Team:Paris Bettencourt/YonatanTest

From 2013.igem.org

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<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Detect">Detect</a></h2>
+
    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Detect">Detect</a></h2>
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<div class="overbox" style="height:500px;">
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    <div class="overbox">
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    <div class="bkgr">
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      <div class="bkgr">
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      <h2>Background</h2>
+
<h2>Background</h2>
-
      <p>CRISPR/Cas systems generate site-specific double strand breaks and have recently been used for genome editing.  </p>
+
<p>CRISPR/Cas systems generate site-specific double strand breaks and have recently been used for genome editing.  </p>
 +
      </div>
 +
      <div class="results">
 +
<h2>Results</h2>
 +
<ul>
 +
          <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>Testing the new assembly standard for our cloning.</li>
 +
</ul><h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Assembly_Standard">Assembly Standard</h2>
 +
<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 class="biocriks">
 +
<h2>BioBricks</h2>
 +
<ol>
 +
          <li><a href="http://parts.igem.org/Part:BBa_K1137012" target="_blank">BBa_K1137012 (gRNA anti-KAN)</a></li>
 +
          <li><a href="http://parts.igem.org/Part:BBa_K1137013" target="_blank">BBa_K1137013 (crRNA anti-KAN)</a></li>
 +
          <li><a href="http://parts.igem.org/Part:BBa_K1137014" target="_blank">BBa_K1137014 (tracrRNA-Cas9)</a></li>
 +
          <li><a href="http://parts.igem.org/Part:BBa_K1137015" target="_blank">BBa_K1137015 (pRecA-LacZ)</a></li>
 +
</ol>
 +
      </div>
 +
      <div style="clear: both;"></div>
 +
      <div class="aims">
 +
<h2>Aims</h2>
 +
<p>Building a genotype sensor based on CRISPR/Cas that reports existance of an antibiotic resistance gene.</p>
 +
      </div>
 +
      <div style="clear: both;"></div>
     </div>
     </div>
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  <div class="results" style="width:250px;">
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    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Target</a></h2>
-
       <h2>Results</h2>
+
    <div class="overbox">
-
      <ul>
+
      <div class="bkgr">
-
        <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>Background</h2>
-
        <li>Testing the new assembly standard for our cloning.</li>
+
<p>SirA is an essential gene in latent tuberculosis infections</p>
-
      </ul><h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Assembly_Standard">Assembly Standard</h2>
+
       </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 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>
 +
</ol>
 +
      </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>
     </div>
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+
   
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     <div style="clear: both;"></div>
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     <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Infiltrate">Infiltrate</a></h2>
-
    <div class="aims">
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    <div class="overbox">
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      <h2>Aims</h2>
+
      <div class="bkgr">
-
      <p>Building a genotype sensor based on CRISPR/Cas that reports existance of an antibiotic resistance gene.</p>
+
<h2>Background</h2>
 +
<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>
 +
      <div class="results">
 +
<h2>Results</h2>
 +
<ul>
 +
  <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>We expressed the lysteriolyin O (LLO) gene in <i>E. coli</i> and showed that it is capable of entering the macrophage cytosol.</li>
 +
  <li>We co-infected macrophages with both mycobacteria and our engineered <i>E. coli</i> to characterize the resulting phagocytosis and killing.</li>
 +
</ul>
 +
<p></p>
 +
      </div>
 +
      <div class="biocriks">
 +
<h2>BioBricks</h2>
 +
<ol>
 +
  <li><a href="http://parts.igem.org/Part:BBa_K1137008" target="_blank">BBa_K1137008 (TDMH)</a></li>
 +
</ol>
 +
      </div>
 +
      <div style="clear: both;"></div>
 +
      <div class="aims">
 +
<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>
 +
      </div>
 +
      <div style="clear: both;"></div>
     </div>
     </div>
-
 
+
    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Sabotage</a></h2>
-
  <div class="aims">
+
    <div class="overbox">
-
       <h2>BioBricks</h2>
+
       <div class="bkgr">
-
       <ol>
+
<h2>Background</h2>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137012" target="_blank">BBa_K1137012 (gRNA anti-KAN)</a></li>
+
<p>One of the main concern about tuberculosis today is the emergence of antibiotic resistant strain</p>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137013" target="_blank">BBa_K1137013 (crRNA anti-KAN)</a></li>  
+
       </div>
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137014" target="_blank">BBa_K1137014 (tracrRNA-Cas9)</a></li>
+
      <div class="results">
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137015" target="_blank">BBa_K1137015 (pRecA-LacZ)</a></li>
+
<h2>Results</h2>
-
       </ul>
+
<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>
 +
</ol>
 +
      </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>
     </div>
-
 
+
      
-
     <div style="clear: both;"></div>
+
  </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>
+
-
<div class="overbox">
+
-
    <div class="bkgr">
+
-
      <h2>Background</h2>
+
-
      <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>
+
-
    <div class="results">
+
-
      <h2>Results</h2>
+
-
      <ul>
+
-
        <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>We expressed the lysteriolyin O (LLO) gene in <i>E. coli</i> and showed that it is capable of entering the macrophage cytosol.</li>
+
-
        <li>We co-infected macrophages with both mycobacteria and our engineered <i>E. coli</i> to characterize the resulting phagocytosis and killing.</li>
+
-
      </ul>
+
-
      <p></p>
+
-
    </div>
+
-
    <div class="biocriks">
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-
      <h2>BioBricks</h2>
+
-
      <ol>
+
-
        <li><a href="http://parts.igem.org/Part:BBa_K1137008" target="_blank">BBa_K1137008 (TDMH)</a></li>
+
-
      </ul>
+
-
    </div>
+
-
    <div style="clear: both;"></div>
+
-
    <div class="aims">
+
-
      <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>
+
-
    </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>
+
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-
<h2><a href="https://2013.igem.org/wiki/index.php?title=Team:Paris_Bettencourt/Human_Practice/Overview">Human Practice</a></h2>
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<div class="overbox">
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    <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>
+
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      <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>
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-
 
+
-
    <div class="results" style="width:425px;height:340px;">
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      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Gender_Study">Gender Study</h2>
+
-
      <ul>
+
-
        <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>
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-
     
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      </ul>
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      <p></p>
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-
    </div>
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-
    <div class="bkgr" style="width:315px;">
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      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_Gallery"> TB gallery</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 class="bkgr" style="width:315px;margin-bottom:0">
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-
      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_Facts">TB facts</h2>
+
-
      <p> Infographics page containing TB data and facts that captures all you need to know at a glance.</p>
+
-
    </div>
+
-
 
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-
<div style="clear: both;"></div>
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-
    <div class="aims" style="width:315px;height:140px;bottom:143px;margin-bottom:0">
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      <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>
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-
    <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>
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<div class="overbox">
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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>
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-
      <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>
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    </div>
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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/Collaboration">Braunschweig iGEM Team</h2>
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      <ul>
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        <p>Idea, bibliography, and beer sharing!</p>
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-
     
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    </div>
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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/Collaboration">BGU iGEM Team from Israel</h2>
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      <ul>
+
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        <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>
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    </div>
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    <div style="clear: both;"></div>
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  </div>
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<h2><a href="">Modelling</h2>
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<div class="overbox">
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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/Project/Sabotage">Population Dynamics Model</h2>
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      <ul>
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        <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>
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    </div>
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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/Project/Target">Structural analysis of SirA</h2>
+
-
      <ul>
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        <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>
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      <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</h2>
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        <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. </p>
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Revision as of 08:30, 25 October 2013

Detect

Background

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

Results

  • Successfully cloned gRNA anti-KAN, crRNA anti-KAN, tracrRNA-Cas9 and pRecA-LacZ into Biobrick backbones and therefore generated four new BioBricks.
  • Testing the new assembly standard for our cloning.

Assembly Standard

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.

BioBricks

  1. BBa_K1137012 (gRNA anti-KAN)
  2. BBa_K1137013 (crRNA anti-KAN)
  3. BBa_K1137014 (tracrRNA-Cas9)
  4. BBa_K1137015 (pRecA-LacZ)

Aims

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

Target

Background

SirA is an essential gene in latent tuberculosis infections

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 anaylsis

BioBricks

  1. BBa_K1137000 (SirA)
  2. BBa_K1137001 (FprA)
  3. BBa_K1137002 (FdxA)

Aims

To perform an drug screen targeted at the sirA gene from mycobacteria

Infiltrate

Background

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

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 lysteriolyin 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.

BioBricks

  1. BBa_K1137008 (TDMH)

Aim

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

Sabotage

Background

One of the main concern about tuberculosis today is the emergence of antibiotic resistant strain

Results

  • Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins
  • successful conversion of antibiotic resistant population of E. coli to a sensitive state

BioBricks

  1. BBa_K1137009 (sRNA anti Kan)    Characterized
  2. BBa_K1137010 (sRNA anti Cm)    Characterized
  3. BBa_K1137011 (sRNA anti Lac)   

Aims

Our objective is to make an antibiotic-resistant bacterial population sensitive again to those same antibiotics.

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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