Team:Paris Bettencourt/Results

From 2013.igem.org

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    <a href="#Detect">
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<h2>Detect</h2>
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    <a href="#Target">
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<h2>Target</h2>
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<h2>Infiltrate</h2>
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<h2>Sabotage</h2>
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<h2>Modelling</h2>
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<h2>Human Practice</h2>
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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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         <p style="margin-top:-60px;font-size:13px">CRISPR anti-Kan plasmids target kanamycin resistant E. coli. WT (blue) and a kanamycin resistant strain (KanR, red) were co-transformed with a plasmid carrying the Cas9 construct, and a second plasmid carrying the anti-Kanamycin gRNA. WT was successfully transformed with one or both plasmids. KanR E. coli couldn’t be tranformed with both plasmids because of Cas9-induced cleavage of the chromosome specifically at the KanR cassette, with about 99% efficiency.
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         <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.
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  <h2>Results</h2>
  <h2>Results</h2>
  <ul>
  <ul>
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             <li>Produced an E. coli strain which relies upon mycobacterial sirA, fprA and fdxA genes to survive in M9 minimal media</li>
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             <li>Produced an <i>E. coli</i> strain which relies upon mycobacterial sirA, fprA and fdxA genes to survive in M9 minimal media.</li>
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             <li>Demonstrated that E. coli can survive with mycobacterial sulfite reduction pathway with Flux Balance Analysis</li>
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             <li>Demonstrated that <i>E. coli</i> can survive with mycobacterial sulfite reduction pathway with Flux Balance Analysis.</li>
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             <li>Located drug target sites on sirA as well as identified high structural similarity between cysI and sirA through structural anaylsis</li>
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             <li>Located drug target sites on sirA as well as identified high structural similarity between cysI and sirA through structural analysis.</li>
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<li>Identified a potential anti-TB activity of Pyridoxine at high doses.</li>
  </ul>
  </ul>
</div>
</div>
<div class="biocriks">
<div class="biocriks">
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<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>
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<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>
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<a href="http://parts.igem.org/Part:BBa_K1137000" target="_blank"><img width="32%" style="margin-top:15px" src="https://static.igem.org/mediawiki/2013/7/79/Bb_target_sirA.png"/></a>
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  <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>
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         <p style="font-size:13px"> 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  
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         <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  
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     <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Infiltrate">Infiltrate</a></h2>
     <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Infiltrate">Infiltrate</a></h2>
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  <ul>
  <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 enzyme Trehalose Dimycolate Hydrolase (TDMH) in <i>E.coli</i> and showed that it is highly toxic to mycobacteria in culture.</li>
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             <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>
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             <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>
             <li>We co-infected macrophages with both mycobacteria and our engineered <i>E. coli</i> to characterize the resulting phagocytosis and killing.</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>
  </ul>
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  <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>
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         <p style="font-size:13px"> FTDMH 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.
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         <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.
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     <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Sabotage</a></h2>
     <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Sabotage</a></h2>
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  <h2>Results</h2>
  <h2>Results</h2>
  <ul>
  <ul>
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             <li>Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins</li>
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             <li>Construction and characterization of phagemids coding for small RNA targeting antibiotic resistance proteins.</li>
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             <li>Showed theoretically that fitness cost is critical for the stable propagation of a genetic element in a population.</li>
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             <li>Showed theoretically burden of a device is critical for the maintenance of a genetic element in a population.</li>
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             <li>Successful conversion of antibiotic resistant population of E. coli to a sensitive state (on two different antibiotic resistances)</li>
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             <li>Successful conversion of antibiotic resistant population of <i>E. coli</i> to a sensitive state (on two different antibiotic resistances).</li>
  </ul>
  </ul>
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<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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<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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<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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         <p style="font-size:13px">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.
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         <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.
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     <h2><a href="">Modelling</a></h2>
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<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Population Dynamics Model</a></h2>
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Sabotage">Population Dynamics Model</a></h2>
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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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<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>
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        <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>
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        </br>
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        <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>  
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<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Structural analysis of SirA</a></h2>
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<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Structure Based Modelling</a></h2>
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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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<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>
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        <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>
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       <div class="projtile" style="margin-right:0;">
       <div class="projtile" style="margin-right:0;">
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</a></h2>
<h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Target">Flux Balance Analysis</a></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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<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>
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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>
     <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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  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Technology_Transfer">Technology  Transfer</a></h2>
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  <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>
  <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>
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  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/TB_France">TB in France</a></h2>
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  <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.
  <p>Analysis of the social, medical and political aspects of the management of tuberculosis in France.
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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>
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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>
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  <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Human_Practice/Gender_Study">Gender Study</a></h2>
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  <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>
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           <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 supervisor
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           <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>
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          <center><img width="45%" src="https://static.igem.org/mediawiki/2013/d/de/GS_Prize.png"></center><br>
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          <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>
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  <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>
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<div class="aims">
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  <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>
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  <p> A gallery of famous historic figures who had tuberculosis, made to raise awareness to its prevalence of in the past and present .</p>
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    <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">Collaboration</a></h2>
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        <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/SensiGEM">SensiGEM</a></h2>
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        <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.
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        <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">BGU iGEM Team from Israel</a></h2>
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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. 
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        <h2><a href="https://2013.igem.org/Team:Paris_Bettencourt/Collaboration">Braunschweig iGEM Team</h2>
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        <p>Idea, bibliography, and beer sharing!</p>       
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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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