Difference between revisions of "Team:INSA-UPS France/Applied Design"

Line 1: Line 1:
 +
 +
 +
 
{{INSA-UPS_France/Links_new}}
 
{{INSA-UPS_France/Links_new}}
 
{{INSA-UPS_France/Style_new}}
 
{{INSA-UPS_France/Style_new}}
 
{{INSA-UPS_France/Header_new}}
 
{{INSA-UPS_France/Header_new}}
 +
<html>
  
−
 
−
<html>
 
  
 
<!-- C O N T E N T -->
 
<!-- C O N T E N T -->
−
 
+
 
 +
 
 +
 
 
   <main class="site-main">
 
   <main class="site-main">
 
   <div class="main_content">
 
   <div class="main_content">
Line 14: Line 18:
 
   <div class="section_container">
 
   <div class="section_container">
  
−
     <section style="display:table;background:none;padding:0px !important;z-index:100; ">
+
     <section style="background:none;padding:0px !important;z-index:100; ">
−
       <h1 style="vertical-align:bottom;display:table-cell; width:70%;font-size:60pt;letter-spacing: 0.2em;z-index:120;text-align: center;">Description</h1>
+
       <h1 style="font-size:5vw;letter-spacing: 1vw;z-index:120;text-align: center;">Applied Design</h1>
−
       <img style="vertical-align:bottom;display:table-cell; width:100%;" src="https://static.igem.org/mediawiki/2017/e/e8/T--INSA-UPS_France--description_croco.png" alt="">
+
        
−
     </section>
+
     </section>  
−
 
+
−
    <style>
+
−
    /* ASIDE NAV */
+
−
      .left_container{
+
−
        width:25%;
+
−
        position:absolute;
+
−
        top:400px;
+
−
        padding:0;
+
−
        display:inline-block;
+
−
        font-family: 'Quicksand', sans-serif;
+
−
        font-weight: 400;
+
−
        font-size:16pt;
+
−
        text-align: right;
+
−
      }
+
−
 
+
−
      .aside-nav__item + .aside-nav__item{
+
−
        margin-top:20px;
+
−
      }
+
−
      .aside-nav__item{
+
−
        width:100%;
+
−
        position:relative;
+
−
      }
+
−
      .aside-nav__item:after{
+
−
        content:'';
+
−
        border:solid #3377a8 3px;
+
−
        position:absolute;
+
−
        right:-30px;
+
−
        top:40%;
+
−
        width:12px;
+
−
        height:12px;
+
−
        border-radius: 12px;   
+
−
        margin-left:20px;
+
−
      }
+
−
      .aside-nav__item.selected-item:after{
+
−
        background:#3377a8;
+
−
      }
+
−
      .aside-fixed{
+
−
        position:fixed;
+
−
        top: 120px;
+
−
        width: 18%;
+
−
      }
+
−
      .aside-nav__item a, .aside-nav__item a:focus, .aside-nav__item a:visited, .aside-nav__item a:hover{
+
−
        text-decoration: none;
+
−
        color:black;
+
−
      }
+
−
      .aside-nav__item a:hover{
+
−
        font-weight: 700;
+
−
      }
+
−
    </style>
+
−
 
+
−
    <div class="left_container">
+
−
    <div class="left_container__inside">
+
−
      <div class="aside-nav__item">
+
−
      <a href="#a1" data-number="1">
+
−
        Synthetic biology
+
−
      </a>
+
−
      </div>
+
−
      <div class="aside-nav__item">
+
−
      <a href="#a2" data-number="2">
+
−
        A microbial consortium chassis against cholera
+
−
      </a>
+
−
      </div>
+
−
      <div class="aside-nav__item">
+
−
      <a href="#a3" data-number="3">
+
−
        Mimicking <i>Vibrio cholerae</i>
+
−
      </a>
+
−
      </div>
+
−
      <div class="aside-nav__item">
+
−
      <a href="#a4" data-number="4">
+
−
        The sensing organism: <i>Vibrio harveyi</i>
+
−
      </a>
+
−
      </div>
+
−
      <div class="aside-nav__item">
+
−
      <a href="#a5" data-number="5">
+
−
        The effecting organism: <i>Pichia pastoris</i>
+
−
      </a>
+
−
      </div>
+
−
    </div>
+
−
    </div>
+
−
 
+
−
    <style>
+
−
    .right_container{
+
−
        width:70%;
+
−
        margin-left:30%;
+
−
    }
+
−
    .article_offset{
+
−
      margin-bottom:20px;
+
−
      border: solid 1px transparent;
+
−
    }
+
−
    </style>
+
−
 
+
−
   
+
−
    <div class="right_container">
+
−
 
+
−
    <div class="article_offset" id="a1"></div>
+
−
    <section>
+
−
      <h1>Combine to improve: a synthetic biology scale-up</h1>
+
−
      <p>
+
−
        Nature offers us a wide variety of tools in order to sense precise chemical or physical parameters. For example, enzymes and receptors are specialized for unique or restrained range of molecule, or even for specific light wavelength.<sup>1,2,3</sup> Obviously, as mankind progressed in the comprehension of life science, he wanted to take advantage from this extreme diversity and specialization. Synthetic biology was born thanks to those expectations in the early of the twentieth century<sup>4</sup> and made quite notable breakthrough. However, most of those works were based on the insertion of a lot of DNA information on one single model, typically <i>E. coli</i>. We observed that all those informations are not always compatible with the use of a unique microbial chassis : although standard microbial models are quite modular, they have a particular membrane, specific pathways and different ways to do protein maturation.
+
−
      </p>
+
−
      <p>
+
−
        Why should we persist to use a single model when we have access to a wide diversity of organisms?
+
−
      </p>
+
−
      <p>
+
−
        For our iGEM project, we decided to focus on the multi organisms aspect, making communication between prokaryotic and eukaryotic possible.
+
−
      </p>
+
−
    </section>
+
−
 
+
−
   
+
−
    <div class="article_offset" id="a2"></div>
+
−
    <section>
+
−
      <h1>A core: prokaryotic-eukaryotic communication
+
−
</h1>
+
−
      <p>
+
−
        Our first challenge was to design an eukaryote-prokaryote communication system, so we can have a standardized way of communication, with modulable input and output. This system answers to some of the synthetic biology current challenges<sup>8</sup> that are: device modularization and standardisation with the core, using the diversity of living systems and so, using the right cellular chassis, with the right genetics elements.
+
−
      </p>
+
−
      <img src="https://static.igem.org/mediawiki/2017/b/b3/T--INSA-UPS_France--description_sense-effect.png" alt="">
+
−
      <p class="left-p">
+
−
        Team SCUT<sup>26</sup> already described a binding-receptor system built on <i>Saccharomyces cerevisiae</i><sup>18</sup>, based on the Odr-10 receptor, a G Protein Coupled Receptor isolated from Caenorhabditis elegans<sup>19</sup>. The pathway is engaged by the activation of Odr-10 and has been shown to start the mating cascade which ends with  the activation of the pFUS1 promoter by Ste12<sup>20</sup>. After a discussion with Diethard Mattanovich , the supervisor of iGEM Team Boku Vienna, it appears from his transcriptomic data that the mating pathway including Ste12 was also present on Pichia pastoris, a yeast gaining more and more interest for being a robust tool for protein and metabolite production.<sup>33</sup> Once we found a molecule factory, we needed to find a way to induce it, whenever the bacteria sensor we were using. Checking the metabolism of diacetyl on KEGG Pathway, we identified that a simple enzyme, the acetolactate synthase (ALS), processes to produce the diacetyl from pyruvate, a ubiquitous metabolite.
+
−
      </p>
+
−
      <img class="right-img" src="https://static.igem.org/mediawiki/2017/2/24/T--INSA-UPS_France--Description-communicate.png" alt="">
+
−
      <img class="left-img" src="https://static.igem.org/mediawiki/2017/9/91/T--INSA-UPS_France--description_diacetyl.png" alt="">
+
−
      <p class="right-p">
+
−
        As this mechanism relies on diacetyl detection for pFUS1 activation, we needed  the sensing module to produce this molecule. Online tools predict that the missing enzyme to catalyse the production of this molecule is the acetolactate synthase (ALS). Indeed, this enzyme catalyses acetolactate production, which is then oxidized into diacetyl. Thus we decided to add the gene responsible for ALS production in the genetic construction we put in the sensing module.
+
−
      </p>
+
−
    </section>
+
−
 
+
−
 
+
−
    <div class="article_offset" id="a3"></div>
+
−
    <section>
+
−
      <h1>A microbial consortium against cholera</h1>
+
−
      <p>
+
−
        Recently, research teams started to focus on synthetic biology in order to find a way to deal with Vibrio cholerae<sup>5,6</sup>. Additionally, some iGEM teams also took the challenge of detecting <i>V. cholerae</i>, using <i>E. coli</i> as a host for the quorum sensing system, but it seems that this strategy did not succeed7 or showed mixed results<sup>8</sup>. Most of the iGEM teams intended to prevent the cholera infection thanks to gene targeting such as cleaving toxicity genes<sup>9</sup> or inhibiting specific genes on the pathogen<sup>10</sup>. With this lack of successful stories in iGEM on mono-microorganism and the need to have a whole specialised lab in order to build a complex system of synthetic biology, this statement could be perfect to test our core in real conditions and with a useful application.
+
−
      </p>
+
−
    </section>
+
−
 
+
−
    <div class="article_offset" id="a4"></div>
+
−
    <section>
+
−
      <h1>Finding a sensor</h1>
+
−
      <p class="left-p">
+
−
        First we had to detect the initial state of the system in order to activate the core. An interesting property of <i>Vibrio cholerae</i> is its quorum sensing system that depends on the CAI-1 molecule. CAI-1 directly reflects the amount of <i>V. cholerae</i> on water, and thus its virulence. Once CAI-1 is at high concentration, it can be detected and then  provides us a good way of detecting <i>V. cholerae</i> once it becomes pathogenic<sup>19</sup>. <i>Vibrio harveyi</i>, a non-pathogenic strain of <i>Vibrio</i>, showed itself as a perfect sensor of the CAI-1 molecule and thus of the quantity of <i>V. cholerae</i>. This strain fulfilled the requirements we wanted as a good synthetic biology chassis: easy to engineer, already has part of our final system such as the CqsS/CAI-1 pathway<sup>19,20</sup>. We only had to mutate the receptor and integrate the als gene to trigger diacetyl production in presence of CAI-1.
+
−
 
+
−
      </p>
+
−
      <figure>
+
−
        <img src="https://static.igem.org/mediawiki/2017/e/eb/T--INSA-UPS_France--Description-sense-quorum_2.png" alt="" class="right-img">
+
−
        <figcaption><i>Quorum sensing mechanism in</i> V. cholerae</figcaption>
+
−
      </figure>
+
−
      <p>
+
−
        For safety reasons, we were not able to manipulate <i>V. cholerae</i> in our lab. This is why we had to engineer <i>E. coli</i> to mimick <i>V. cholerae</i> in order to further test our system. The idea was to make <i>E. coli</i> produce the specific quorum sensing molecules of <i>V. cholerae</i>: CAI-1.
+
−
      </p>
+
−
    </section>
+
−
 
+
−
    <div class="article_offset" id="a5"></div>
+
−
    <section>
+
−
      <h1>Finding an effector</h1>
+
−
      <p>
+
−
        Because of our will to kill gram-negative bacteria, we assessed that a prokaryotic chassis could not be adequate to achieve the desired effect without drawbacks. So the information of <i>V. cholerae</i> detection must be transmitted  to an eukaryotic protein expressor : <i>Pichia pastoris</i>. Once we had both the sensor, and the core, we had to act on the system. In our application, we aim to reduce the amount of <i>V. cholerae</i>, or even better, to totally kill it. We found the solution thanks to an unorthogonal approach: we looked in the environment of <i>V. cholerae</i> in order to find out a competitor, or an organism not affected by it. It appears quite fast that crocodiles have an impressive immune system, that allows them to resist against lots of  diseases vectors infections<sup>22,23,24</sup>. We used from their amazing immune system promising molecules: antimicrobial peptides that have proven to have a good killing efficiency against <i>V. cholerae</i><sup>13,14</sup>. Moreover, this effector, with a good efficiency against bacteria and the need to be secreted, was a perfect effector to implement in our multi organisms system with specialised tasks.
+
−
 
+
−
      </p>
+
−
      <p>
+
−
        Those peptides are cationic molecules and can target bacterium membranes, to create pores in it, leading to the lysis of the cells<sup>24</sup>.
+
−
      </p>
+
−
      <img src="https://static.igem.org/mediawiki/2017/8/80/T--INSA-UPS_France--Description-kill.png" alt="">
+
−
      <p class="left-p">
+
−
        The fact that literature described the robustness of <i>Pichia pastoris</i><sup>16,17</sup> for the production of antimicrobial peptide made us definitively enthousiast about using this yeast as part of the core.
+
−
      </p>
+
−
      <img src="https://static.igem.org/mediawiki/2017/0/0b/T--INSA-UPS_France--Description-kill-MICAMP.png" alt="" class="right-img">
+
−
    </section>
+
−
 
+
−
    <div class="article_offset" id="a6"></div>
+
−
    <section style="background: none;">
+
−
      <h1 style="text-align:left;">Our system</h1>     
+
−
      <!--<p>
+
−
        See design for more informations of the genetic engineering we used!
+
−
      </p>-->
+
−
      <img src="https://static.igem.org/mediawiki/2017/b/b8/T--INSA-UPS_France--description_loop.png" alt="">     
+
−
    </section>
+
−
 
+
−
    </div>
+
−
    <!-- fin section -->   
+
  
 
   </div>
 
   </div>
−
  </div>
+
</div>
−
    <style>
+
−
 
+
−
footer{
+
−
  position:relative;
+
−
  text-align:center;
+
−
  margin-top:20px;
+
−
  background: #323537;
+
−
  width:100%;
+
−
}
+
−
 
+
−
/* CONTACT ICONS */
+
−
 
+
−
.icons{ 
+
−
  display:inline-block;
+
−
  margin:40px 0;
+
−
 
+
−
 
+
−
}
+
−
 
+
−
.icons > a{
+
−
  color:black;
+
−
  margin:10px;
+
−
  text-shadow:2px 2px 0px white;
+
−
}
+
−
 
+
−
#fbIcon:hover{
+
−
  color:#3b5998;
+
−
  text-shadow:2px 2px 0 #000000;
+
−
}
+
−
 
+
−
#twitterIcon:hover{
+
−
  color:#55acee;
+
−
  text-shadow:2px 2px 0 #000000;
+
−
}
+
−
 
+
−
#contactIcon:hover{
+
−
  color:#e5e5e5;
+
−
  text-shadow:2px 2px 0 #000000;
+
−
}
+
−
#instaIcon:hover{
+
−
  color:#8a3ab9;
+
−
  text-shadow:2px 2px 0 #000000;
+
−
}
+
−
 
+
−
/* SPONSORS IMG */
+
−
 
+
−
.footer_sponsors img{
+
−
  max-height:50px;
+
−
  display:inline-block;
+
−
  margin:10px;
+
−
  opacity:0.5;
+
−
}
+
−
.footer_sponsors img:hover{
+
−
  opacity:1;
+
−
}
+
  
−
</style>
 
 
   <footer>
 
   <footer>
 
      
 
      
Line 293: Line 61:
 
   </div>
 
   </div>
 
   </main>
 
   </main>
−
 
−
<!--
 
−
  -->
 
−
 
−
</div>
 
  
  
Line 303: Line 66:
  
 
<!-- C O N T E N T -->
 
<!-- C O N T E N T -->
−
<script type="text/javascript">
 
−
  $('.js-sticky').addClass('is-sticky');
 
−
</script>
 
  
−
 
−
<script type="text/javascript">
 
−
  $('.main_content').scroll(function(){
 
−
    console.log($('.main_content').scrollTop());
 
−
    console.log("position 1 :");
 
−
    console.log($("#a1").position().top);
 
−
    console.log("position 2 :");
 
−
    console.log($("#a2").position().top);
 
−
    var pos = $('.main_content').scrollTop();
 
−
    // BOLD ASIDE NAV
 
−
    if(pos>$("#a1").position().top-10){
 
−
      $('*[data-number="1"]').css("font-weight", "bold");
 
−
      $('*[data-number="1"]').parent().addClass("selected-item");
 
−
      $('*[data-number="2"]').css("font-weight", "normal");
 
−
      $('*[data-number="2"]').parent().removeClass("selected-item");
 
−
      $('*[data-number="3"]').css("font-weight", "normal");
 
−
      $('*[data-number="3"]').parent().removeClass("selected-item");
 
−
      $('*[data-number="4"]').css("font-weight", "normal");
 
−
      $('*[data-number="4"]').parent().removeClass("selected-item");
 
−
      $('*[data-number="5"]').css("font-weight", "normal");
 
−
      $('*[data-number="5"]').parent().removeClass("selected-item");
 
−
      $('*[data-number="6"]').css("font-weight", "normal");
 
−
      $('*[data-number="6"]').parent().removeClass("selected-item");
 
−
      if(pos>$("#a2").position().top-10){
 
−
        $('*[data-number="1"]').css("font-weight", "normal");
 
−
        $('*[data-number="1"]').parent().removeClass("selected-item");
 
−
        $('*[data-number="2"]').css("font-weight", "bold");
 
−
        $('*[data-number="2"]').parent().addClass("selected-item");
 
−
        $('*[data-number="3"]').css("font-weight", "normal");
 
−
        $('*[data-number="3"]').parent().removeClass("selected-item");
 
−
        $('*[data-number="4"]').css("font-weight", "normal");
 
−
        $('*[data-number="4"]').parent().removeClass("selected-item");
 
−
        $('*[data-number="5"]').css("font-weight", "normal");
 
−
        $('*[data-number="5"]').parent().removeClass("selected-item");
 
−
        $('*[data-number="6"]').css("font-weight", "normal");
 
−
        $('*[data-number="6"]').parent().removeClass("selected-item");
 
−
        if(pos>$("#a3").position().top-10){
 
−
          $('*[data-number="1"]').css("font-weight", "normal");
 
−
          $('*[data-number="1"]').parent().removeClass("selected-item");
 
−
          $('*[data-number="2"]').css("font-weight", "normal");
 
−
          $('*[data-number="2"]').parent().removeClass("selected-item");
 
−
          $('*[data-number="3"]').css("font-weight", "bold");
 
−
          $('*[data-number="3"]').parent().addClass("selected-item");
 
−
          $('*[data-number="4"]').css("font-weight", "normal");
 
−
          $('*[data-number="4"]').parent().removeClass("selected-item");
 
−
          $('*[data-number="5"]').css("font-weight", "normal");
 
−
          $('*[data-number="5"]').parent().removeClass("selected-item");
 
−
          $('*[data-number="6"]').css("font-weight", "normal");
 
−
          $('*[data-number="6"]').parent().removeClass("selected-item");
 
−
          if(pos>$("#a4").position().top-10){
 
−
            $('*[data-number="1"]').css("font-weight", "normal");
 
−
            $('*[data-number="1"]').parent().removeClass("selected-item");
 
−
            $('*[data-number="2"]').css("font-weight", "normal");
 
−
            $('*[data-number="2"]').parent().removeClass("selected-item");
 
−
            $('*[data-number="3"]').css("font-weight", "normal");
 
−
            $('*[data-number="3"]').parent().removeClass("selected-item");
 
−
            $('*[data-number="4"]').css("font-weight", "bold");
 
−
            $('*[data-number="4"]').parent().addClass("selected-item");
 
−
            $('*[data-number="5"]').css("font-weight", "normal");
 
−
            $('*[data-number="5"]').parent().removeClass("selected-item");
 
−
            $('*[data-number="6"]').css("font-weight", "normal");
 
−
            $('*[data-number="6"]').parent().removeClass("selected-item");
 
−
            if(pos>$("#a5").position().top-10){
 
−
              $('*[data-number="1"]').css("font-weight", "normal");
 
−
              $('*[data-number="1"]').parent().removeClass("selected-item");
 
−
              $('*[data-number="2"]').css("font-weight", "normal");
 
−
              $('*[data-number="2"]').parent().removeClass("selected-item");
 
−
              $('*[data-number="3"]').css("font-weight", "normal");
 
−
              $('*[data-number="3"]').parent().removeClass("selected-item");
 
−
              $('*[data-number="4"]').css("font-weight", "normal");
 
−
              $('*[data-number="4"]').parent().removeClass("selected-item");
 
−
              $('*[data-number="5"]').css("font-weight", "bold");
 
−
              $('*[data-number="5"]').parent().addClass("selected-item");
 
−
              $('*[data-number="6"]').css("font-weight", "normal");
 
−
              $('*[data-number="6"]').parent().removeClass("selected-item");
 
−
              if(pos>$("#a6").position().top-10){
 
−
                $('*[data-number="1"]').css("font-weight", "normal");
 
−
                $('*[data-number="1"]').parent().removeClass("selected-item");
 
−
                $('*[data-number="2"]').css("font-weight", "normal");
 
−
                $('*[data-number="2"]').parent().removeClass("selected-item");
 
−
                $('*[data-number="3"]').css("font-weight", "normal");
 
−
                $('*[data-number="3"]').parent().removeClass("selected-item");
 
−
                $('*[data-number="4"]').css("font-weight", "normal");
 
−
                $('*[data-number="4"]').parent().removeClass("selected-item");
 
−
                $('*[data-number="5"]').css("font-weight", "normal");
 
−
                $('*[data-number="5"]').parent().removeClass("selected-item");
 
−
                $('*[data-number="6"]').css("font-weight", "bold");
 
−
                $('*[data-number="6"]').parent().addClass("selected-item");
 
−
              }
 
−
            }
 
−
          }
 
−
        }
 
−
      }
 
−
    }
 
−
    // FIXED ASIDE NAV
 
−
    if(pos>371){
 
−
      $('.left_container').addClass("aside-fixed");
 
−
    }
 
−
    else{
 
−
      $('.left_container').removeClass("aside-fixed");
 
−
    }
 
−
  });
 
−
 
−
</script>
 
−
 
−
<script type="text/javascript">
 
−
 
−
    // NAV BAR SUBNAV CLICK
 
−
 
−
  $(document).on("click",".cat_name", function(){
 
−
    if($(this).parent().children('.subnav').css("max-height")=="0px"){
 
−
      $('.subnav').css("max-height","0px");
 
−
      $(this).parent().children('.subnav').css("max-height","1000px");
 
−
    }
 
−
    else{
 
−
      $(this).parent().children('.subnav').css("max-height","0px");
 
−
    }   
 
−
  });
 
−
</script>
 
−
 
−
<script type="text/javascript">
 
−
  var contentSections = $('.article_offset'),
 
−
  navigationItems = $('.left_container .aside-nav__item:after');
 
−
 
−
  updateNavigation();
 
−
  $('.main_content').on('scroll', function(){
 
−
    updateNavigation();
 
−
    });
 
−
 
−
 
−
  function updateNavigation() {
 
−
    contentSections.each(function(){
 
−
      $this = $(this);
 
−
 
−
      var activeSection = $('.left_container a[href="#'+$this.attr('id')+'"]').data('number') - 1;
 
−
    });
 
−
  }
 
−
 
−
  function smoothScroll(target) {
 
−
        $('body,html').animate(
 
−
          {'scrollTop':target.offset().top},
 
−
          600
 
−
        );
 
−
  }
 
−
</script>
 
  
 
</body>
 
</body>
 
</html>
 
</html>
 +
 
{{INSA-UPS_France/General_script}}
 
{{INSA-UPS_France/General_script}}
 
{{INSA-UPS_France/Header_script}}
 
{{INSA-UPS_France/Header_script}}

Revision as of 20:20, 21 October 2017


Croc'n Cholera
iGEM UPS-INSA Toulouse 2017

Applied Design