Team:Evry/FrenchFrog

From 2012.igem.org

(Difference between revisions)
 
(140 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:Evry/template_v1}}
{{:Team:Evry/template_v1}}
-
 
<html>
<html>
-
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.6.2/jquery.min.js" type="text/javascript"></script>
+
<center><h1><b><i>Xenopus tropicalis</i>: A new multicellular chassis</b></h1></center>
-
<script type="text/javascript">
+
-
$(function(){
+
-
  $('#btn_up').click(function() {
+
-
    $('html,body').animate({scrollTop: 0}, 'slow');
+
-
  });
+
-
  $(window).scroll(function(){
+
<h2>Establishment of a new chassis</b></h2><br/>
-
    if($(window).scrollTop()<500){
+
-
        $('#btn_up').fadeOut();
+
-
    }else{
+
-
        $('#btn_up').fadeIn();
+
-
    }
+
-
  });
+
-
});
+
-
</script>
+
-
<div id="btn_up" style="position: fixed; bottom: 15px; right: 25px; cursor: pointer; display:none;">
+
-
<img alt="Top_arrow" title="Top" src="http://image.noelshack.com/fichiers/2012/26/1341100852-fleche.png" width="40" />
+
-
</div>
+
-
<h1><b>The French froggies:</b> an artificial hormonal system in tadpoles</h1>
+
<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>
 +
<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>
-
<center>The Evry iGEM team is proud to introduce you to our new project: <b>The French Froggies!</b>
+
                <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.
-
<table>
+
-
<tr>
+
-
<td>
+
-
</html>
+
-
[[File:FrenchTouch.jpg|center|300px]]
+
-
<html>
+
-
</td>
+
-
<td>
+
-
</html>
+
-
[[File:Frogncorn.png|center|300px]]
+
-
<html>
+
-
</td>
+
-
</tr>
+
-
</table>
+
-
</center>
+
-
<h2>Establishment of a new chassis</b></h2>
+
<!-- <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> -->
-
</html>
+
-
<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:
 +
<a href="https://2012.igem.org/Team:Evry/AIDSystem">An orthogonal hormonal system</a>.
 +
</p><br/>
-
[[File:Igem-logo.png|left|130px]]
 
-
<p>So far, the engineering of living organisms has mostly been focused on bacteria, as being the simplest organism to engineer. iGEM teams and laboratories have focused on unicellular organisms in order to understand the principles underlying biology and has developed a quite comprehensive database of molecular part. Some work has been started on engineering mammalian cells and a few iGEM team had followed this trend. It is generally admitted that synthetic biology is now heading toward rational design of multicellular organisms with numerous applications ranging from gene therapy, drug production or environmental applications. This year, our team would like to be part of that challenge.</p>
+
<a name="plasmid" /><h3>The simple molecular strategy to build eukaryotic plasmid ready to use: </h3></a>
 +
<p>
 +
<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/></p>
 +
<a href="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" target="_blank">
 +
<img src="https://static.igem.org/mediawiki/2012/0/0e/French_froggies_scheme2.1.png" alt="Image unavailable" width="950px" /> </a><br/>
-
 
+
<ul>
-
[[File:tadpole.png|right|200px]]
+
<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/>
-
 
+
<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/>
-
<p>Frogs, as well as nematodes, flies and mice have been used for a long time as organisms of choice to study the fundamental principles of biology in multicellular organisms, and an all range of genetic and micro injection techniques have been developed for them. But so far, very little work has been done in engineering <i>de-novo</i> systems in these organisms, as we are aiming at in synthetic biology.</p>
+
<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/>
-
 
+
<li><b>Antibiotic resistance genes</b> : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic</li><br/>
-
[[File:parts.png|left]]
+
<li><b>Biobrick prefix and suffix</b></li><br/>
-
 
+
<li><b>Origin of replication</b> : This origin of replication is bacterial, this sequence initiates the replication of DNA</li><br/>
-
<p>This year, the <b>Evry iGEM team</b> is going to be the very first iGEM team to work on a vertebrate, and our work is focused both on developing genetic tools and standard protocols for the iGEM community. We believe the tadpole is a chassis of choice for iGEM on multi cellular organisms, and we would like to demonstrate the feasibility of engineering <i>Xenopus Laevis</i> and <i>Xenopus trocicalis</i> in the iGEM time and technological constraints through the development of a very original project: the development of a new orthogonal hormonal system in <i>Xenopus</i>.</p>
+
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/>
-
 
+
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/>
-
<html>
+
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.
-
<h2>Engineering a new orthogonal hormonal system</h2>
+
<br/>
-
</html>
+
<br/>
 +
So far we have made 3 new plasmid backbones with different promoters :
 +
<br/><br/>
 +
<li>With a <b>CMV promoter</b> for an ubiquitous expression :
 +
(<a href="http://partsregistry.org/Part:BBa_K812000" target="_blank">BBa_K812000</a>),
 +
<li>With a <b>Hsp70 promoter</b> for an inducible expression :
 +
(<a href="http://partsregistry.org/Part:BBa_K812300" target="_blank">BBa_K812300</a>),
 +
<li>With a <b>Elastase promoter</b> for a tissue specific expression :
 +
(<a href="http://partsregistry.org/Part:BBa_K812200" target="_blank">BBa_K812200</a>). </p></li>
<br/>
<br/>
-
<p>Our project this year is to demonstrate the feasibility of building <i>de-novo</i> a new hormonal system, in <i>Xenopus Tropicalis</i>, orthogonal to any endogenous hormonal system existing in the tadpole. A hormone (from Greek ὁρμή, "impetus") is a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism. In essence, it is a chemical messenger that transports a signal from one tissue to another. In a synthetic biology approach, it is a communication device, and an extensive work has been done on bacteria to engineer such systems, mostly using quorum sensing molecules.</p>
+
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.
 +
</ul>
-
<p>We had to choose 2 organs we would like to make communicate. The choice of these organs has been set on the specific properties of the tissues in term of function and blood irrigation as well as on the existence of reported functioning tissue specific promoters. As an emitter, we chose to use the skin, and as a receiver, the kidney. We are going to described the reason of these choices now.</p>
 
-
[[File:general_hormonal_schematic.png|center|750px]]
+
<br/><br/><br/>
-
<center><i><b>Fig 1:</b> Main schematic of our system. The skin is used as an emitter, the kidney as a receiver;</i></center>
+
-
<br />
+
-
<p>In order to trigger the emission of the hormone in our synthetic hormonal system we wanted to dissolve a chemical in the water of the tadpole that would activate an indicible promoter. The most exposed tissue to the chemical environment is undoubtely the epithelium, because of the important surface exposed to the water. On the top of it, this tissue is highly vascularized, which is important to acheive a high concentration of auxin in the blood. An important library of promoter has also been identified for this tissue.</p>
 
-
<br />
 
-
[[File:promoter_skin.png|center]]
 
-
<center><i><b>Fig 2:</b> Picture of a tadpole expression GFP through a skin specific promoter.</i></center>
 
-
<p>The problem of introducing a non native hormon into the blood is that the kidney is likely to eliminate it from the blood. The kidney works as an inverted filter, in the sense that it takes out every molecule from the blood and reintroduce only the one it knows, and our hormon does not nessarily belongs to these molecule. Therefore, we can anticipate that the course of your molecule will ends up there and it will be the place where it is the most concentrated. This organ seems to be the best place for expressing our receiver system. There are also good promoters coming from the different ion channels that are known to work there.</p>
+
<h2>Example of GFP expression in <i>Xenopus</i></h2><br/>
-
<br />
+
-
[[File:promoter_kidney.png|center|300px]]
+
-
<center><i><b>Fig 3:</b> Image of a tadpole kidney.</i></center>
+
-
<br />
+
-
<p>This project is the first known example of a rationally designed homonal system in a pluricellular organism. On the top of being an important technological acheivement, it demonstrates the capability to engineer deeply fundamental mechanisms in pluricellular organisms and demonstrate further that the tadpole is a good system to engineer biosensors</p>
+
<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 />
+
<h3>Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter</h3><br/>
-
<html>
+
<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/>
-
<h2>Using the auxin as an orthogonal hormone</h2>
+
-
</html>
+
<img src="https://static.igem.org/mediawiki/2012/c/cc/Tadpole_de_la_mort.png" alt="Image unavailable" width="950px" />  
 +
</b></b>
 +
<p>
 +
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>
 +
</p>
-
<br />
+
We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70.
-
<p>The molecule we have choosen to use is a plant hormone called auxin (IAA), well known for beeing responsible for the plant and the roots growth. A very extensive work has been done on this hormon in <i>E. coli</i> and <i>Arabidopsis Thaliana</i> last year by the  [https://2011.igem.org/Team:Imperial_College_London/Tour 2011 Imperial College of London iGEM team].</p>
+
Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.<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>
-
<p>Auxin is a molecule of choice for working on tadpole. It is amphiphilic and hydrophobic so we assume it can cross the biological membrane easily and its toxicity is reported to be very weak. It can be synthetized in a two steps pathway from a tryprophane precursor and a cytosolic receptor for this hormone from the rice has been shown to work in mammalian cells successfully [https://2012.igem.org/Team:Evry/FrenchFrog#references].</p>
+
<h2>Conclusion</h2><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>
-
[[File:auxin_patw.png|center|600px]]
+
-
<center><i><b>Fig 4:</b> The auxinsynthetic pathway, developped by the 2011 Imperial College iGEM Team</i></center>
+
-
<br />
+
-
<p>The first part of the project consists in reengineering the auxin synthetic pathway for it to be expressed in the tadpole and produce auxin. Once the system will be functionnal, we will put it under the control of an inducible skin specific promoter. We anticipate that the auxine produced will diffuse through the membrane and gets in the blood and would reach the receiver in the kidney.</p>
+
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>
-
<html>
+
<p>
-
<h2>Auxin Inductible Degron system</h2>
+
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.
-
</html>
+
</p>
-
<br />
+
-
<p>One key requirement for the creation of a synthetic hormonal system was to find a cytosolic hormone receptor. We came across a very ingenious system developped by Masato Kanemaki laboratory coming from rice and that has been reported to work and patented in mammalian cells [https://2012.igem.org/Team:Evry/FrenchFrog#references] but not in tadpoles.</p>
+
<p>
 +
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.
 +
</p>
-
<p>This system is based on the E3 ubiquitinase SCF-TIR1, that is capable, in the presence of auxin to recognise a GFP tagged with the AID degron. When auxin is present in the cytosol, TIR1 binds to the degron and recruits the E2 ubiquitinase that adds the ubiquitine tag to the GFP. Then, the GFP is gedraded by the proteasome, giving a decrease in the fluorescence of the tissue.</p>
+
<p>
 +
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.
 +
</p>
-
<br />
+
<p>
 +
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.
 +
</p>
-
[[File:Auxin-degron.png|center|750px]]
+
<p>
-
<center><i><b>Fig 5:</b> The SRC-TIR1 GFP-degron system</i></center>
+
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 />
 
-
 
-
<p>The first step of this part of the project is to reconstruct the TIR1-degron system in the tadpole under the contol of a CMV promoter and tests is the system can react to the auxine diluted in the water of the tadpole. Then, we will move the system under the control of a kidney specific promoter and test its response to the auxin secreted in the blood.</p> 
 
-
 
-
<br />
 
-
<html>
 
-
<h2>Modeling, Human practice and Safety</h2>
 
-
<br />
 
-
 
-
<p>Modeling an integrated system at the organism level is something that is not nessarily new, because some intensive work has been done in the past in modeling physiological functions, but it is the first time that people are going to model synthetic physological function. In this work, using a combination of differential equation and agent based modeling we are going to tackle the entire system, and provide modeling tools and ideas for the future generation of iGEMers that are going to work on multicellular organisms.</p>
 
-
 
-
<p>This project has also a lot of ethical and safety implications that we are aware of and that we will also address. Please visit our Safety and Human practice pages for more details.</p>
 
-
 
-
<!-- contents -->
 
-
 
-
<div id="contourmenu" style="position: relative; margin-left: auto; margin-right: auto; width: 400px; text-align: left; background-color: #cee9f4; border-radius: 7px;">
 
-
<h3 style="text-align: left; padding-top:10px;">Link out</h3>
 
-
<div id="item" style="margin-left:10px;">
 
-
<a href="https://2012.igem.org/Team:Evry/HumanPractice" style="text-decoration:none;">Human Practice</a><br>
 
-
<a href="https://2012.igem.org/Team:Evry/Safety" style="text-decoration:none;">Safety</a><br>
 
-
<a href="https://2012.igem.org/Team:Evry/Modeling" style="text-decoration:none;">Modeling</a><br>
 
-
</div>
 
-
</font>
 
-
<br>
 
-
</div>
 
-
 
-
 
-
 
-
<br />
 
-
 
-
<html>
 
<div id="citation_box">
<div id="citation_box">
<p id="references">References:</p>
<p id="references">References:</p>
<ol>
<ol>
-
<li><i>Inducible control of tissue-specific transgene expression in Xenopus tropicalis transgenic lines.</i>, Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002</li>
+
<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>
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li>
<li><i>Xenopus: a prince among models for pronephric kidney development.</i>, Jones E., JASN 16:2, 2005</li>
-
<li><i>An auxin-based degron system for the rapid depletion of proteins in nonplant cells</i>, Nishimura K., Fukagawa T., Takisawa H., Kakimoto T., Kanemaki M., Nature Methods 6:12, 2009</li>
+
<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>
</ol>
</ol>
</div>
</div>
<br>
<br>
-
 
+
<script type="text/javascript">writeFooter()</script>  
-
<!-- PAGE FOOTER -- ITEMS FROM COLUMN ! HAVE BEEN MOVED HERE  -- RDR  -->
+
-
 
+
-
        <div id="footer-wrapper">
+
-
        <div id="footer">
+
-
              <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">
+
-
+
-
 
+
-
  <!-- Recentchanges is not handles well DEBUG -->
+
-
    <li id="t-recentchanges"><a href="/Special:RecentChanges"
+
-
      title='Recent changes'>Recent changes</a></li>
+
-
 
+
-
    <li id="t-whatlinkshere"><a href="/Special:WhatLinksHere/Team:Paris_Bettencourt/Modeling"
+
-
      title="List of all wiki pages that link here [j]" accesskey="j">What links here</a></li>
+
-
 
+
-
                        <li id="t-recentchangeslinked"><a href="/Special:RecentChangesLinked/Team:Paris_Bettencourt/Modeling"
+
-
                          title="Recent changes in pages linked from this page [k]" accesskey="k">Related changes</a></li>
+
-
 
+
-
 
+
-
 
+
-
                <li id="t-upload"><a href="/Special:Upload"
+
-
                  title="Upload files [u]" accesskey="u">Upload file</a>
+
-
                </li>
+
-
                <li id="t-specialpages"><a href="/Special:SpecialPages"
+
-
                  title="List of all special pages [q]" accesskey="q">Special pages</a>
+
-
 
+
-
                </li>
+
-
                <li><a href='/Special:Preferences'>My preferences</a></li>
+
-
            </ul>
+
-
        </div> <!-- close footer -->
+
-
        <div id='footer'>
+
-
    <ul id="f-list">
+
-
 
+
-
            <li id="t-print"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;printable=yes"
+
-
              title="Printable version of this page [p]" accesskey="p">Printable version</a>
+
-
 
+
-
            </li>
+
-
 
+
-
            <li id="t-permalink"><a href="/wiki/index.php?title=Team:Paris_Bettencourt/Modeling&amp;oldid=86565"
+
-
              title="Permanent link to this revision of the page">Permanent link</a>
+
-
            </li>
+
-
 
+
-
 
+
-
        <li id="privacy"><a href="/2011.igem.org:Privacy_policy" title="2011.igem.org:Privacy policy">Privacy policy</a></li>
+
-
        <li id="disclaimer"><a href="/2011.igem.org:General_disclaimer" title="2011.igem.org:General disclaimer">Disclaimers</a></li>
+
-
    </ul>
+
-
 
+
-
</div> <!-- close footer -->
+
-
</div> <!-- close footer-wrapper -->
+
-
</div>
+
-
</div>
+
-
</div>
+
-
</body>
+
</html>
</html>

Latest revision as of 01:22, 27 September 2012

Xenopus tropicalis: A new multicellular chassis

Establishment of a new chassis


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.

The arrival of Xenopus 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 Xenopus for building multicellular systems.

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. Xenopus can be used as a biosensor, Organisation for Economic Co-operation and Development (OECD) plan to validate an assay capable of detecting thyroid disruptor using Xenopus. With our plasmid it is easy to test in 5 days a promoter or/and a reporter in the new chassis xenopus because it contains a working immune/vascular/neurologic/nephrologic/digestive systems.

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 Xenopus in one summer for an iGEM project, and to create a great tool for multicellular synthetic biology: An orthogonal hormonal system.


The simple molecular strategy to build eukaryotic plasmid ready to use:


Xenopus tropicalis 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 Xenopus tropicalis (but also others vertebrate and fish). The plasmid is produced in bacteria then purified and injected into Xenopus's eggs. The plasmid can not replicate in eukaryotic cells. As origins of replication are cryptic in Xenopus, 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.

Image unavailable
  • Kozac : 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

  • Promoter : The promoter of a gene is located upstream of this gene and initiate its transcription. The promoter is surrounded by the enzyme restriction sites SalI and HindIII in order to be able to switch more easily to other promoters

  • 5'UTR and 3’UTR : 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

  • SV40 PolyA signal : 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

  • Antibiotic resistance genes : This sequence is necessary for the selection of transformed bacteria exposed to the antibiotic

  • Biobrick prefix and suffix

  • Origin of replication : This origin of replication is bacterial, this sequence initiates the replication of DNA

    • 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 Xenopus tropicalis after a single cloning.
    It is possible to easily change promoter with the restriction sites SalI and HindIII.
    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.

    To test it, inject 2.3 nL of 100 ng.uL-1 plasmid solution into the one cell embryo following the injecting tutorial.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.

    So far we have made 3 new plasmid backbones with different promoters :

  • With a CMV promoter for an ubiquitous expression : (BBa_K812000),
  • With a Hsp70 promoter for an inducible expression : (BBa_K812300),
  • With a Elastase promoter for a tissue specific expression : (BBa_K812200).


    • 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.



Example of GFP expression in Xenopus


The injection tutorial 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 stage 48-50. The GFP (or other fluorescent protein) is expressed few hours after the fertilization to the end of the week (see below).

Plasmid injected: pCS2+ with CMV promoter and GFP-aid reporter


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 BBa_K812010, and it was integrated into our Eucaryotic plasmid BBa_K812000.We injected about 3.78E+7 plasmids.


Image unavailable

GFP-aid expression from the embryo at stage 20 (one day after injection )to a tadpole at stage ~46 (four days after injection). For this tadpole the expression is localized in the skin.

We characterize the promoter CMV and elastase, not yet for the inducible promoter HSP70. Reporters characterized: sfGFP, mCitrine, mCFP and GFP-aid.

The characterization of all reporter and promoters is here.


Conclusion


This new BioBricked plasmid is ready to use in Xenopus tropicalis. 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 Xenopus tropicalis as pCS2+. This pCS2+ was Biobricked to be compatible with the registry.
The pCS2+ plasmid was characterized and different reporters were expressed under the control of different promoters: here.

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.

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 model. Another reason could be that the metabolism of each differentiated cell is different and changes during the tadpole's development.

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 Xenopus'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.

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.

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 Human Practice.


References:

  1. Inducible control of tissue-specific transgene expression in Xenopus tropicalis transgenic lines., Chae J., Zimmerman L.B., Grainger R.M., Mechanisms of development 117:1-2, 2002
  2. Xenopus: a prince among models for pronephric kidney development., Jones E., JASN 16:2, 2005
  3. REMI (Restriction Enzyme Mediated Integration) and its Impact on the Isolation of Pathogenicity Genes in Fungi Attacking Plants
    4. Kahmann R., Basse C., European Journal of Plant Pathology

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