Team:Paris Bettencourt/Results

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    <a href="#Detect">
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      <div class="hlink" style="width:355px">
 +
<h2>Detect</h2>
 +
      </div>
 +
    </a>
 +
    <a href="#Target">
 +
      <div class="hlink" style="width:355px">
 +
<h2>Target</h2>
 +
      </div>
 +
    </a>
 +
    <a href="#Infiltrate">
 +
      <div class="hlink" style="width:355px;margin-right:0">
 +
<h2>Infiltrate</h2>
 +
      </div>
 +
    </a>
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    <div style="clear: both;"></div>
   </div>
   </div>
 +
  <div style="height:68px">
 +
    <a href="#Sabotage">
 +
      <div class="hlink" style="width:355px">
 +
<h2>Sabotage</h2>
 +
      </div>
 +
    </a>
 +
    <a href="#Modelling">
 +
      <div class="hlink" style="width:355px">
 +
<h2>Modelling</h2>
 +
      </div>
 +
    </a>
 +
    <a href="#Human_Practice">
 +
      <div class="hlink" style="width:355px;margin-right:0">
 +
<h2>Human Practice</h2>
 +
      </div>
 +
    </a>
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    <div style="clear: both;"></div>
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  </div>
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   <div id="page">
   <div id="page">
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<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Detect">Detect</a></h2>
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  <div id="Detect"></id>
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<div class="overbox">
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  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Detect">Detect</a></h2>
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    <div class="bkgr">
+
    <div class="overbox">
-
      <h2>Background</h2>
+
      <div class="subbox1">
-
      <p>CRISPR/Cas systems generate site-specific double strand breaks and have recently be used for genome editing.  </p>
+
<div class="bkgr">
-
    </div>
+
  <h2>Background</h2>
-
    <div class="results">
+
  <p>CRISPR/Cas systems generate site-specific double strand breaks and have recently been used for genome editing.  </p>
-
       <h2>Results</h2>
+
</div>
-
      <ul>
+
<div class="aims">
-
        <li>Successfully cloned gRNA anti-KAN, crRNA anti-KAN, tracrRNA-Cas9 and pRecA-LacZ into Biobrick backbones and therefore generated four new BioBricks. </li>
+
  <h2>Aims</h2>
-
        <li>Testing the new assembly standard for our cloning.</li>
+
  <p>Building a genotype sensor based on CRISPR/Cas that reports existance of an antibiotic resistance gene.</p>
-
      </ul><h2>Assembly Standard</h2>
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</div>
-
      <p>We offer a new assembly standard. It enables keeping the BioBrick standard while providing the needed tools to perform assembly of several parts in one step. BBG is a fusion of the BioBrick standard cloning and Gibson isothermal assembly.</p>
+
       </div>
-
    </div>
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      <div class="subbox2">
-
    <div class="biocriks">
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<div class="results">
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      <h2>BioBricks</h2>
+
  <h2>Results</h2>
-
      <ol>
+
  <ul>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137012" target="_blank">BBa_K1137012 (gRNA anti-KAN)</a></li>
+
            <li>Successfully cloned gRNA anti-KAN, crRNA anti-KAN, tracrRNA-Cas9 and pRecA-LacZ into Biobrick backbones and therefore generated four new BioBricks. </li>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137013" target="_blank">BBa_K1137013 (crRNA anti-KAN)</a></li>  
+
<li> Confirmation of site-specific binding and DNA double-strand breaks generated by the gRNA-Cas9 complex in the kanamycin resistance casette. </li>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137014" target="_blank">BBa_K1137014 (tracrRNA-Cas9)</a></li>
+
<li>Testing the new assembly standard for our cloning.</li>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137015" target="_blank">BBa_K1137015 (pRecA-LacZ)</a></li>
+
  </ul>
-
       </ul>
+
</div>
 +
<div class="biocriks">
 +
 
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137014" target="_blank"><img width="24%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/a/ab/Bb_detect_cas9.png"/></a>
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137013" target="_blank"><img width="24%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/9/97/Bb_detect_crRNAKan.png"/></a>
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137012" target="_blank"><img width="24%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/7/7b/Bb_detect_gRNAkan.png"/></a>
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137015" target="_blank"><img width="24%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/0/05/Bb_detect_LacZ.png"/></a>
 +
 
 +
 +
 
 +
 
 +
</div>
 +
       </div>
 +
      <div class="mainfig">
 +
        <center> <img width="80%" src="https://static.igem.org/mediawiki/2013/0/01/PB_13_Results_detect_killing_assay.png"/></center>
 +
<br>
 +
 
 +
        <p style="margin-top:-60px;font-size:13px"><b>CRISPR anti-Kan plasmids target specifically kanamycin resistant <i>E. coli</i>. </b>We introduced our CRISPR-based DNA cleavage system to two strains of <i>E. coli</i> : one WT (blue bars) and one carrying a genomically integrated kanamycin resistance casette (KanR, blue bars). The strains were co-transformed with two plasmids. One with the Cas9 construct, the other with the anti-Kanamycin gRNA. WT <i>E. coli</i> could be efficiently transformed with one or both plasmids, as determined by selective plating. However, KanR <i>E. coli</i> could not be efficiently transformed with both. We attribute this to Cas9-induced cleavage of the chromosome specifically at the KanR casette, with about 99% efficiency.
 +
</p>
 +
      </div>
     </div>
     </div>
     <div style="clear: both;"></div>
     <div style="clear: both;"></div>
-
     <div class="aims">
+
   
-
       <h2>Aims</h2>
+
    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Target</a></h2>
-
      <p>Building a genotype sensor based on CRISPR/Cas that reports existance of an antibiotic resistance gene.</p>
+
     <div class="overbox">
 +
       <div class="subbox1">
 +
<div class="bkgr">
 +
  <h2>Background</h2>
 +
  <p>SirA is an essential gene in latent tuberculosis infections.  </p>
 +
</div>
 +
<div class="aims">
 +
  <h2>Aims</h2>
 +
  <p>To perform a drug screen targeted at the sirA gene from mycobacteria.</p>
 +
</div>
 +
      </div>
 +
      <div class="subbox2">
 +
<div class="results">
 +
  <h2>Results</h2>
 +
  <ul>
 +
            <li>Produced an <i>E. coli</i> strain which relies upon mycobacterial sirA, fprA and fdxA genes to survive in M9 minimal media.</li>
 +
            <li>Demonstrated that <i>E. coli</i> can survive with mycobacterial sulfite reduction pathway with Flux Balance Analysis.</li>
 +
            <li>Located drug target sites on sirA as well as identified high structural similarity between cysI and sirA through structural analysis.</li>
 +
<li>Identified a potential anti-TB activity of Pyridoxine at high doses.</li>
 +
  </ul>
 +
</div>
 +
<div class="biocriks">
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137000" target="_blank"><img height="80%" style="margin-top:15px;margin-left:30px" src="https://static.igem.org/mediawiki/2013/7/79/Bb_target_sirA.png"/></a>
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137001" target="_blank"><img height="80%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/c/cb/Bb_target_fprA.png"/></a>
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K1137002" target="_blank"><img height="80%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/4/40/Bb_target_fdxA.png"/></a>
 +
 
 +
</div>
 +
      </div>
 +
      <div class="mainfig">
 +
        <center> <img width="100%" src="https://static.igem.org/mediawiki/2013/3/31/PB_fig_target1.png"/></center>
 +
        <p style="font-size:13px"> <b>MycoSIR <i>E. coli</i> depend on our synthetic pathway for growth.</b> <i>E. coli</i> strain BL21(DE3) was deleted for cysI and transformed with the three genes of the mycoSIR pathway expressed from IPTG-inducible T7 promoters (red). Wild-type (blue), uninduced (purple) and pathway-minus (gold) strains were used as controls. Both time course growth curves (A) and final ODs (B) reveal that the complete, induced pathway is required for growth
 +
</p>
 +
      </div>
     </div>
     </div>
     <div style="clear: both;"></div>
     <div style="clear: both;"></div>
-
  </div>
 
-
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Target</a></h2>
 
-
<div class="overbox">
 
-
    <div class="bkgr">
 
-
      <h2>Background</h2>
 
-
      <p>SirA is an essential gene in latent tuberculosis infections</p>
 
-
    </div>
 
-
    <div class="results">
 
-
      <h2>Results</h2>
 
-
      <ul>
 
-
        <li>Produced an E. coli strain which relies upon mycobacterial sirA, fprA and fdxA genes to survive in M9 minimal media</li>
 
-
        <li>Demonstrated that E. coli can survive with mycobacterial sulfite reduction pathway with Flux Balance Analysis</li>
 
-
        <li>Located drug target sites on sirA as well as identified high structural similarity between cysI and sirA through structural anaylsis</li>
 
-
      </ul>
 
-
      <p></p>
 
-
    </div>
 
-
    <div class="biocriks">
 
-
      <h2>BioBricks</h2>
 
-
      <ol>
 
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137000">BBa_K1137000 (SirA)</a></li>
 
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137001">BBa_K1137001 (FprA)</a></li>
 
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137002">BBa_K1137002 (FdxA)</a></li>
 
-
      </ul>
 
-
    </div>
 
-
    <div style="clear: both;"></div>
 
-
    <div class="aims">
 
-
      <h2>Aims</h2>
 
-
      <p>To perform an drug screen targeted at the sirA gene from mycobacteria</p>
 
-
    </div>
 
-
    <div style="clear: both;"></div>
 
-
  </div>
 
-
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Infiltrate">Infiltrate</a></h2>
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    <div id="Infiltrate"></id>
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<div class="overbox">
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    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Infiltrate">Infiltrate</a></h2>
-
    <div class="bkgr">
+
    <div class="overbox">
-
      <h2>Background</h2>
+
      <div class="subbox1">
-
      <p>Latent tuberculosis persists inside macrophages of the lungs, where it is partially protected from both the host immune system and conventional antibiotics.</p>
+
<div class="bkgr">
-
    </div>
+
  <h2>Background</h2>
-
    <div class="results">
+
  <p>Latent tuberculosis persists inside macrophages of the lungs, where it is partially protected from both the host immune system and conventional antibiotics. </p>
-
       <h2>Results</h2>
+
</div>
-
      <ul>
+
<div class="aims">
-
        <li>We expressed the enzyme Trehalose Dimycolate Hydrolase (TDMH) in <i>E.coli</i> and showed that it is highly toxic to mycobacteria in culture.</li>
+
  <h2>Aims</h2>
-
        <li>We expressed the lysteriolyin O (LLO) gene in <i>E. coli</i> and showed that it is capable of entering the macrophage cytosol.</li>
+
  <p>To create an <i>E. coli</i> strain capable of entering the macrophage cytosol and delivering a lytic enzyme to kill mycobacteria.</p>
-
        <li>We co-infected macrophages with both mycobacteria and our engineered <i>E. coli</i> to characterize the resulting phagocytosis and killing.</li>
+
</div>
-
      </ul>
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       </div>
-
      <p></p>
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      <div class="subbox2">
-
    </div>
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<div class="results">
-
    <div class="biocriks">
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  <h2>Results</h2>
-
      <h2>BioBricks</h2>
+
  <ul>
-
      <ol>
+
            <li>We expressed the enzyme Trehalose Dimycolate Hydrolase (TDMH) in <i>E.coli</i> and showed that it is highly toxic to mycobacteria in culture.</li>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137008" target="_blank">BBa_K1137008 (TDMH)</a></li>
+
            <li>We expressed the listeriolyin O (LLO) gene in <i>E. coli</i> and showed that it is capable of entering the macrophage cytosol.</li>
-
      </ul>
+
            <li>We co-infected macrophages with both mycobacteria and our engineered <i>E. coli</i> to characterize the resulting phagocytosis and killing.</li>
-
    </div>
+
  </ul>
-
    <div style="clear: both;"></div>
+
</div>
-
    <div class="aims">
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<div class="biocriks">
-
      <h2>Aim</h2>
+
 
-
      <p>To create an <i>E. coli</i> strain capable of entering the macrophage cytosol and delivering a lytic enzyme to kill mycobacteria.</p>
+
  <a href="http://parts.igem.org/Part:BBa_K1137008" target="_blank"><img height="80%" style="margin-top:15px; margin-left:150px" src="https://static.igem.org/mediawiki/2013/a/a0/Bb_infiltrate_tdmh.png"/></a>
 +
 
 +
</div>
 +
      </div>
 +
      <div class="mainfig">
 +
        <center><br> <img width="95%" src="https://static.igem.org/mediawiki/2013/b/bb/PB_fig_Infil.png"/></center>
 +
        <p style="font-size:13px"> <b>TDMH expression kills mycobacteria in culture.</b> We mixed <i>E. coli</i> and WT <i>M.smegmatis</i> in LB media. Plating assays were used to count specifically <i>M.smegmatis</i> after the indicated times. When TDMH-expression was fully induced, more than 98% of mycobacteria were killed after 6 hours (red line). Populations of mycobacteria alone (black line) and mycobacteria mixed with uninduced <i>E. coli</i> (blue line) were stable.
 +
</p>
 +
      </div>
     </div>
     </div>
     <div style="clear: both;"></div>
     <div style="clear: both;"></div>
-
  </div>
 
-
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Sabotage</a></h2>
 
-
<div class="overbox">
 
-
    <div class="bkgr">
 
-
      <h2>Background</h2>
 
-
      <p>One of the main concern about tuberculosis today is the emergence of antibiotic resistant strain</p>
 
-
    </div>
 
-
    <div class="results">
 
-
      <h2>Results</h2>
 
-
      <ul>
 
-
        <li>Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins</li>
 
-
        <li>successful conversion of antibiotic resistant population of E. coli to a sensitive state</li>
 
-
      </ul>
 
-
      <p></p>
 
-
    </div>
 
-
    <div class="biocriks">
 
-
      <h2>BioBricks</h2>
 
-
      <ol>
 
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137009" target="_blank">BBa_K1137009 (sRNA anti Kan)&nbsp;&nbsp;&nbsp; Characterized </a></li>
 
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137010" target="_blank">BBa_K1137010 (sRNA anti Cm)&nbsp;&nbsp;&nbsp; Characterized</a></li>
 
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137011" target="_blank">BBa_K1137011 (sRNA anti Lac)&nbsp;&nbsp;&nbsp;</a></li>
 
-
      </ul>
 
-
    </div>
 
-
<div style="clear: both;"></div>
 
-
    <div class="aims">
 
-
      <h2>Aims</h2>
 
-
      <p>Our objective is to make an antibiotic-resistant bacterial population sensitive again to those same antibiotics.</p>
 
-
    </div>
 
-
    <div style="clear: both;"></div>
 
-
  </div>
 
-
<h2><a href="https://2013.igem.org/wiki/index.php?title=Team:Paris_Bettencourt/Human_Practice/Overview">Human Practice</a></h2>
 
-
<div class="overbox">
 
-
    <div class="bkgr" style="width:315px;height:184px;">
 
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    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Technology_Transfer">Technology  Transfer</h2>
 
-
      <p> An essay that addresses the issue of designing a technology aimed at "developing" countries, rather than at “developed” ones: a typical case of technology transfer.</p>
 
-
    </div>
 
-
     <div class="results" style="width:425px;height:340px;">
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     <div id="Sabotage"></id>
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Gender_Study">Gender Study</h2>
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    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Sabotage</a></h2>
-
      <ul>
+
    <div class="overbox">
-
        <p>A comprehensive and quantitative study of gender equality(equality) in iGEM and synthetic biology. A database was gathered to depict sex ratio in teams' students and supervisors in all iGEM teams as well as other available information. This was statistically analysed to investigate gender in(equality) in iGEM, as well as SB conferences and synthetic biology labs.</p>
+
      <div class="subbox1">
-
     
+
<div class="bkgr">
-
      </ul>
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  <h2>Background</h2>
-
      <p></p>
+
  <p>One of the main concerns about tuberculosis today is the emergence of antibiotic resistant strains.</p>
-
    </div>
+
</div>
-
    <div class="bkgr" style="width:315px;">
+
<div class="aims">
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_Gallery"> TB gallery</h2>
+
  <h2>Aims</h2>
-
      <p> A gallery of famous historic figures who had tuberculosis, made to raise awareness to its prevalence of in the past and present .</p>
+
  <p>Our objective is to make an antibiotic-resistant bacterial population sensitive again to the selfsame antibiotics.</p>
-
    </div>
+
</div>
 +
      </div>
 +
      <div class="subbox2">
 +
<div class="results">
 +
  <h2>Results</h2>
 +
  <ul>
 +
            <li>Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins.</li>
 +
            <li>Showed theoretically burden of a device is critical for the maintenance of a genetic element in a population.</li>
 +
            <li>Successful conversion of antibiotic resistant population of <i>E. coli</i> to a sensitive state (on two different antibiotic resistances).</li>
-
    <div class="bkgr" style="width:315px;margin-bottom:0">
+
  </ul>
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_Facts">TB facts</h2>
+
</div>
-
      <p> Infographics page containing TB data and facts that captures all you need to know at a glance.</p>
+
<div class="biocriks">
-
    </div>
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-
<div style="clear: both;"></div>
+
<a href="http://parts.igem.org/Part:BBa_K1137009" target="_blank"><img height="80%" style="margin-top:15px;margin-left:30px" src="https://static.igem.org/mediawiki/2013/3/37/Bb_sabotage_aKAN.png"/></a>
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    <div class="aims" style="width:315px;height:140px;bottom:143px;margin-bottom:0">
+
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_France">TB in France</h2>
+
-
      <p>An analysis of the social and political aspects of the management of Tuberculosis in France.</p>
+
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    </div>
+
-
    <div style="clear: both;"></div>
+
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  </div>
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-
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">Collaboration</a></h2>
+
<a href="http://parts.igem.org/Part:BBa_K1137010" target="_blank"><img height="80%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/6/66/Bb_sabotage_aCm.png"/></a>
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<div class="overbox">
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<a href="http://parts.igem.org/Part:BBa_K1137011" target="_blank"><img height="80%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/7/72/Bb_sabotage_aLac.png"/></a>
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    <div class="results" style="width:349px;height:340px;">
+
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      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/SensiGEM">Sensigem</h2>
+
-
      <ul>
+
-
        <p>SensiGEM is the iGEM Biosensor database generated by the teams Paris Bettencourt 2013 and Calgary 2013. In this database you can find fast and easy what biosensor projects were already done by past iGEM Teams. To be able to select the projects that fit into the database, we also collaborated to compose a joint definition a biosensor.</p>
+
-
     
+
-
     
+
-
    </div>
+
-
    <div class="results" style="width:349px;height:340px;">
 
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">Braunschweig iGEM Team</h2>
 
-
      <ul>
 
-
        <p>Idea, bibliography, and beer sharing!</p>
 
-
     
 
-
     
 
-
    </div>
 
-
<div class="results" style="width:349px;height:340px;">
 
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">BGU iGEM Team from Israel</h2>
 
-
      <ul>
 
-
        <p> A mutual part characterization.  We characterize the promoter units produced by the lac/ara-1 promoter of cI, a repressor of their constructed kill switch. In return, BGU characterizes our TDMH biobrick protein expression levels by Western Blot.  </p>
 
-
     
 
-
     
 
-
    </div>
 
-
<h2><a href="">Modelling</h2>
 
-
<div class="overbox">
 
-
 
-
    <div class="results" style="width:349px;height:340px;">
 
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Population Dynamics Model</h2>
 
-
      <ul>
 
-
        <p>This model investigates the effects of the fitness-cost of a genetic element on it's spread in a bacterial population, based on a phagemid helper system</p>
 
-
     
 
-
     
 
-
    </div>
 
-
    <div class="results" style="width:349px;height:340px;">
+
</div>
-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Structural analysis of SirA</h2>
+
      </div>
-
      <ul>
+
      <div class="mainfig">
-
         <p>Using Swiss pdb we demonstrated the superimposed 3D structures of Mycobacterium tuberculosis SirA and Escherichia coli CysI highlighting their similarities and differences. Both proteins are important in their respective sulphite reduction pathways. We then predicted the effect of a small drug target based on SirA's structure. </p>
+
        <center><br> <img width="70%" src="https://static.igem.org/mediawiki/2013/b/b2/Newfiguresabotagepresentation.png"/></center>
-
     
+
         <p style="font-size:13px"><b>Our synthetic phage conveys antibiotic-sensitivity to an antbiotic-resistant population. </b>The anti-Chloramphenicol phage system effectively killed 99.1% of the Chloramphenicol resistant population and the anti- Kanamycine phage effictevely killed 99,5% of the Kanamycine resistant population.
-
        
+
</p>
 +
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     </div>
     </div>
 +
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 +
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 +
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 +
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 +
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<div class="results" style="width:349px;height:340px;">
+
    <div id="Modelling"></id>
-
       <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</h2>
+
    <h2><a href="">Modelling</a></h2>
-
      <ul>
+
    <div class="overbox" style="">
-
        <p>We used an E. coli model iJR904 obtained from BiGG database as a starting model and obtained a growth rate represented by the f value of 0.9129. We then deleted the reaction ‘SULR’ which encodes for the sulphite reduction pathway involving cysI and obtained a f value of -8.63596783409936e-13 indicating that the sulphite reduction pathway is required for growth. Finally we introduced two new reactions for sirA and fprA and a new species fdxA. We found that growth was restored with the mycobacteria pathway resulting in a f value of 0.9105</p>
+
      <div class="projtile" style="">
-
     
+
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Population Dynamics Model</a></h2>
-
        
+
<p>This model investigates the propagation of horizontal gene-transfer via phagemid/helper system. We study the effect of the burden of a desired device on the maintenance of the system in time.</p>
 +
        </br>
 +
        <center><a href="https://static.igem.org/mediawiki/2013/3/38/PB_Model_diagram3.png" target="_blank"><img src="https://static.igem.org/mediawiki/2013/3/38/PB_Model_diagram3.png" width="80%"/></a></center>
 +
        </br>
 +
        <p style="font-size:13px">Left: scheme representing the regular non-lytic M13 bacteriophage horizontal spread. Right: scheme representing the main processes of the phagemid/helper system.</p>   
 +
      </div>
 +
      <div class="projtile" style="">
 +
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Structure Based Modelling</a></h2>
 +
<p><b>SirA: </b>Using Swiss pdb we demonstrated the superimposed 3D structures of <i>Mycobacterium tuberculosis</i> SirA and <i>Escherichia coli</i> CysI highlighting their similarities and differences. Both proteins are important in their respective sulphite reduction pathways. We then predicted the effect of a small drug target based on SirA's structure. </p>
 +
       
 +
        <p><b>FprA: </b>Using LigandScout 3.1, we searched over 8100 drug compounds from the BindingDB and Chembl databases for drugs targetting mycobacterial Ferredoxin NADP reductase (FprA). We have modelled Pyridoxine's interaction to its active site. </p>
 +
       </div>
 +
      <div class="projtile" style="margin-right:0;">
 +
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</a></h2>
 +
<p>We used an <i>E. coli</i> model iJR904 obtained from BiGG database as a starting model and obtained a growth rate represented by the f value of 0.9129. We then deleted the reaction which encodes for the sulphite reduction pathway and obtained a f value of -8.63e-13 indicating that the sulphite reduction pathway is essential. We wrote a program which finds all essential reactions in <i>M. tuberculosis</i> and <i>E. coli</i> SBML models and attempts to restore growth for each essential <i>E. coli</i> model with essential reactions from M. tuberculosis to identify other metabolic pathways we could apply a targeted drug screen to. We identified <a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target/FBA">100 other essential reactions</a> we can target.</p>
 +
       </div>
     </div>
     </div>
 +
    <div style="clear: both;"></div>
 +
   
 +
    <div id="Human_Practice"></id>
 +
    <h2><a href="https://2013.igem.org/wiki/index.php?title=Team:Paris_Bettencourt/Human_Practice/Overview">Human Practice</a></h2>
 +
    <style>
 +
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 +
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 +
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 +
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 +
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 +
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 +
    </style>
 +
    <div class="overbox">
 +
      <div class="subbox3">
 +
<div class="bkgr">
 +
  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Technology_Transfer">Technology  Transfer  <img height="100%" src="https://static.igem.org/mediawiki/2013/6/6d/PB_logotransferttechno.png"/></a></h2>
 +
  <p> An essay that addresses the issue of designing a technology aimed at "developing" countries, rather than at “developed” ones: a typical case of technology transfer.</p>
 +
        </div>
 +
<div class="aims">
 +
  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_France">TB in France  <img height="100%" src="https://static.igem.org/mediawiki/2013/c/cf/PB_logofrance.png"/></a></h2>
 +
  <p>Analysis of the social, medical and political aspects of the management of tuberculosis in France.
 +
Synthetic biology may help in many ways such as treatments, drug development, diagnostic. We also give advice on how to introduce it in clinics. </p>
 +
        </div>
 +
      </div>
 +
      <div class="subbox4">
 +
<div class="aims" style="height:100%">
 +
  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Gender_Study">Gender Study  <img height="100%" src="https://static.igem.org/mediawiki/2013/d/da/PB_logogender.png"/></a></h2>
 +
          <p >A comprehensive and quantitative study of gender (in)equality in iGEM and synthetic biology. A database was gathered and statistically analysed in order to depict sex ratio of iGEM teams' students and supervisors.</p>
 +
          <br>
 +
          <center><img width="45%" src="https://static.igem.org/mediawiki/2013/d/de/GS_Prize.png"></center><br>
 +
          <p style="margin-top:-10px;font-size:13px"><b>Gender balance and success in iGEM</b><br>Winning teams have a significantly higher number of women and are more Gender balanced.</p>
 +
         
 +
        </div>       
 +
      </div>
 +
<div class="subbox3" style="margin-right:0">
 +
<div class="bkgr">
 +
  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_Facts">TB Facts  <img height="100%" src="https://static.igem.org/mediawiki/2013/6/69/PB_logoTBfacts.png"/></a></h2>
 +
  <p> Infographics page containing TB data and facts that captures all you need to know at a glance.</p>
 +
        </div>
 +
<div class="aims">
 +
  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_Gallery"> TB Gallery <img height="100%" src="https://static.igem.org/mediawiki/2013/d/de/PB_logoTBgallery.png"/><a/></h2>
 +
  <p> A gallery of famous historic figures who had tuberculosis, made to raise awareness to its prevalence of in the past and present .</p>
 +
        </div>
 +
      </div>
 +
    </div>
 +
    <div style="clear: both;"></div>
-
 
+
    <div id="Collaboration"></id>
-
 
+
    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">Collaboration</a></h2>
 +
    <div class="overbox" style="height:300px">
 +
      <div class="projtile" style="height:300px">
 +
        <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/SensiGEM">SensiGEM</a></h2>
 +
        <p>SensiGEM is the iGEM Biosensor database generated by the teams Paris Bettencourt 2013 and Calgary 2013. In this database you can find fast and easy what biosensor projects were already done by past iGEM Teams. To be able to select the projects that fit into the database, we also collaborated to compose a joint definition a biosensor.
 +
        </p>
 +
      </div>
 +
      <div class="projtile" style="height:300px">
 +
        <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">BGU iGEM Team from Israel</a></h2>
 +
        <p> A mutual part characterization.  We characterize the promoter units produced by the lac/ara-1 promoter of cI, a repressor of their constructed kill switch. In return, BGU characterizes our TDMH biobrick protein expression levels by Western Blot. 
 +
        </p>
 +
      </div>
 +
      <div class="projtile" style="height:300px;margin-right:0;">
 +
        <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">Braunschweig iGEM Team</h2>
 +
        <p>Idea, bibliography, and beer sharing!</p>       
 +
      </div>
 +
    </div>
 +
    <div style="clear: both;"></div>
 +
  </div>
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Latest revision as of 03:37, 29 October 2013

Detect

Target

Infiltrate

Sabotage

Modelling

Human Practice

Detect

Background

CRISPR/Cas systems generate site-specific double strand breaks and have recently been used for genome editing.

Aims

Building a genotype sensor based on CRISPR/Cas that reports existance of an antibiotic resistance gene.

Results

  • Successfully cloned gRNA anti-KAN, crRNA anti-KAN, tracrRNA-Cas9 and pRecA-LacZ into Biobrick backbones and therefore generated four new BioBricks.
  • Confirmation of site-specific binding and DNA double-strand breaks generated by the gRNA-Cas9 complex in the kanamycin resistance casette.
  • Testing the new assembly standard for our cloning.

CRISPR anti-Kan plasmids target specifically kanamycin resistant E. coli. We introduced our CRISPR-based DNA cleavage system to two strains of E. coli : one WT (blue bars) and one carrying a genomically integrated kanamycin resistance casette (KanR, blue bars). The strains were co-transformed with two plasmids. One with the Cas9 construct, the other with the anti-Kanamycin gRNA. WT E. coli could be efficiently transformed with one or both plasmids, as determined by selective plating. However, KanR E. coli could not be efficiently transformed with both. We attribute this to Cas9-induced cleavage of the chromosome specifically at the KanR casette, with about 99% efficiency.

Target

Background

SirA is an essential gene in latent tuberculosis infections.

Aims

To perform a drug screen targeted at the sirA gene from mycobacteria.

Results

  • Produced an E. coli strain which relies upon mycobacterial sirA, fprA and fdxA genes to survive in M9 minimal media.
  • Demonstrated that E. coli can survive with mycobacterial sulfite reduction pathway with Flux Balance Analysis.
  • Located drug target sites on sirA as well as identified high structural similarity between cysI and sirA through structural analysis.
  • Identified a potential anti-TB activity of Pyridoxine at high doses.

MycoSIR E. coli depend on our synthetic pathway for growth. E. coli strain BL21(DE3) was deleted for cysI and transformed with the three genes of the mycoSIR pathway expressed from IPTG-inducible T7 promoters (red). Wild-type (blue), uninduced (purple) and pathway-minus (gold) strains were used as controls. Both time course growth curves (A) and final ODs (B) reveal that the complete, induced pathway is required for growth

Infiltrate

Background

Latent tuberculosis persists inside macrophages of the lungs, where it is partially protected from both the host immune system and conventional antibiotics.

Aims

To create an E. coli strain capable of entering the macrophage cytosol and delivering a lytic enzyme to kill mycobacteria.

Results

  • We expressed the enzyme Trehalose Dimycolate Hydrolase (TDMH) in E.coli and showed that it is highly toxic to mycobacteria in culture.
  • We expressed the listeriolyin O (LLO) gene in E. coli and showed that it is capable of entering the macrophage cytosol.
  • We co-infected macrophages with both mycobacteria and our engineered E. coli to characterize the resulting phagocytosis and killing.

TDMH expression kills mycobacteria in culture. We mixed E. coli and WT M.smegmatis in LB media. Plating assays were used to count specifically M.smegmatis after the indicated times. When TDMH-expression was fully induced, more than 98% of mycobacteria were killed after 6 hours (red line). Populations of mycobacteria alone (black line) and mycobacteria mixed with uninduced E. coli (blue line) were stable.

Sabotage

Background

One of the main concerns about tuberculosis today is the emergence of antibiotic resistant strains.

Aims

Our objective is to make an antibiotic-resistant bacterial population sensitive again to the selfsame antibiotics.

Results

  • Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins.
  • Showed theoretically burden of a device is critical for the maintenance of a genetic element in a population.
  • Successful conversion of antibiotic resistant population of E. coli to a sensitive state (on two different antibiotic resistances).

Our synthetic phage conveys antibiotic-sensitivity to an antbiotic-resistant population. The anti-Chloramphenicol phage system effectively killed 99.1% of the Chloramphenicol resistant population and the anti- Kanamycine phage effictevely killed 99,5% of the Kanamycine resistant population.

Modelling

Population Dynamics Model

This model investigates the propagation of horizontal gene-transfer via phagemid/helper system. We study the effect of the burden of a desired device on the maintenance of the system in time.



Left: scheme representing the regular non-lytic M13 bacteriophage horizontal spread. Right: scheme representing the main processes of the phagemid/helper system.

Structure Based Modelling

SirA: Using Swiss pdb we demonstrated the superimposed 3D structures of Mycobacterium tuberculosis SirA and Escherichia coli CysI highlighting their similarities and differences. Both proteins are important in their respective sulphite reduction pathways. We then predicted the effect of a small drug target based on SirA's structure.

FprA: Using LigandScout 3.1, we searched over 8100 drug compounds from the BindingDB and Chembl databases for drugs targetting mycobacterial Ferredoxin NADP reductase (FprA). We have modelled Pyridoxine's interaction to its active site.

Flux Balance Analysis

We used an E. coli model iJR904 obtained from BiGG database as a starting model and obtained a growth rate represented by the f value of 0.9129. We then deleted the reaction which encodes for the sulphite reduction pathway and obtained a f value of -8.63e-13 indicating that the sulphite reduction pathway is essential. We wrote a program which finds all essential reactions in M. tuberculosis and E. coli SBML models and attempts to restore growth for each essential E. coli model with essential reactions from M. tuberculosis to identify other metabolic pathways we could apply a targeted drug screen to. We identified 100 other essential reactions we can target.

Human Practice

Technology Transfer

An essay that addresses the issue of designing a technology aimed at "developing" countries, rather than at “developed” ones: a typical case of technology transfer.

TB in France

Analysis of the social, medical and political aspects of the management of tuberculosis in France. Synthetic biology may help in many ways such as treatments, drug development, diagnostic. We also give advice on how to introduce it in clinics.

Gender Study

A comprehensive and quantitative study of gender (in)equality in iGEM and synthetic biology. A database was gathered and statistically analysed in order to depict sex ratio of iGEM teams' students and supervisors.



Gender balance and success in iGEM
Winning teams have a significantly higher number of women and are more Gender balanced.

TB Facts

Infographics page containing TB data and facts that captures all you need to know at a glance.

TB Gallery

A gallery of famous historic figures who had tuberculosis, made to raise awareness to its prevalence of in the past and present .

Collaboration

SensiGEM

SensiGEM is the iGEM Biosensor database generated by the teams Paris Bettencourt 2013 and Calgary 2013. In this database you can find fast and easy what biosensor projects were already done by past iGEM Teams. To be able to select the projects that fit into the database, we also collaborated to compose a joint definition a biosensor.

BGU iGEM Team from Israel

A mutual part characterization. We characterize the promoter units produced by the lac/ara-1 promoter of cI, a repressor of their constructed kill switch. In return, BGU characterizes our TDMH biobrick protein expression levels by Western Blot.

Braunschweig iGEM Team

Idea, bibliography, and beer sharing!

Centre for Research and Interdisciplinarity (CRI)
Faculty of Medicine Cochin Port-Royal, South wing, 2nd floor
Paris Descartes University
24, rue du Faubourg Saint Jacques
75014 Paris, France
+33 1 44 41 25 22/25
team2013@igem-paris.org
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Copyright (c) 2013 igem.org. All rights reserved.

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