_left<br />
{<br />
display:block;<br />
height:350px;<br />
width:140px;<br />
background-color:transparent;<br />
z-index:400;<br />
position:fixed;<br />
top:400px;<br />
left:5px;<br />
}<br />
<br />
#scroll_left a<br />
{<br />
font-size:11px;<br />
color:#273572;<br />
font-weight:bold;<br />
}<br />
<br />
#scroll_right<br />
{<br />
display:block;<br />
height:350px;<br />
width:100px;<br />
background-color:transparent;<br />
z-index:400;<br />
position:fixed;<br />
top:400px;<br />
right:5px;<br />
}<br />
<br />
#scroll_right a<br />
{<br />
font-size:11px;<br />
color:#273572;<br />
font-weight:bold;<br />
}<br />
<br />
<br />
<br />
/*TEXT formating*/<br />
.legende_schema<br />
{<br />
font-style:italic;<br />
text-align: center;<br />
}<br />
<br />
a<br />
{<br />
text-decoration:none;<br />
}<br />
<br />
#title<br />
{<br />
display:block;<br />
top:-400px;<br />
left:60px;<br />
}<br />
<br />
h1<br />
{<br />
font-style: normal;<br />
text-decoration: none;<br />
border: none;<br />
line-height:1em;<br />
padding:15px 0px 15px 0px;<br />
font-weight:bold;<br />
font-size: 30px;<br />
color:#cb6228;<br />
}<br />
<br />
h2<br />
{<br />
font-style: normal;<br />
font-weight:bold;<br />
font-style:italic;<br />
font-size: 22px;<br />
line-height:1em;<br />
text-decoration:none;<br />
border:none;<br />
padding:0px 0px 10px 0px;<br />
color:#364d01;<br />
margin-top:25px;<br />
}<br />
<br />
h3<br />
{<br />
padding-left:25px;<br />
font-style:bold;<br />
font-size: 18px;<br />
text-decoration:none;<br />
border:none;<br />
line-height:1em;<br />
padding:0px 0px 5px 5px;<br />
margin-top:20px;<br />
}<br />
<br />
h4<br />
{<br />
font-style:italic;<br />
}<br />
<br />
/*block for paper citations*/<br />
#citation_box<br />
{<br />
margin-top:30px;<br />
padding:10px;<br />
border-style:none;<br />
border-width:2px;<br />
border-color:#BDFEBC;<br />
background-color:#ECECEC;<br />
text-align:left;<br />
}<br />
<br />
#citation_box ol,li<br />
{<br />
text-style:italic;<br />
}<br />
<br />
#references<br />
{<br />
text-style:bold;<br />
text-size:14px;<br />
}<br />
<br />
table.parameter<br />
{<br />
width:100%; <br />
display: block; <br />
margin-left: auto; <br />
margin-right: auto; <br />
cellpadding:0px; <br />
cellspacing:0px;Experimentals_Parameters <br />
align:middle; <br />
}<br />
<br />
table.parameter td<br />
{<br />
padding:5px;<br />
}<br />
<br />
#table-fixed-size<br />
{<br />
table-layout:fixed;<br />
word-wrap: break-word;<br />
width:100px;<br />
}<br />
<br />
em {<br />
color: #cb6228;<br />
font-style: normal;<br />
font-weight:bold;<br />
}<br />
<br />
strong {<br />
color: #364d01;<br />
}<br />
<br />
.orange, a.orange:visited<br />
{<br />
color:#cb6228;<br />
}<br />
<br />
.green, a.green:visited<br />
{<br />
color:#364d01;<br />
}<br />
<br />
#param<br />
{<br />
border-collapse:collapse;<br />
text-align:center;<br />
}<br />
<br />
#param td, #param th<br />
{<br />
border: 1px solid black;<br />
padding:10px;<br />
}<br />
<br />
#team<br />
{<br />
padding:5px;<br />
}<br />
<br />
#team td<br />
{<br />
align:left;<br />
vertical-align:top;<br />
}<br />
<br />
.moredetails<br />
{<br />
width: 300px;<br />
text-align: left;<br />
background-color: #CEE9F4;<br />
border-radius: 7px;<br />
}<br />
<br />
.moredetails a<br />
{<br />
font-style: italic;<br />
font-weight: bold;<br />
}<br />
<br />
.moredetails a:hover<br />
{<br />
text-decoration:underline<br />
}<br />
<br />
.ania<br />
{<br />
color:#cb6228;<br />
}</div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-26T23:44:11Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" class="moredetails" style="position: relative; margin-left: auto; margin-right: auto; width: 400px; text-align: left; background-color: #cee9f4; border-radius: 7px; align: left"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/0/0f/French_frog.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog">More details here...</a><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem">More details here...</a><br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-26T23:43:15Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" style="position: relative; margin-left: auto; margin-right: auto; width: 400px; text-align: left; background-color: #cee9f4; border-radius: 7px; align: left"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/0/0f/French_frog.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog">More details here...</a><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem">More details here...</a><br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/ProjectTeam:Evry/Project2012-09-26T23:41:59Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<br />
<!-- contents --><br />
<br />
<html><br />
<h1>Project overview</h1><br />
<p><br />
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 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.<br />
</p><br />
<br />
<p><br />
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>. <br />
</p><br />
<br />
<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"><br />
<h3 style="text-align: center; padding-top:10px;">The French Froggies Project</h3><br><br />
<div id="item" style="margin-left:20px;"><br />
<ul><br />
<a href="#xenopus" style="text-decoration:none;"><li><i>Xenopus</i>: A new multicellular chassis</li></a><br />
<a href="#hormone" style="text-decoration:none;"><li>Intertissue communication: An orthogonal hormonal system </li></a><br />
<a href="#goldenBrick" style="text-decoration:none;"><li>GoldenBrick: A new biobrick cloning format</li></a><br />
<a href="#modeling" style="text-decoration:none;"><li>Modeling a tadpole: A multi-level approach</li></a><br />
<a href="#human" style="text-decoration:none;"><li>Human pratice: What does it mean to be a chassis?</a><br><br><br />
</ul><br />
</div><br />
</font><br />
</div><br><br><br />
<br />
<!-- Bannière Grenouille --><br />
<center> <img src="http://image.noelshack.com/fichiers/2012/27/1341654981-gregre.gif" width=800 /> </center><br />
<!-- #Bannière Grenouille --><br />
<br />
<br><br><br><br />
<!-- Xenopus Tropicalis --><br />
<h2 id="xenopus"><i>Xenopus</i>: A new multicellular chassis</h2><br />
<br />
<p><br />
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.<br />
</p><br />
<br />
<p><br />
<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.<br />
</p><br />
<br />
<br><br />
<div id="contourmenu" style="position: relative; margin-left: auto; margin-right: auto; width: 400px; text-align: left; background-color: #cee9f4; border-radius: 7px; align: left"><br />
<br />
<table style="background:transparent";><br />
<tr><td><img style="padding-top:10px;padding-left:10px;" src="https://static.igem.org/mediawiki/2012/0/0f/French_frog.png" width=80px></td><br />
<td><br />
<h3 style="text-align:center; padding-left:20px;"></u><br />
<br />
<a href="https://2012.igem.org/Team:Evry/FrenchFrog"><center>More details here...</center></a><br />
<br />
</u></h3></td><br />
</tr></table><br />
<br /><br />
</font><br />
</div><br />
<br />
<br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/FrenchFrog">More details here...</a><br />
<br />
<!-- AID System --><br />
<h2 id="hormone">Intertissue communication: An orthogonal hormonal system </h2><br />
<p><br />
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. <br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/AIDSystem">More details here...</a><br />
<br />
<!-- GoldenBrick --><br />
<h2 id="goldenBrick">GoldenBrick: A new biobrick cloning format</h2><br />
<p><br />
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!<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/GB">More details here...</a><br />
<br />
<!-- Modeling --><br />
<h2 id="modeling">Modeling a tadpole: A multi-level approach</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/Modeling">More details here...</a><br />
<br />
<!-- Human Practice --><br />
<h2 id="human">Human practice: What does it mean to be a chassis?</h2><br />
<p><br />
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.<br />
</p><br />
<a class="moredetails" target="_blank" href="https://2012.igem.org/Team:Evry/HumanPractice">More details here...</a><br />
<br><br><br />
<br />
<!--<br />
<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 />
<br /><br />
<p><a href="https://2012.igem.org/Team:Evry/Modeling">Visit the project page ></a></p><br />
<br /><br />
</font><br />
</div><br />
<br />
<h2 id="design"> style="text-decoration:none; color: white;"><b>Biotic games:</b> Better understanding of tadpole behavior through gaming</a></h2><br />
<p><a href="https://2012.igem.org/Team:Evry/BGame">Visit the project page ></a></p><br />
!--><br />
<br />
<br />
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE -- RDR --><br />
<br />
<div id="footer-wrapper"><br />
<div id="footer"><br />
<div id="f-poweredbyico"><a href="http://www.mediawiki.org/"><img src="/wiki/skins/common/images/poweredby_mediawiki_88x31.png" height="31" width="88" alt="Powered by MediaWiki" /></a></div> <div id="f-copyrightico"><a href="http://creativecommons.org/licenses/by/3.0/"><img src="http://i.creativecommons.org/l/by/3.0/88x31.png" alt="Attribution 3.0 Unported" width="88" height="31" /></a></div> <ul id="f-list"><br />
<br />
<br />
<!-- Recentchanges is not handles well DEBUG --><br />
<li id="t-recentchanges"><a href="/Special:RecentChanges"<br />
title='Recent changes'>Recent changes</a></li><br />
<br />
<li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"<br />
title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li><br />
<br />
<li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"<br />
title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li><br />
<br />
<br />
<br />
<li id="t-upload"><a href="/Special:Upload"<br />
title="Upload files [u]" accesskey="u">Upload file</a><br />
</li><br />
<li id="t-specialpages"><a href="/Special:SpecialPages"<br />
title="List of all special pages [q]" accesskey="q">Special pages</a><br />
<br />
</li><br />
<li><a href='/Special:Preferences'>My preferences</a></li><br />
</ul><br />
</div> <!-- close footer --><br />
<div id='footer'><br />
<ul id="f-list"><br />
<br />
<li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"<br />
title="Printable version of this page [p]" accesskey="p">Printable version</a><br />
<br />
</li><br />
<br />
<li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"<br />
title="Permanent link to this revision of the page">Permanent link</a><br />
</li><br />
<br />
<br />
<li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li><br />
<li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li><br />
</ul><br />
<br />
</div> <!-- close footer --><br />
</div> <!-- close footer-wrapper --><br />
</div><br />
</div><br />
</div><br />
</body><br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/FrenchFrogTeam:Evry/FrenchFrog2012-09-26T23:07:06Z<p>Tiff: </p>
<hr />
<div>{{:Team:Evry/template_v1}}<br />
<html><br />
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center><br />
<br />
<h2>Establishment of a new chassis</b></h2><br/><br />
<br />
<p>So far, synthetic biology has mostly focused on bacteria, since they are simple to engineer. iGEM teams and laboratories have met synthetic biology laboratories on unicellular organisms in order to understand the underlying biology and have developed an impressive database of molecular parts. Some work has also been done on engineering mammalian cells and a few iGEM teams have followed this trend. Synthetic biologists are now imagining the rational design of multicellular organisms with numerous applications ranging from gene therapy or drug production to environmental monitoring. This year, our team would like to be part of that challenge.</p><br />
<br />
<p>The arrival of <i>Xenopus</i> as a chassis in synthetic biology requires the creation of new standards and protocols that the community will be able to build on. We provided the registry with such tools that allow rapid construction and characterization of devices in vivo, and include debugging tools. We think they will be very useful for later iGEM teams and synthetic biologists who wish to work with <i>Xenopus</i> for building multicellular systems.</p><br />
<br />
<p>A multi-tissular systems allows testing protein effect into an animal. The expression/degradation of a protein (a protein fused to GFP in example) can be followed in the organism. <i>Xenopus</i> can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of <a href="http://www.oecd.org/chemicalsafety/testingofchemicals/41620749.pdf">detecting thyroid disruptor using <i>Xenopus</i></a>. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis <i>xenopus</i> because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.<br />
<br />
<!-- <p>You want to make the move from bacteria to multicellular synthetic biology ? Make sure you check out our Introduction to <i>Xenopus</i> page, and our Frogs for dummies page to make sure you are aware of all the differences between genetic engineering in eukaryotes.</p> --><br />
<br />
<p>This year, the Evry iGEM team is going to be the one of the first iGEM team to work on a vertebrate. Our work is focused both on developing a system for intercellular and intertissue communication, and creating the tools for the iGEM community to easily express genes in specific tissues. We believe the tadpole is a chassis of choice for iGEM on multicellular organisms, as experiments can be conducted in one week using microinjection methods. We hope to demonstrate the feasibility of engineering <i> Xenopus </i> in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: <br />
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.<br />
</p><br/><br />
<br />
<br />
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a><br />
<p><br />
<br/><i>Xenopus tropicalis</i> represents a challenge as it is a vertebrate but also because it's a new chassis in the iGEM competition. To make sure we meet iGEM’s expectations on time, we have had to develop a new biobrick plasmid backbone compatible with<i> Xenopus tropicalis</i> (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into <i>Xenopus</i>'s eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in <i>Xenopus</i>, the plasmid does not replicate. Therefore, it is only active in the first two or three weeks of development, as the injected plasmid is passed on randomly to daughter cells. After that, it becomes too diluted. <br />
<br/><br/></p><br />
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank"><br />
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/><br />
<br />
<ul><br />
<li><b>Kozac</b> : The Kozak consensus sequence is essential for the initiation of the translation process in eukaryotes. The sequence is the following (gcc)gccRccAUGG, where upper case letters are highly-conserved bases, and lower case letter can vary</li><br/><br />
<li><b>Promoter </b>: The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites <b>SalI</b> and <b>HindIII</b> in order to be able to switch more easily to other promoters</li><br/><br />
<li><b>5'UTR and 3’UTR</b> : UTRs are Untranslated Region. The B-globin 5' UTR is located upstream of the coding sequence and is involved in 5'RNA capping. The 3'UTR is located downstream of the coding sequence and may contain sequences for the regulation of translation efficiency, mRNA stability, and polyadenylation signals</li><br/><br />
<li><b>SV40 PolyA signal</b> : The simian virus 40 polyadenylation signal is involved in the maturation of the mRNA for translation and is composed of a succession of adenine bases </li><br/><br />
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/><br />
<li><b>Biobrick prefix and suffix</b></li><br/><br />
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/><br />
By putting all the parts necessary for expression in eukaryotes, we have made plasmids where any coding biobrick (containing Kozak sequence) can be cloned in directly without having to transfer each parts individually. These plasmids can be used to rapidly test genetic constructions in<i> Xenopus tropicalis</i> after a single cloning.<br/> It is possible to easily change promoter with the restriction sites SalI and HindIII. <br/><br />
The plasmid also contains tools to calibrate the system in combination with a model. For instance, it contains sites for in vitro transcription (sp6 sites) of genes to make RNA that can then be injected directly in the embryo, allowing a much finer control of the ratio between levels of different genes during construct testing. <br/><br />
<br/><br />
To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the <a href="https://2012.igem.org/Team:Evry/InjectionTuto" target="_blank">injecting tutorial</a>.For a plasmid of 4kb it represents approximately 45 million of plasmids per injection. As the cell divides, plasmids are shared between cells but not replicated so a high concentration of DNA is necessary to ensure there will be DNA in most of the organism. Once the transcription machinery turns on during the development, plasmids are transcribed and translated. Since the tadpole stage starts after a few days, we can work on a whole vertebrate with most organs formed within a week. With different tissues it is possible to diversify the type of expression with different promoters.<br />
<br/><br />
<br/><br />
So far we have made 3 new plasmid backbones with different promoters :<br />
<br/><br/><br />
<li>With a <b>CMV promoter</b> for an ubiquitous expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>), <br />
<li>With a <b>Hsp70 promoter</b> for an inducible expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),<br />
<li>With a <b>Elastase promoter</b> for a tissue specific expression :<br />
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li><br />
<br/><br />
<br />
Our goal was to provide tools which would allow to rapidly build and characterize constructs in the embryos (along with a synthetic hormone to make them communicate), with tools for debugging (by injecting mRNA) and with ubiquitous, inducible and tissue specific promoters.<br />
</ul><br />
<br />
<br />
<br/><br/><br/><br />
<br />
<br />
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/><br />
<br />
<p>The <a href="https://2012.igem.org/Team:Evry/InjectionTuto">injection tutorial</a> explains very simply with diagram how we did injection and how take care about your embryos and tadpole. The experiment carries on 5 days, from the unfertilized egg to a swimming tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).<br />
<br />
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/><br />
<br />
<p>pCS2+ GFP-aid: this plasmid contains the constitutive and ubiquitous promoter CMV and the aid sequenced of the aid system fusionned to GFP (Green Fluorescent Protein)(Nishimura et al., 2009), this Biobrick created by our team is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812010">BBa_K812010</a>, and it was integrated into our Eucaryotic plasmid <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K812000">BBa_K812000</a>.We injected about 3.78E+7 plasmids.</p><br/><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" /> <br />
</b></b><br />
<p><br />
GFP-aid expression from the embryo at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> 20 (one day after injection )to a tadpole at <a href="https://2012.igem.org/Team:Evry/Stages">stage</a> ~46 (four days after injection). For this tadpole the expression is localized in the skin.</b></b></b><br />
</p><br />
<br />
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.<br />
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<br><br><br />
<h4><b>The characterization of all reporter and promoters is <u><a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a></u>.</b></h4><br><br />
<br />
<h2>Conclusion</h2><br/><br />
<br />
<p>This new BioBricked plasmid is ready to use in <i>Xenopus tropicalis</i>. As you can see above the plasmid pCS2+ with the CMV pomoter express the fluorescent protein GFP-aid, but this plasmid carry on important things to express a gene into eukaryotic calls. The 5'UTR region and the 3' UTR region was needed for gene expression in euklaryotic organism. The simplest way to do that was to use a plasmid already used in eukaryotic cells, vertebrate and especially <i>Xenopus tropicalis</i> as pCS2+. This pCS2+ was Biobricked to be compatible with the registry. <br><br />
<br />
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: <a href="https://2012.igem.org/Team:Evry/Tadpole_injection1">here</a>.<br><br />
<br />
<p><br />
Nevertheless we expected a more uniform expression of the reporters with the CMV promoter. Within tadpole, fluorescent proteins were observed in one to four different tissues, and tissues were different between tadpoles.<br />
</p><br />
<br />
<p><br />
Explanation: The plasmid DNA does not diffuse in the egg and stay in the same area around the injection site. This means that depending on the injection site, the plasmid will be inherited by a given set of cells within the tadpole. This question was raised in our <a href="https://2012.igem.org/Team:Evry/plasmid_splitting">model</a>. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.<br />
</p><br />
<br />
<p><br />
Our experiment showed us that plasmids injected do not diffuse in the whole organism. To express a protein with a promoter tissue specific it is a problem, because of the very low the probability to have the plasmid into the expected tissue. To solve the problem it is possible to easily integrate promoters and genes into the <i>Xenopus</i>'s chromosome with the REMI technic [3]. A new plasmid pCS2+ with I-SceI sites upstream the promoter and downstream of the reporter could allow the integration of the sequence between this two I-SceI restriction sites. This plasmid could be useful for the eukaryotic community, they could change promoters easily with SalI and HindIII and the reporter is compatible with the registry (with BB prefix and suffix), and they would have the choice to test a construction by plasmid injection or DNA chromosome integration.<br />
</p><br />
<br />
<p><br />
Moreover, the expression of reporters decreases during time, because plasmid DNA is subjected to a catabolic activity during development but also plasmid DNA gets diluted as cells proliferate and the quantity of plasmid DNA decreases for each cell. Integration into the chromosome could prevent it. <br />
</p><br />
<br />
<p><br />
Our project raised important ethics question because the team use tadpole, an animal. We reflect that working with tadpole involved new questions about the animal pain but also about using animals in iGEM and in Synthetic Biology. It made us think about these questions, our reflection is in <a href="https://2012.igem.org/Team:Evry/HumanPractice">Human Practice</a>.</p><br><br />
<br />
<div id="citation_box"><br />
<p id="references">References:</p><br />
<ol><br />
<li><i>Inducible control of tissue-specific transgene expression in <i>Xenopus</i> tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li><br />
<br />
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li><br />
<br />
<li><i>REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants</li> Kahmann R., Basse C., European Journal of Plant Pathology</li><br />
</ol><br />
</div><br />
<br><br />
<br />
<script type="text/javascript">writeFooter()</script> <br />
</html></div>Tiffhttp://2012.igem.org/Team:Evry/main-img.jsTeam:Evry/main-img.js2012-09-26T21:32:08Z<p>Tiff: </p>
<hr />
<div>(function($){<br />
<br />
var Renderer = function(elt){<br />
var dom = $(elt)<br />
var canvas = dom.get(0)<br />
var ctx = canvas.getContext("2d");<br />
var gfx = arbor.Graphics(canvas)<br />
var sys = null<br />
<br />
var _vignette = null<br />
var selected = null,<br />
nearest = null,<br />
_mouseP = null;<br />
<br />
<br />
var that = {<br />
init:function(pSystem){<br />
sys = pSystem<br />
sys.screen({size:{width:dom.width(), height:dom.height()},padding:[36,60,36,60]})<br />
<br />
$(window).resize(that.resize)<br />
that.resize()<br />
that._initMouseHandling()<br />
<br />
if (document.referrer.match(/Goldenbricks|Plasmids|AIDSystem/)){<br />
// if we got here by hitting the back button in one of the Benchwork, <br />
// start with the Benchwork section pre-selected<br />
that.switchSection('Benchwork')<br />
}<br />
},<br />
resize:function(){<br />
// canvas.width = .5* $(window).width()<br />
// canvas.height = .5* $(window).height()<br />
sys.screen({size:{width:canvas.width, height:canvas.height}})<br />
_vignette = null<br />
that.redraw()<br />
},<br />
redraw:function(){<br />
gfx.clear()<br />
sys.eachEdge(function(edge, p1, p2){<br />
if (edge.source.data.alpha * edge.target.data.alpha == 0) return<br />
gfx.line(p1, p2, {stroke:"#b2b19d", width:3, alpha:edge.target.data.alpha})<br />
})<br />
sys.eachNode(function(node, pt){<br />
var w = Math.max(20, 20+gfx.textWidth(node.name) )<br />
if (node.data.alpha===0) return<br />
<br />
if (node.data.shape=='img'){<br />
var img_elem = new Image();<br />
img_elem.src = node.data.url;<br />
ctx.drawImage(img_elem, pt.x-w/2, pt.y-w/2, w, w); // Redimensionnement de l'image prévue comme tu le souhaitais !<br />
gfx.oval(pt.x-w/2, pt.y-w/2, w, w, {fill:node.data.color, alpha:0})<br />
}<br />
<br />
else if (node.data.shape=='dot'){<br />
gfx.oval(pt.x-w/2, pt.y-w/2, w, w, {fill:node.data.color, alpha:node.data.alpha})<br />
gfx.text(node.name, pt.x, pt.y+7, {color:"white", align:"center", font:"Arial", weight:"bold", size:12}) <br />
}<br />
<br />
else{<br />
gfx.rect(pt.x-w/2, pt.y-8, w, 20, 4, {fill:node.data.color, alpha:node.data.alpha})<br />
gfx.text(node.name, pt.x, pt.y+9, {color:"white", align:"center", font:"Arial", size:12})<br />
gfx.text(node.name, pt.x, pt.y+9, {color:"white", align:"center", font:"Arial", size:12})<br />
}<br />
})<br />
that._drawVignette()<br />
},<br />
<br />
_drawVignette:function(){<br />
var w = canvas.width<br />
var h = canvas.height<br />
var r = 20<br />
<br />
if (!_vignette){<br />
var top = ctx.createLinearGradient(0,0,0,r)<br />
top.addColorStop(0, "#e0e0e0")<br />
top.addColorStop(.7, "rgba(255,255,255,0)")<br />
<br />
var bot = ctx.createLinearGradient(0,h-r,0,h)<br />
bot.addColorStop(0, "rgba(255,255,255,0)")<br />
bot.addColorStop(1, "white")<br />
<br />
_vignette = {bot:bot}<br />
}<br />
<br />
// top<br />
ctx.fillStyle = _vignette.top<br />
ctx.fillRect(0,0, w,r)<br />
<br />
// bot<br />
ctx.fillStyle = _vignette.bot<br />
ctx.fillRect(0,h-r, w,r)<br />
},<br />
<br />
switchMode:function(e){<br />
if (e.mode=='hidden'){<br />
dom.stop(true).fadeTo(e.dt,0, function(){<br />
if (sys) sys.stop()<br />
$(this).hide()<br />
})<br />
}else if (e.mode=='visible'){<br />
dom.stop(true).css('opacity',0).show().fadeTo(e.dt,1,function(){<br />
that.resize()<br />
})<br />
if (sys) sys.start()<br />
}<br />
},<br />
<br />
switchSection:function(newSection){<br />
var parent = sys.getEdgesFrom(newSection)[0].source<br />
var children = $.map(sys.getEdgesFrom(newSection), function(edge){<br />
return edge.target<br />
})<br />
<br />
sys.eachNode(function(node){<br />
if (node.data.shape=='dot') return // skip all but leafnodes<br />
if (node.data.shape=='img') return // skip all but leafnodes<br />
var nowVisible = ($.inArray(node, children)>=0)<br />
var newAlpha = (nowVisible) ? 1 : 0<br />
var dt = (nowVisible) ? .5 : .5<br />
sys.tweenNode(node, dt, {alpha:newAlpha})<br />
<br />
if (newAlpha==1){<br />
node.p.x = parent.p.x + .05*Math.random() - .025<br />
node.p.y = parent.p.y + .05*Math.random() - .025<br />
node.tempMass = .001<br />
}<br />
})<br />
},<br />
<br />
<br />
_initMouseHandling:function(){<br />
// no-nonsense drag and drop (thanks springy.js)<br />
selected = null;<br />
nearest = null;<br />
var dragged = null;<br />
var oldmass = 1<br />
<br />
var _section = null<br />
<br />
var handler = {<br />
moved:function(e){<br />
var pos = $(canvas).offset();<br />
_mouseP = arbor.Point(e.pageX-pos.left, e.pageY-pos.top)<br />
nearest = sys.nearest(_mouseP);<br />
<br />
if (!nearest.node) return false<br />
<br />
// if (nearest.node.data.shape!='dot'){<br />
selected = (nearest.distance < 50) ? nearest : null<br />
if (selected){<br />
dom.addClass('linkable')<br />
window.status = selected.node.data.link//.replace(/^\//,"http://"+window.location.host+"/")//.replace(/^#/,'')<br />
}<br />
else{<br />
dom.removeClass('linkable')<br />
window.status = ''<br />
}<br />
// }else <br />
if ($.inArray(nearest.node.name, ['The French Froggies Project!','Xenopus as a chassis','Hormonal Communication','Modeling','GoldenBricks', 'Human Practice', 'The Team']) >=0 ){<br />
if (nearest.node.name!=_section){<br />
_section = nearest.node.name<br />
that.switchSection(_section)<br />
}<br />
dom.removeClass('linkable')<br />
window.status = ''<br />
}<br />
<br />
return false<br />
},<br />
clicked:function(e){<br />
var pos = $(canvas).offset();<br />
_mouseP = arbor.Point(e.pageX-pos.left, e.pageY-pos.top)<br />
nearest = dragged = sys.nearest(_mouseP);<br />
<br />
if (nearest && selected && nearest.node===selected.node){<br />
var link = selected.node.data.link<br />
if (link.match(/^#/)){<br />
$(that).trigger({type:"navigate", path:link.substr(1)})<br />
}else{<br />
window.location = link<br />
}<br />
return false<br />
}<br />
<br />
<br />
if (dragged && dragged.node !== null) dragged.node.fixed = true<br />
<br />
$(canvas).unbind('mousemove', handler.moved);<br />
$(canvas).bind('mousemove', handler.dragged)<br />
$(window).bind('mouseup', handler.dropped)<br />
<br />
return false<br />
},<br />
dragged:function(e){<br />
var old_nearest = nearest && nearest.node._id<br />
var pos = $(canvas).offset();<br />
var s = arbor.Point(e.pageX-pos.left, e.pageY-pos.top)<br />
<br />
if (!nearest) return<br />
if (dragged !== null && dragged.node !== null){<br />
var p = sys.fromScreen(s)<br />
dragged.node.p = p<br />
}<br />
<br />
return false<br />
},<br />
<br />
dropped:function(e){<br />
if (dragged===null || dragged.node===undefined) return<br />
if (dragged.node !== null) dragged.node.fixed = false<br />
dragged.node.tempMass = 1000<br />
dragged = null;<br />
// selected = null<br />
$(canvas).unbind('mousemove', handler.dragged)<br />
$(window).unbind('mouseup', handler.dropped)<br />
$(canvas).bind('mousemove', handler.moved);<br />
_mouseP = null<br />
return false<br />
}<br />
<br />
<br />
}<br />
<br />
$(canvas).mousedown(handler.clicked);<br />
$(canvas).mousemove(handler.moved);<br />
<br />
}<br />
}<br />
<br />
return that<br />
}<br />
<br />
<br />
var Nav = function(elt){<br />
var dom = $(elt)<br />
<br />
var _path = null<br />
<br />
var that = {<br />
init:function(){<br />
$(window).bind('popstate',that.navigate)<br />
dom.find('> a').click(that.back)<br />
$('.more').one('click',that.more)<br />
<br />
$('#Model dl:not(.datastructure) dt').click(that.reveal)<br />
that.update()<br />
return that<br />
},<br />
more:function(e){<br />
$(this).removeAttr('href').addClass('less').html('&nbsp;').siblings().fadeIn()<br />
$(this).next('h2').find('a').one('click', that.less)<br />
<br />
return false<br />
},<br />
less:function(e){<br />
var more = $(this).closest('h2').prev('a')<br />
$(this).closest('h2').prev('a')<br />
.nextAll().fadeOut(function(){<br />
$(more).text('creation & use').removeClass('less').attr('href','#')<br />
})<br />
$(this).closest('h2').prev('a').one('click',that.more)<br />
<br />
return false<br />
},<br />
reveal:function(e){<br />
$(this).next('dd').fadeToggle('fast')<br />
return false<br />
},<br />
back:function(){<br />
_path = "/"<br />
if (window.history && window.history.pushState){<br />
window.history.pushState({path:_path}, "", _path);<br />
}<br />
that.update()<br />
return false<br />
},<br />
navigate:function(e){<br />
var oldpath = _path<br />
if (e.type=='navigate'){<br />
_path = e.path<br />
if (window.history && window.history.pushState){<br />
window.history.pushState({path:_path}, "", _path);<br />
}else{<br />
that.update()<br />
}<br />
}else if (e.type=='popstate'){<br />
var state = e.originalEvent.state || {}<br />
_path = state.path || window.location.pathname.replace(/^\//,'')<br />
}<br />
if (_path != oldpath) that.update()<br />
},<br />
update:function(){<br />
var dt = 'slow'<br />
if (_path===null){<br />
// this is the original page load. don't animate anything just jump<br />
// to the proper state<br />
_path = window.location.pathname.replace(/^\//,'')<br />
dt = 0<br />
dom.find('p').css('opacity',0).show().fadeTo('slow',1)<br />
}<br />
<br />
switch (_path){<br />
case '':<br />
case '/':<br />
// dom.find('p').text('a graph visualization library using web workers and jQuery')<br />
dom.find('> a').removeClass('active').attr('href','#')<br />
<br />
$('#Model').fadeTo('fast',0, function(){<br />
$(this).hide()<br />
$(that).trigger({type:'mode', mode:'visible', dt:dt})<br />
})<br />
document.title = "The French Froggies Project!"<br />
break<br />
<br />
}<br />
<br />
}<br />
}<br />
return that<br />
}<br />
<br />
$(document).ready(function(){<br />
var CLR = {<br />
branch:"#b2b19d",<br />
level3benchwork:"#FFBF3E",<br />
level3model:"#4B86C7"<br />
}<br />
/*Thibault BEGIN*/<br />
var theUI = {<br />
<br />
// ['The French Froggies Project!','Xenopus as a chassis','Hormonal Communication','Modeling','GoldenBricks', 'Human Practices', 'The Team']<br />
<br />
nodes:{"The French Froggies Project!":{color:"#51C215", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/Project', url:'https://static.igem.org/mediawiki/2012/1/19/Button1.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
<br />
"Xenopus as a chassis":{color:"#1A5291", shape:"dot", alpha:1, link:'FrenchFrog', url:'ResultsbuttonLowRes.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"Creation of new Xenopus plasmids":{color:CLR.level3model, alpha:0, link:'FrenchFrog#plasmid'},<br />
"How to micro inject in Xenopus eggs":{color:CLR.level3model, alpha:0, link:'InjectionTuto'},<br />
"Development stages":{color:CLR.level3model, alpha:0, link:'Stages'},<br />
"Characterization of plasmids and reporters":{color:CLR.level3model, alpha:0, link:'Tadpole_injection1'},<br />
<br />
"Hormonal Communication":{color:"#1A5291", shape:"img", alpha:1, link:'AIDSystem', url:'https://static.igem.org/mediawiki/2012/a/a0/Button6.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"The auxin emmiter":{color:CLR.level3model, alpha:0, link:'AIDSystem#auxin'},<br />
"The auxin receiver":{color:CLR.level3model, alpha:0, link:'AIDSystem#AID'},<br />
"Auxin toxicity":{color:CLR.level3model, alpha:0, link:'AuxinTOX'},<br />
"Auxin Uptake":{color:CLR.level3model, alpha:0, link:'auxin_uptake'},<br />
<br />
"Modeling":{color:"#1A5291", shape:"img", alpha:1, link:'Modeling', url:'https://static.igem.org/mediawiki/2012/5/55/Button5.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"General Model":{color:CLR.level3model, alpha:0, link:'ODE_model'},<br />
"Rigorous derivations of ODEs":{color:CLR.level3model, alpha:0, link:'auxin_pde'},<br />
"Diffusion in a realistic geometry":{color:CLR.level3model, alpha:0, link:'Auxin_diffusion'},<br />
"Auxin production":{color:CLR.level3model, alpha:0, link:'auxin_production'},<br />
"Auxin reception":{color:CLR.level3model, alpha:0, link:'auxin_detection'},<br />
"Plasmid diffusion":{color:CLR.level3model, alpha:0, link:'plasmid_splitting'},<br />
"Model integration":{color:CLR.level3model, alpha:0, link:'model_integration'},<br />
<br />
"GoldenBricks":{color:"#1A5291", shape:"img", alpha:1, link:'GB', url:'https://static.igem.org/mediawiki/2012/f/fd/Button3.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
<br />
"Human Practice":{color:"#1A5291", shape:"img", alpha:1, link:'https://2012.igem.org/Team:Evry/HumanPractice/HumanPractice', url:'https://static.igem.org/mediawiki/2012/8/8f/Button2.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"Hi Xenope!":{color:CLR.level3model, alpha:0, link:'Team:Evry/HumanPractice/Introduction'},<br />
"Would you be my chassis?":{color:CLR.level3model, alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/HumanPractice/modelorganism'},<br />
"Freed the frogs!":{color:CLR.level3model, alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/freedthefrogs'},<br />
"I'm a chassis, really?":{color:CLR.level3model, alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/HumanPractice/chassis'},<br />
"Should we work with Xenopus again?":{color:CLR.level3model, alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/HumanPractice/future'},<br />
"What the laws says...":{color:CLR.level3model, alpha:0, link:'https://2012.igem.org/Team:Evry/HumanPractice/HumanPractice/others'},<br />
<br />
"The Team":{color:"#1A5291", shape:"img", alpha:1, link:'Team', url:'https://static.igem.org/mediawiki/2012/5/53/Button4.png'}, //Attribut url pour l'image ajouté /*Thibault*/<br />
"Our Team":{color:CLR.level3model, alpha:0, link:'Team'},<br />
"Our Sponsors":{color:CLR.level3model, alpha:0, link:'Sponsors'},<br />
"Attributions":{color:CLR.level3model, alpha:0, link:'Attributions'},<br />
"Official profile":{color:CLR.level3model, alpha:0, link:'https://igem.org/Team.cgi?year=2012'},<br />
"Collaborations":{color:CLR.level3model, alpha:0, link:'Collaboration'}<br />
},<br />
<br />
edges:{<br />
<br />
<br />
"The French Froggies Project!":{<br />
"Xenopus as a chassis":{"length":0.4,"weight":2},<br />
"Hormonal Communication":{"length":0.6,"weight":2},<br />
"Modeling":{"length":0.4,"weight":2},<br />
"GoldenBricks":{"length":1.5,"weight":2},<br />
"Human Practice":{"length":0.75,"weight":2},<br />
"The Team":{"length":0.5,"weight":2}<br />
},<br />
<br />
<br />
"Xenopus as a chassis":{<br />
"Creation of new Xenopus plasmids":{"length":0.75,"weight":1},<br />
"How to micro inject in Xenopus eggs":{"length":0.75,"weight":2},<br />
"Development stages":{"length":0.75,"weight":2},<br />
"Characterization of plasmids and reporters":{"length":0.75,"weight":2}<br />
},<br />
"Hormonal Communication":{<br />
"The auxin emmiter":{"length":1,"weight":2},<br />
"The auxin receiver":{"length":1,"weight":2},<br />
"Auxin toxicity":{"length":1,"weight":2},<br />
"Auxin Uptake":{"length":1,"weight":2}<br />
<br />
},<br />
<br />
"Modeling":{<br />
"General Model":{"length":0.5,"weight":2},<br />
"Rigorous derivations of ODEs":{"length":0.5,"weight":2},<br />
"Diffusion in a realistic geometry":{"length":0.75,"weight":2},<br />
"Auxin production":{"length":0.5,"weight":2},<br />
"Auxin reception":{"length":0.5,"weight":2},<br />
"Plasmid diffusion":{"length":0.5,"weight":2},<br />
"Model integration":{"length":0.5,"weight":2}<br />
<br />
},<br />
<br />
"GoldenBricks":{},<br />
<br />
<br />
"Human Practice":{<br />
"Hi Xenope!":{"length":0.5,"weight":2},<br />
"Would you be my chassis?":{"length":0.5,"weight":2},<br />
"Freed the frogs!":{"length":0.5,"weight":2},<br />
"I'm a chassis, really?":{"length":0.5,"weight":2},<br />
"Should we work with Xenopus again?":{"length":0.5,"weight":2},<br />
"What the laws says...":{"length":0.5,"weight":2}<br />
},<br />
<br />
"The Team":{<br />
"Our Team":{"length":0.5,"weight":2},<br />
"Our Sponsors":{"length":0.5,"weight":2},<br />
"Attributions":{"length":0.5,"weight":2},<br />
"Official profile":{"length":0.5,"weight":2},<br />
"Collaborations":{"length":0.5,"weight":2}<br />
}<br />
}<br />
}<br />
/*Thibault END*/<br />
<br />
var sys = arbor.ParticleSystem()<br />
sys.parameters({stiffness:900, repulsion:50, gravity:true, dt:0.015})<br />
sys.renderer = Renderer("#sitemap")<br />
sys.graft(theUI)<br />
<br />
var nav = Nav("#nav")<br />
$(sys.renderer).bind('navigate', nav.navigate)<br />
$(nav).bind('mode', sys.renderer.switchMode)<br />
nav.init()<br />
})<br />
})(this.jQuery)</div>Tiff