Team:Evry/Achievements

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<h1>iGEM Evry 2013 achievements</h1>
<h1>iGEM Evry 2013 achievements</h1>
<br>
<br>
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<p>Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum:</p><br/>
 
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<div class="jamboree">
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  <header>Since European Jamboree!</header>
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  <p>
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<div align="center"><h2><img title="Gold Medal" src='https://static.igem.org/mediawiki/2013/c/c4/Or-01%281%29.png' alt="Gold Medal" width="7%"/>Gold Medal</h2></div>
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<table>
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<img src="https://static.igem.org/mediawiki/2013/7/71/IGEM_Lyon.png" width=200px style="padding: 5px;"/>
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</td>
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<td>
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<table>
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<td colspan=2>
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<p>We worked hard since the last european Jamboree, taking into account the remarks from the juges and continuing on our own ideas. Here are the our main acheivements:<p>
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</td>
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<br />
<ul>
<ul>
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<li>(Improve the function of an existing BioBrick Part or Device) => LacO RFP
+
<li><b>Biology:</b></li>
-
<li>Help any registered iGEM team
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  <ul>
-
<li class="tick">Your project may have implications for the environment, security, safety and ethics and/or ownership and sharing.
+
      <li>Proceed to new inverter constructions</li>
 +
      <li>Cloned an periplasm located iron chelating protein coming from <i>Nesseria</i></li>
 +
    </ul>
 +
<li><b>Modeling:</b></li>
 +
  <ul>
 +
      <li>We parametrized all our models with the experimental parameters of the iron sensor</li>
 +
      <li>We created a cellular automaton based model of the treatment in the upper intestine</li>
 +
  </ul>
 +
<li><b>Human Practice:</b></li>
 +
  <ul>
 +
      <li>We estimated the cost of the capsule, the benefits for the company producing it and the gain of the French national care system</li>
 +
      <li>We consulted SANOFI, a world leader drug maker</li>
 +
  </ul>
</ul>
</ul>
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<br/>
 
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</p>
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</td>
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<div align="center"><h2><img title="Silver Medal" src='https://static.igem.org/mediawiki/2013/d/dc/Argent-01.png'  alt="Silver Medal" width="7%"/>Silver Medal</h2></div>
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<td style="vertical-align:top;">
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<img src="https://static.igem.org/mediawiki/2013/d/df/Improved.png" align="center" width=81px>
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</td>
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<td>
<p>
<p>
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<br />
<ul>
<ul>
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<li class="tick">We <b>experimentally validate</b> AceB-sfGFP <b> Biobricks we submitted</b> to the iGEM Parts registry, using <a href="https://2013.igem.org/Team:Evry/Results" target='_blank'>TECAN and microfluidic experiment</a> notably.
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  <li><b>Biology:</b></li>
-
<li class="tick">We <b>document the characterization</b> in the "Main Page"
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      <ul>
-
<small>
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          <li>We improved the characterization of our best iron sensor</li>
-
<ul>
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      </ul>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163102:Experience" target='_blank'>BBa_K1163102</a>: AceB-sfGFP characterization
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  <li><b>Modeling:</b></li>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163103:Experience" target='_blank'>BBa_K1163103</a>: AceB-LacI characterization
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      <ul>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163105:Experience" target='_blank'>BBa_K1163105</a>: FepA-sfGFP characterization
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        <li>We reviewed the math, the code and improved the description of all our models for further re-use in iGEM</li>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163106:Experience" target='_blank'>BBa_K1163106</a>: FepA-LacI characterization
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      </ul>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163108:Experience" target='_blank'>BBa_K1163108</a>: Fes-sfGFP characterization
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  <li><b>Human Practice:</b></li>
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<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163109:Experience" target='_blank'>BBa_K1163109</a>: Fes-LacI characterization
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      <ul>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163111:Experience" target='_blank'>BBa_K1163111</a>: YncE-sfGFP characterization
+
            <li>We extended our survey of patient to the rest of the world</li>
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163112:Experience" target='_blank'>BBa_K1163112</a>: YncE-LacI characterization
+
      </ul>
-
</ul>
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<li><b>Wiki:</b></li>
-
</small>    <li class="tick">Our project have implications for <b><a href='https://2013.igem.org/Team:Evry/Safety' target='_blank'>safety</a></b> and <b><a href='https://2013.igem.org/Team:Evry/Philosophy target='_blank'>ethics</a></b>
+
  <ul>
 +
      <li>We made a simplified french version of our Wiki that could be accessible for french patients</li>
 +
      <li>We survived a second Wiki-freeze but without coffee this time !!</li>
 +
  </ul>
 +
 
</ul>
</ul>
-
<br/>
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</p>
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</td>
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</tr>
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</table>
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<div align="center"><h2><img title="Bronze Medal" src='https://static.igem.org/mediawiki/2013/b/bc/Bronze-01.png' width="7%" alt="Bronze Medal"/>Bronze Medal</h2></div>
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</td>
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</table>
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<p><ul>
+
 
-
<li class="tick">We <b><a https://igem.org/Team.cgi?id=1163' target='_blank'>register</a> the team</b>, have a great summer, and plan to have fun at the Regional Jamboree
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</div>
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<li>We <b>complete</b> and <b>submit 
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</p>
-
<a href='https://igem.org/2013_Judging_Form?id=1163' target='_blank'>Judging form</a></b>
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-
<li class="tick">We <b>make</b> an awesome and accessible <b>team Wiki</b>. We manage to make it the more educational and scientific as we can !
+
-
<li class="tick">We will <b>present a poster</b> and a <b>talk at the iGEM Jamboree</b>
+
-
<li class="tick">We <b>document xx <a href='https://2013.igem.org/Team:Evry/Parts' target='_blank'>BioBricks</a></b> and <b>submit 8 news BioBricks</b> used in our project:
+
-
<small>
+
-
<ul>
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163102" target='_blank'>BBa_K1163102</a>: AceB-sfGFP
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163103" target='_blank'>BBa_K1163103</a>: AceB-LacI
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163105" target='_blank'>BBa_K1163105</a>: FepA-sfGFP
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163106" target='_blank'>BBa_K1163106</a>: FepA-LacI
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163108" target='_blank'>BBa_K1163108</a>: Fes-sfGFP
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163109" target='_blank'>BBa_K1163109</a>: Fes-LacI
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163111" target='_blank'>BBa_K1163111</a>: YncE-sfGFP
+
-
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163112" target='_blank'>BBa_K1163112</a>: YncE-LacI
+
-
</ul>
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-
</small>
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-
</ul>
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-
<br/>
+
<br />
-
<br/>
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<br />
-
<h1>And more precisely ?!</h1>
+
<p>
 +
Here we detail how we fulfilled each of the <a href="https://2013.igem.org/Judging/Awards" target='_blank'><em>iGEM medal requirements</em></a>.
 +
</p>
-
<div align="center"><h2>Biology</h2></div>
+
<h2  align="center"><img title="Gold Medal" src='https://static.igem.org/mediawiki/2013/c/c4/Or-01%281%29.png' alt="Gold Medal" width="7%"/>Gold Medal (requires any one of the following goals)</h2>
<ul>
<ul>
-
    <li class="tick">We <b>design</b> and <b>create 4 Iron sensing systems</b>, that could also works with an <b>invertor</b> !
 
-
    <li class="tick">We <b>design an Iron chelating system</b> and isolate genes of the enterobactins biosynthesis pathway !
 
-
    <li class="tick">We use <b>TECAN</b> and <b>microfluidic</b> to analyse our systems and show that <b>they work</b> !
 
-
    <li class="tick">We created a <b><a href="https://2013.igem.org/Team:Evry/Pill_design!" target='_blank'>pill</a></b> adapted to our project and that fulfilled basic requirements of the European Pharmacopeia !
 
 +
<li class="tick">We improved the function of an existing BioBrick Part or Device. First, we re-characterize the LacO-RFP BioBrick <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_J04450:Experience" target='_blank'><em>BBa_J04450</em></a> (<a href="https://2013.igem.org/Team:Evry/Results#recharacterization_LacO_RFP" target='_blank'><em>Biology Results Section</em></a>) and improve it by integrating it with an aceB-LacI iron sensor (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163102:Experience" target='_blank'><em>Biobrick BBa_K1163102</em></a>). Together, these Biobricks create a <a href="https://2013.igem.org/Team:Evry/Inverter" target='_blank'><em>Fur Inverter</em></a> (see <a href="https://2013.igem.org/Team:Evry/Results#Inverter" target='_blank'><em>Biology Results Section</em></a>) that activates gene expression in response to iron.</li>
 +
 +
<li class="tick">We <a href="https://2013.igem.org/Team:Evry/Collaborations"><em>collaborated</em></a> with other iGEM teams: we participated to <b>Purdue</b> and <b>UGent</b> online survey and had a nice workshop with <b>Paris-Saclay</b> team. </br>
 +
We are also setting up a scientific collaboration with the <b>Edimburgh</b> iGEM team that is working on and environmental sensor using the Fur System. </li>
 +
 +
<li class="tick">As our project involves treating a human genetic disorder using genetically-engineered bacteria, it has numerous implications for human health, safety and security, and ethics. To enable safe delivery of therapeutic bacteria to the human intestine, we designed and constructed a <a href="https://2013.igem.org/Team:Evry/Pill_design"target='_blank'><em>polymer-based capsule</em></a>. We also explored safety and ethics consequences of our project as the Human Practices studies:
 +
<ol>
 +
 +
<li > We discussed the medical feasibility and implications of this treatment in a <a href="https://2013.igem.org/Team:Evry/HumanPractice/Expert_consultation" target='_blank'><em>series of interviews and discussions</em></a> with renowned experts on iron overload diseases.</li>
 +
 +
<li>We carefully analyzed the <a href="https://2013.igem.org/Team:Evry/Safety" target='_blank'><em>safety issues</em></a> and potential consequences of our bacteria using consequence-based decision tree.</li>
 +
 +
<li>We organized and hosted a <a href="https://2013.igem.org/Team:Evry/Seminar" target='_blank'><em>scientific conference</em></a> on iron overload disorders and perceptions of our our project on 18 September 2013. This conference was attended by both medical experts and iron disorder patients.</li>
 +
 +
<li> We prepared and disseminated a <a href="https://2013.igem.org/Team:Evry/HumanPractice/Patients_perceptions" target='_blank'><em> patient perception survey</em></a> about how our treatment could potentially help hemochromatosis patients. We received and analyzed the results from over 250 patients who responded to our survey.</li>
 +
 +
<li>We wrote an extensive report on our <a href="https://2013.igem.org/Team:Evry/Philosophy" target='_blank'><em>conclusions about  synthetic biology </em></a>, which is the fruit of our many discussions over the summer.</li>
 +
 +
</ol>
</ul>
</ul>
 +
<br/>
-
<div align="center"><h2>Model</h2></div>
 
 +
<h2 align="center"><img title="Silver Medal" src='https://static.igem.org/mediawiki/2013/d/dc/Argent-01.png'  alt="Silver Medal" width="7%"/>Silver Medal (requires each of the four following goals)</h2>
-
<div align="center"><h2>Human Practices</h2></div>
+
<p>
 +
<ul>
 +
<li class="tick">We experimentally validated that the aceB-sfGFP biobrick acts as an iron-reponsive biosensor (<a href="https://2013.igem.org/Team:Evry/Results#AceB_GFP" target='_blank'><em>see Biology Results Section</em></a>). 
 +
<li class="tick">We document the characterization of our aceB-sfGFP and other BioBricks in "Main Page" section of the Parts Registry.
 +
 +
<li class="tick">We submitted the following BioBricks parts to the iGEM Parts Registry. The 4 sfGFP constructs function as <a href="https://2013.igem.org/Team:Evry/Sensor" target='_blank'><em>iron sensors</em></a> and the lacI constructs are used to build a <a href="https://2013.igem.org/Team:Evry/Inverter" target='_blank'><em>Fur-based genetic inverter</em></a> that activates gene expression in response to iron. These 8 Biobricks have been <a href="http://parts.igem.org/cgi/dna_transfer/batch_list.cgi?group_id=1475" target='_blank'><em>received and accepted</em></a> by the Registry of Standard Biological Parts.
 +
<small>
<ul>
<ul>
-
<li class="tick">We make a <a href="https://2013.igem.org/Team:Evry/HumanPractice/Expert_consultation" target='_blank'>series of <b>interviews and discussion</b></a> with <b>experts on iron overload diseases</b>.
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163102:Experience" target='_blank'><em>BBa_K1163102</em></a>: AceB-sfGFP
-
<li class="tick">We make <b>reflexion</b> about the <b><a href="https://2013.igem.org/Team:Evry/Safety" target='_blank'>safety</a></b> of potential consequences of our bacteria, including a <b>consequence tree</b>.
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163103:Experience" target='_blank'><em>BBa_K1163103</em></a>: AceB-lacI
-
<li class="tick">We had discussion with hemochromatosis patient and held a <b><a href="https://2013.igem.org/Team:Evry/Seminar" target='_blank'>seminar</a></b> on <b>iron overload</b> and on <b>our project</b> on 18 September 2013.<br/>
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163105:Experience" target='_blank'><em>BBa_K1163105</em></a>: FepA-sfGFP
-
<b>Scientists</b> working on iron overload, <b>patients</b>, and <b>students</b> attended to it !
+
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163106:Experience" target='_blank'><em>BBa_K1163106</em></a>: FepA-lacI
 +
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163108:Experience" target='_blank'><em>BBa_K1163108</em></a>: Fes-sfGFP
 +
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163109:Experience" target='_blank'><em>BBa_K1163109</em></a>: Fes-lacI
 +
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163111:Experience" target='_blank'><em>BBa_K1163111</em></a>: YncE-sfGFP
 +
<li><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1163112:Experience" target='_blank'><em>BBa_K1163112</em></a>: YncE-LacI
 +
</ul>
-
<li class="tick">We make a <b><a href="https://2013.igem.org/Team:Evry/HumanPractice/Patients_perceptions" target='_blank'>survey</a></b> about hemochromatosis and about our potential treatment. <br/>We <b>received and analyzed</b> more than <b>250 answers from patients</b> !
+
</small>    <li class="tick">We describe how our project has implications for <b><a href='https://2013.igem.org/Team:Evry/Safety' target='_blank'><em>safety</em></a></b> and <b><a href="https://2013.igem.org/Team:Evry/Philosophy" target='_blank'><em>ethics</em></a></b>
-
<li class="tick">We submitted an <b><a href="https://2013.igem.org/Team:Evry/Philosophy">extensive report</a> of our conclusions about synthetic biology</b> , which is the fruit of our long reflection we conducted over the summer.</li>
+
</ul>
</ul>
 +
<br/>
-
 
 +
<h2 align="center"><img title="Bronze Medal" src='https://static.igem.org/mediawiki/2013/b/bc/Bronze-01.png' width="7%" alt="Bronze Medal"/>Bronze Medal (requires each of the five following goals)</h2>
 +
 +
<p>
 +
<ul>
 +
<li class="tick">We <a href="https://igem.org/Team_List?year=2013" target='_blank'><em> registered our team</em></a> for iGEM 2013 and are attending the European Regional Jamboree.
 +
<li class="tick">We completed and submitted the <a href='https://igem.org/2013_Judging_Form?id=1163' target='_blank'><em>Judging form</em></a>.
 +
<li class="tick">We made a comprehensive and accessible <a href="https://2013.igem.org/Team:Evry" target='_blank'><em>iGEM Evry 2013 Wiki</em></a> to convey our educational and scientific advances.
 +
<li class="tick">We will present a poster and give an oral presentation at the iGEM European Jamboree in Lyon, France.</b>
 +
<li class="tick">We <a href='https://2013.igem.org/Team:Evry/Parts' target='_blank'><em>document 22 BioBricks</em></a></b> used in our project and submit 8 news BioBricks to the Parts Registry (see 8 submitted Biobricks in Silver Medal Requirements).
 +
</ul>
 +
 +
<br/>
 +
<br/>
</div>
</div>

Latest revision as of 03:53, 29 October 2013

Iron coli project

iGEM Evry 2013 achievements


Since European Jamboree!

We worked hard since the last european Jamboree, taking into account the remarks from the juges and continuing on our own ideas. Here are the our main acheivements:


  • Biology:
    • Proceed to new inverter constructions
    • Cloned an periplasm located iron chelating protein coming from Nesseria
  • Modeling:
    • We parametrized all our models with the experimental parameters of the iron sensor
    • We created a cellular automaton based model of the treatment in the upper intestine
  • Human Practice:
    • We estimated the cost of the capsule, the benefits for the company producing it and the gain of the French national care system
    • We consulted SANOFI, a world leader drug maker


  • Biology:
    • We improved the characterization of our best iron sensor
  • Modeling:
    • We reviewed the math, the code and improved the description of all our models for further re-use in iGEM
  • Human Practice:
    • We extended our survey of patient to the rest of the world
  • Wiki:
    • We made a simplified french version of our Wiki that could be accessible for french patients
    • We survived a second Wiki-freeze but without coffee this time !!



Here we detail how we fulfilled each of the iGEM medal requirements.

Gold MedalGold Medal (requires any one of the following goals)

  • We improved the function of an existing BioBrick Part or Device. First, we re-characterize the LacO-RFP BioBrick BBa_J04450 (Biology Results Section) and improve it by integrating it with an aceB-LacI iron sensor (Biobrick BBa_K1163102). Together, these Biobricks create a Fur Inverter (see Biology Results Section) that activates gene expression in response to iron.
  • We collaborated with other iGEM teams: we participated to Purdue and UGent online survey and had a nice workshop with Paris-Saclay team.
    We are also setting up a scientific collaboration with the Edimburgh iGEM team that is working on and environmental sensor using the Fur System.
  • As our project involves treating a human genetic disorder using genetically-engineered bacteria, it has numerous implications for human health, safety and security, and ethics. To enable safe delivery of therapeutic bacteria to the human intestine, we designed and constructed a polymer-based capsule. We also explored safety and ethics consequences of our project as the Human Practices studies:
    1. We discussed the medical feasibility and implications of this treatment in a series of interviews and discussions with renowned experts on iron overload diseases.
    2. We carefully analyzed the safety issues and potential consequences of our bacteria using consequence-based decision tree.
    3. We organized and hosted a scientific conference on iron overload disorders and perceptions of our our project on 18 September 2013. This conference was attended by both medical experts and iron disorder patients.
    4. We prepared and disseminated a patient perception survey about how our treatment could potentially help hemochromatosis patients. We received and analyzed the results from over 250 patients who responded to our survey.
    5. We wrote an extensive report on our conclusions about synthetic biology , which is the fruit of our many discussions over the summer.

Silver MedalSilver Medal (requires each of the four following goals)


Bronze MedalBronze Medal (requires each of the five following goals)

  • We registered our team for iGEM 2013 and are attending the European Regional Jamboree.
  • We completed and submitted the Judging form.
  • We made a comprehensive and accessible iGEM Evry 2013 Wiki to convey our educational and scientific advances.
  • We will present a poster and give an oral presentation at the iGEM European Jamboree in Lyon, France.
  • We document 22 BioBricks used in our project and submit 8 news BioBricks to the Parts Registry (see 8 submitted Biobricks in Silver Medal Requirements).