Difference between revisions of "Team:WashU StLouis/team"

 
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{{:Team:WashU_StLouis/Header}}
 
{{:Team:WashU_StLouis/Header}}
 
<html>
 
<html>
 +
 
   <!-- Navigation -->
 
   <!-- Navigation -->
 
   <nav class="navbar navbar-default navbar-fixed-top">
 
   <nav class="navbar navbar-default navbar-fixed-top">
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           <span class="icon-bar"></span>
 
           <span class="icon-bar"></span>
 
         </button>
 
         </button>
         <a class="navbar-brand page-scroll" href="#page-top">Nitrogen</a>
+
         <a class="navbar-brand page-scroll" href="#page-top">Nitrogenius</a>
        <a class="navbar-brand" href="https://2015.igem.org">
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          <img id="igemLogo" class="img-responsive" src="https://static.igem.org/mediawiki/2014/0/09/Aalto_Helsinki_Logov_iGEM.png" alt="Igem Logo">
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        </a>
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       </div>
 
       </div>
  
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           </li>
 
           </li>
 
           <li>
 
           <li>
             <a class="page-scroll" href="#overview">Overview</a>
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             <a class="page-scroll" href="#Team">Team</a>
 
           </li>
 
           </li>
 
           <li>
 
           <li>
             <a class="page-scroll" href="#team">Team</a>
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             <a href="mailto:ayekedavidr@wustl.edu?subject=Bug">Report Bugs</a>
          </li>
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          <li>
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            <a class="page-scroll" href="#collaboration">Collaboration</a>
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          </li>
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          <li>
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            <a class="page-scroll" href="#sponsors">Sponsors</a>
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          </li>
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+
          <li>
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            <a class="page-scroll" href="#contact">Contact</a>
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          </li>
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          <li>
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            <a href="#reportBugsModal" class="overview-link" data-toggle="modal">Report Bugs</a>
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          </li>
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          <li>
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            <a class="page-scroll" href="#sitemap">More</a>
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           </li>
 
           </li>
 
         </ul>
 
         </ul>
 
       </div>
 
       </div>
      <!-- iGEM Logo -->
 
 
       <!-- /.navbar-collapse -->
 
       <!-- /.navbar-collapse -->
 
     </div>
 
     </div>
 
     <!-- /.container-fluid -->
 
     <!-- /.container-fluid -->
 
   </nav>
 
   </nav>
  <div class="container">
 
  
  
  
    <!-- Project Overview -->
 
    <!-- Main container -->
 
    <section id="overview" class="bg-light-gray row sectionNum1">
 
      <div class="container">
 
        <div class="row">
 
          <div class="col-lg-12 text-center">
 
            <h2 class="section-heading">Project Overview</h2>
 
            <h3 class="section-subheading text-muted">Washington University and Penn State iGEM</h3>
 
          </div>
 
        </div>
 
        <div class="row">
 
          <!-- Previously on Wustl iGEM -->
 
          <div class="col-md-4 col-sm-6 overview-item">
 
            <a href="#overviewModal1" class="overview-link" data-toggle="modal">
 
              <div class="overview-hover">
 
                <div class="overview-hover-content">
 
                  <i class="fa fa-plus fa-3x"></i>
 
                </div>
 
              </div>
 
              <img src="https://static.igem.org/mediawiki/2015/7/76/Calendar52.png" class="img-responsive" alt="">
 
  
            </a>
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  <!-- Project Overview -->
            <div class="overview-caption">
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  <!-- Main container -->
              <h4>Last Year</h4>
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  <div class="container">
              <p class="text-muted">Learn from history</p>
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     <section id="team"  class="bg-light-gray row sectionNum1 sectionNum2 sectionNum3 sectionNum4 sectionNum5 sectionNum6 ">
            </div>
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          </div>
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          <!-- Mission statement -->
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          <div class="col-md-4 col-sm-6 overview-item">
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            <a href="#overviewModal2" class="overview-link" data-toggle="modal">
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              <div class="overview-hover">
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                <div class="overview-hover-content">
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                  <i class="fa fa-plus fa-3x"></i>
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                </div>
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              </div>
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              <img src="https://static.igem.org/mediawiki/2015/7/72/Bullseye.png" class="img-responsive" alt="">
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            </a>
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            <div class="overview-caption">
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              <h4>Mission Statement</h4>
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              <p class="text-muted">The goal in a sentence</p>
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            </div>
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          </div>
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          <!-- Nitrogen Project -->
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          <div class="col-md-4 col-sm-6 overview-item">
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            <a href="#overviewModal3" class="overview-link" data-toggle="modal">
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              <div class="overview-hover">
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                <div class="overview-hover-content">
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                  <i class="fa fa-plus fa-3x"></i>
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                </div>
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              </div>
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              <img src="https://static.igem.org/mediawiki/2015/a/a9/Earth17.png" class="img-responsive" alt="">
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            </a>
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            <div class="overview-caption">
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              <h4>Nitrogen Project</h4>
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              <p class="text-muted">Ain't broke, but we got to fix it</p>
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            </div>
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          </div>
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          <!-- The Big picture -->
+
          <div class="col-md-4 col-sm-6 overview-item">
+
            <a href="#overviewModal4" class="overview-link" data-toggle="modal">
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              <div class="overview-hover">
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                <div class="overview-hover-content">
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                  <i class="fa fa-plus fa-3x"></i>
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                </div>
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              </div>
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              <img src="https://static.igem.org/mediawiki/2015/c/cf/Zoom27.png" class="img-responsive" alt="">
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            </a>
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            <div class="overview-caption">
+
              <h4>The Big Picture</h4>
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              <p class="text-muted">Why did we do this?</p>
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            </div>
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          </div>
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          <!-- Materials and Methods -->
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          <div class="col-md-4 col-sm-6 overview-item">
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            <a href="#overviewModal5" class="overview-link" data-toggle="modal">
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              <div class="overview-hover">
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                <div class="overview-hover-content">
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                  <i class="fa fa-plus fa-3x"></i>
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                </div>
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              </div>
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              <img src="https://static.igem.org/mediawiki/2015/9/9f/Beaker2.png" class="img-responsive" alt="">
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            </a>
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            <div class="overview-caption">
+
              <h4>Materials and Methods</h4>
+
              <p class="text-muted">Imitation is the sincerest form of flattery.</p>
+
            </div>
+
          </div>
+
          <!-- Discussion -->
+
          <div class="col-md-4 col-sm-6 overview-item">
+
            <a href="#overviewModal6" class="overview-link" data-toggle="modal">
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              <div class="overview-hover">
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                <div class="overview-hover-content">
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                  <i class="fa fa-plus fa-3x"></i>
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                </div>
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              </div>
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              <img src="https://static.igem.org/mediawiki/2015/0/0a/Comments16.png" class="img-responsive" alt="">
+
            </a>
+
            <div class="overview-caption">
+
              <h4>Discussion</h4>
+
              <p class="text-muted">Explaining the results</p>
+
            </div>
+
          </div>
+
        </div>
+
      </div>
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    </section>
+
 
+
    <!-- Team Section -->
+
     <section id="team"  class="bg-white row sectionNum2">
+
 
       <div class="container">
 
       <div class="container">
 
         <div class="row">
 
         <div class="row">
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         </div>
 
         </div>
 
         <div class="row">
 
         <div class="row">
          <div class="col-lg-12">
+
        <div class="col-lg-12 text-center">
            <ul class="timeline">
+
          <img height="255" width="255" class="img-responsive img-circle img-centered" src="https://static.igem.org/mediawiki/2015/1/1d/Charlotte.JPG" alt="Charlotte Bourg Picture"/>
              <li class="row">
+
          <h2 class="section-heading">Charlotte Bourg</h2>
                <div class="timeline-image">
+
          <h3 class="section-subheading text-muted">Biochemistry and Spanish @ Washington University</h3>
                  <img class="img-circle img-responsive" src="http://placehold.it/200x200" alt="">
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          <p>
                </div>
+
            Hi, I’m Charlotte Bourg and I’m a rising senior (eek) at Wash U. I’m double majoring in biochemistry and Spanish. I’m working with David in the Zhang lab, doing a lot of cloning with the Cyanothece nif cluster in E. coli. Outside of lab, I enjoy running, reading, cooking, watching movies, and exploring the St. Louis area.
                <div class="timeline-panel">
+
          </p>
                  <div class="timeline-heading">
+
        </div>
                    <h4>Jessica O'Callaghan</h4>
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      </div>
                    <h4 class="subheading">Chemical Engineering</h4>
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                  </div>
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                  <div class="timeline-body">
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                    <!-- lead -->
+
                    <p class="text-muted">Penn State</p>
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                  </div>
+
                </div>
+
              </li>
+
              <li class="row timeline-inverted">
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                <div class="timeline-image">
+
                  <img class="img-circle img-responsive" src="https://static.igem.org/mediawiki/2015/3/32/Laura.jpg" alt="Laura">
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                </div>
+
                <div class="timeline-panel">
+
                  <div class="timeline-heading">
+
                    <h4>Laura Beebe</h4>
+
                    <h4 class="subheading">Biochemistry and Molecular Biology</h4>
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                  </div>
+
                  <div class="timeline-body">
+
                    <!-- Lead -->
+
                    <p class="text-muted">Penn State</p>
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                  </div>
+
                </div>
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              </li>
+
              <li class="row ">
+
                <div class="row timeline-image">
+
                  <img class="img-circle img-responsive" src="https://static.igem.org/mediawiki/2015/5/5c/Blake_actkinson.png" alt="Blake Actkinson">
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                </div>
+
                <div class="timeline-panel">
+
                  <div class="timeline-heading">
+
                    <h4>Blake Actkinson</h4>
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                    <h4 class="subheading">Biomedical Engineering</h4>
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                  </div>
+
                  <div class="timeline-body">
+
                    <p class="text-muted">Washington University in St. Louis</p>
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                  </div>
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                </div>
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              </li>
+
              <li class="row timeline-inverted">
+
                <div class="row timeline-image">
+
                  <img class="img-circle img-responsive" src="https://static.igem.org/mediawiki/2015/1/1d/Charlotte.JPG" alt="Charlotte">
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                </div>
+
                <div class="timeline-panel">
+
                  <div class="timeline-heading">
+
                    <h4>Charlotte Bourg</h4>
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                    <h4 class="subheading">Biochemistry and Spanish</h4>
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                  </div>
+
                  <div class="timeline-body">
+
                    <p class="text-muted">Washington University in St. Louis</p>
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                  </div>
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                </div>
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              </li>
+
              <li class="row ">
+
                <div class="row timeline-image">
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                  <img class="img-circle img-responsive" src="https://static.igem.org/mediawiki/2015/c/c6/David_ayeke.jpg" alt="">
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                </div>
+
                <div class="timeline-panel">
+
                  <div class="timeline-heading">
+
                    <h4>David Ayeke</h4>
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                    <h4 class="subheading">Computer Engineering</h4>
+
                  </div>
+
                  <div class="timeline-body">
+
                    <p class="text-muted">Washington University in St. Louis</p>
+
                  </div>
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                </div>
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              </li>
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              <li class="row  timeline-inverted">
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                <div class="row timeline-image">
+
                  <img class="img-circle img-responsive" src="https://static.igem.org/mediawiki/2015/6/6b/Mike_toomey.png" alt="">
+
                </div>
+
                <div class="timeline-panel">
+
                  <div class="timeline-heading">
+
                    <h4>Mike Toomey</h4>
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                    <h4 class="subheading">Biomedical Engineering</h4>
+
                  </div>
+
                  <div class="timeline-body">
+
                    <p class="text-muted">Washington University in St. Louis</p>
+
                  </div>
+
                </div>
+
  
              </li>
+
      <div class="row">
              <li class="row ">
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      <div class="col-lg-12 text-center">
                <div class="row timeline-image">
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        <img height="255" width="255" class="img-responsive img-circle img-centered" src="https://static.igem.org/mediawiki/2015/6/6b/Mike_toomey.png" alt="Mike Picture"/>
                  <img class="img-circle img-responsive" src="https://static.igem.org/mediawiki/2015/4/4b/Caroline_focht.jpg" alt="">
+
        <h2 class="section-heading">Mike Toomey</h2>
                </div>
+
        <h3 class="section-subheading text-muted">Biomedical Engineering @ Washington University</h3>
                <div class="timeline-panel">
+
        <p>
                  <div class="timeline-heading">
+
          Hello! My name is Mike Toomey and I’m a rising sophomore majoring in Biomedical Engineering at Washington University in Saint Louis. This summer, I’m working in Dr. Tae Sook Moon’s lab in the Department of Energy, Environmental, and Chemical Engineering trying to assess the minimal genes necessary for expression of the enzyme nitrogenase from the Cyanothece sp. 51142 nif cluster. Other than iGEM, I’m Professional Outreach Chair for WashU’s Biomedical Engineering Society, I write for WashU’s student newspaper, and I serve as a Washington University Student Associate. I enjoy reading, watching movies, and running in my free time.
                    <h4>Caroline Focht</h4><span class="text-muted">- 2014 iGEM Team Member</span>
+
      </p>
                    <h4 class="subheading">Chemistry and Biochemistry</h4>
+
      </div>
                  </div>
+
    </div>
                  <div class="timeline-body">
+
                    <p class="text-muted">Washington University in St. Louis</p>
+
                  </div>
+
                </div>
+
  
              </li>
+
    <div class="row">
              <li class="row">
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    <div class="col-lg-12 text-center">
                <div class=" col-lg-12" style="text-align:center;" >
+
      <img height="255" width="255"  class="img-responsive img-circle img-centered" src="https://static.igem.org/mediawiki/2015/5/5c/Blake_actkinson.png" alt="Ba la ke Picture"/>
                  <br>
+
      <h2 class="section-heading">Blake Actkinson</h2>
                  <h4>Be Part
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      <h3 class="section-subheading text-muted">Biomedical Engineering @ Washington University</h3>
                    <br>Of Our
+
      <p>
                    <br>Story!</h4>
+
    Hi, I’m Blake Actkinson, and I’m a rising junior from Houston, Texas. I study Biomedical Engineering in WashU’s School of Engineering and Applied Science. When I’m not in lab, I enjoy playing video games and listening to music. My interests largely revolve around engineering microorganisms to produce novel compounds.
                    <a href="#collaboration" class="page-scroll btn btn-sm btn-warning">Collaboration</a>
+
    </p>
                  </div>
+
    </div>
 +
  </div>
  
                </li>
+
  <div class="row">
              </ul>
+
  <div class="col-lg-12 text-center">
            </div>
+
    <img height="255" width="255"  class="img-responsive img-circle img-centered" src="https://static.igem.org/mediawiki/2015/c/c6/David_ayeke.jpg" alt="David Picture"/>
          </div>
+
    <h2 class="section-heading">David Ayeke</h2>
        </div>
+
    <h3 class="section-subheading text-muted">Computer Engineering @ Washington University</h3>
      </section>
+
    <p>
 +
      Hi, I'm David Ayeke, and I'm a rising junior from St. Louis Missouri. Now you may be wondering what a computer scientist is doing among biologist, and the answer is very simple: making this website. I enjoy programming all sorts of stuff, and I usually spend my time reading computer science papers, and on personal projects. I love building novel systems, and it doesn't get more novel than biological machines.
 +
  </p>
 +
  </div>
 +
</div>
  
      <!-- Collaboration Section -->
+
<div class="row">
      <section id="collaboration" class="bg-light-gray row sectionNum3">
+
<div class="col-lg-12 text-center">
        <div class="container">
+
  <img height="255" width="255"  class="img-responsive img-circle img-centered" src="https://static.igem.org/mediawiki/2015/1/1b/Jessica.jpg" alt="Jessica Picture"/>
          <div class="row">
+
  <h2 class="section-heading">Jessica O'Callaghan</h2>
            <div class="col-lg-12 text-center">
+
  <h3 class="section-subheading text-muted">Chemical Engineering @ Penn State</h3>
              <h2 class="section-heading">Collaboration</h2>
+
  <p>
              <h3 class="section-subheading text-muted"><a class="page-scroll" href="#contact">:{ Looking for Collaborators</a></h3>
+
    Hello! My name is Jessica O’Callaghan and I’m currently a rising sophomore majoring in chemical engineering with a minor in spanish. I’m working under Dr. Maranas studying various strains of Escherichia coli to maximize ATP production and produce excess microbial energy. This is my first major-specific internship, and I look forward to learning more about the sub-disciplines of my field, specifically biochemistry. On campus, I am involved in several organizations, including SHC student council and Engineers Without Borders (EWB). In my free time, I enjoy playing lacrosse and reading.
 +
</p>
 +
</div>
 +
</div>
  
              </div>
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<div class="row">
            </div>
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<div class="col-lg-12 text-center">
            <div class="row text-center">
+
  <img height="255" width="255"  class="img-responsive img-circle img-centered" src="https://static.igem.org/mediawiki/2015/3/32/Laura.jpg" alt="Laura Picture"/>
              <div class="col-lg-12">
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  <h2 class="section-heading">Laura Beebe</h2>
                <span class="fa-stack fa-4x">
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  <h3 class="section-subheading text-muted">Biochemistry and Molecular Biology @ Penn State</h3>
                  <i class="fa fa-circle fa-stack-2x text-primary"></i>
+
  <p>
                  <i class="fa fa-gears fa-stack-1x fa-inverse"></i>
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Hi! My name is Laura Beebe, and I am a rising junior at Penn State majoring in BMB (Biochemistry and Molecular Biology) and minoring in math.  I am working with metabolic models of the bacterial strains used to optimize nitrogen fixation in the labs at Wash U.  Through a computational approach, I can identify interesting and quantitative features of the strains to help experimentation go as well as possible.  Outside of iGEM, I work in the Center for Eukaryotic Gene Regulation on campus, and I enjoy running, caving, reading, and watching movies on Netflix.
                </span>
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                <h4 class="collaboration-heading">Vanderbilt</h4>
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  <h2 class="section-heading">Caroline Focht </h2>
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  <h3 class="section-subheading text-muted">Chemistry and Biochemistry @ Washington University</h3>
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Hello there! I'm Caroline, and I am a rising junior pursuing a major in chemistry with a biochemistry concentration and a minor in ancient studies. I was a member of the WashU_StLouis 2014 iGEM team, and this summer, I am working as the 2015 team’s undergraduate advisor while continuing my own research on light-regulated systems. Whenever I am not in the lab, I like to bake cookies, go out with friends, and binge watch shows on Netflix.</p>
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  <h2 class="section-heading">Cheryl Immethun</h2>
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  <h3 class="section-subheading text-muted">PhD candidate @ Washington University</h3>
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Hi, I’m Cheryl, a PhD candidate in the Moon Research Group. I am developing synthetic biology tools for cyanobacteria, mainly utilizing transcriptional regulation. Through their millions of years of evolution, cyanobacteria have developed amazing capabilities that I would like to employ for societal needs. By unlocking the secrets of nitrogen fixation in a photosynthetic cell, we could one day transform agriculture to keep up with the demands of our ever expanding population. My passions are solving puzzles (in and out of the lab,) as well as exciting students about the mysteries of science and helping them develop the tools to become society’s problem solvers.
                  <h4>Tae Seok Moon</h4>
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                  <p class="text-muted">Faculty Advisor - Washington University</p>
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                  <h4>Fuzhong Zhang</h4>
 
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                  <h4>Costas Maranas</h4>
 
                  <p class="text-muted">Faculty Advisor - Pennsylvania State University</p>
 
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                  <p class="text-muted">Washington University iGEM Advisor</p>
 
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                  <h4>Andrea Balassy</h4>
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  <h2 class="section-heading">Thomas Mueller</h2>
                  <p class="text-muted">Washington University iGEM Advisor</p>
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  <h3 class="section-subheading text-muted">Graduate Student @ Penn State</h3>
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    Hello, my name is Tom Mueller, I am a graduate student in chemical engineering working for Dr. Costas D. Maranas at Penn State University. I work in computational modeling of both metabolic and regulatory networks, focusing predominantly on cyanobacteria. I spend much of my free time volunteering for the Penn State Dance Marathon.
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    <h2 class="section-heading">Graduate Student Mentors</h2>
                  <h4>Carlos Barba</h4>
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    <h3 class="section-subheading text-muted"></h3>
                  <p class="text-muted">Washington University iGEM Advisor</p>
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  <h3 class="section-subheading text-muted">Graduate Student @ Washington University</h3>
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  <h4>Zhang Lab</h4>
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  <h3 class="section-subheading text-muted">Graduate Student @ Washington University</h3>
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 +
  <h2 class="section-heading">Young Je Lee</h2>
 +
  <h3 class="section-subheading text-muted">Graduate Student @ Washington University</h3>
 +
  <h4>Moon Lab</h4>
 +
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                  <h4>Yi Xiao</h4>
+
                  <p class="text-muted">Washington University iGEM Advisor</p>
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                  <h4>Ray Henson</h4>
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                  <p class="text-muted">Washington University iGEM Advisor</p>
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                    <h2>2014 iGEM Project</h2>
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                    <p class="item-intro text-muted">Fixing Nitrogen and Sensing Light</p>
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                    <img class="img-responsive img-centered" src="https://static.igem.org/mediawiki/2014/4/4e/WashU_Project_Overview.png" alt="">
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                    <h4> What was our goal?</h4>
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                    <p>There were two key components of our project: </p>
+
                    <p>Richard and Caroline were working in the <a href="https://pages.wustl.edu/photo.synth.bio">Pakrasi </a>lab, and had been using genes from cyanobacteria to get nitrogen fixation working in <em>E. coli</em>. They were testing nitrogen fixation by running acetylene reduction assays and designing experiments to test the optimal criteria (ie. <em>E. coli</em> strains, temperature, nitrogen source) to get maximal results.
+
                    </p>
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                    <strong> Read more <a href="https://2014.igem.org/Team:WashU_StLouis/Project/nif"> here </a> </strong>
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                    <p>Ben and Jeffery worked in the <a href="http://moon.eece.wustl.edu/"> Moon </a> lab, and cloned plasmids to create a system that represses and expresses a fluorescent protein with the presence and absence of light, and were running experiments to test the induction levels compared to various positive and negative controls.</p>
+
 
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                    <strong> Read more <a href="https://2014.igem.org/Team:WashU_StLouis/Project/light"> here </a> </strong>
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                    <h2>Mission Statement</h2>
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                    <p class="item-intro text-muted">tl;dr Fix Nitrogen</p>
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                      <video controls class="embed-responsive-item">
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                        <source src="https://static.igem.org/mediawiki/2015/7/7f/Nitrogenius_intro.mp4" type=video/mp4>
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                      <span>Caroline Focht</span><p class="text-muted">- 2014 Washington University iGEM member</p>
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                      <a href="https://www.youtube.com/watch?v=5B73_8vcENI&list=PL6fJjAsbg4Sz1V-Xu0moedDxG9Hbbqx8N">More Videos!!!</a>
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                      <p> The goal of this year's project is to take the nitrogen fixing <em>nif</em> cluster from <em>Cyanothece</em>, a cyanobacterium, minify it, and make it work in <em>E. coli</em>. </p>
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                      <ul style="text-align:left;">
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                        <li><a href="#">Designing the plasmid TODO ADD LINkS</a>
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                          <li><a href="#">Making it work in E. Coli TODO ADD LINKS</a>
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                          </ul>
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                          <h2>Summary of the project to date</h2>
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                          <h3> Phase 1: Electro-Transformation of plasmid pNif51142 into E. Coli strains</h3><em> - 2014 </em>
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                          <img class="img-responsive img-centered" src="https://static.igem.org/mediawiki/2015/4/4b/WashU_nifcluster_size.png" alt="Nif Cluster"/>
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                          <p>To successfully transform pNif51142, we used Electro-Transformation, also known as Electroporation.  Electroporation provides a method of transforming E. coli to efficiencies greater than are possible with the best chemical methods. By subjecting mixtures of cells and DNA to exponentially decaying fields of very high initial amplitude, we were able to deliver the plasmid into all of E. coli strains that were tested in the project.</p>
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                          <strong>Results</strong><p>According to the gel running and antibiotic testing, bands in the gel and the survival of all strains transformed in antibiotic Kanamycin (there was an cluster of Kanamycin-resistant marker gene in sequence of pNif51142) both prove that the Electro-Transformation was successful.</p>
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                          <h3> Phase 2: Determine the optimal conditions for cell survival with plasmid pNif51142 in <em>E. Coli</em></h3><em> - 2014</em>
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                          <p>Due to the oxidative properties of oxygen, most nitrogenases are irreversibly inhibited by dioxygen, which degradatively oxidizes the Fe-S cofactors. This requires mechanisms for nitrogen fixers to protect nitrogenase from oxygen in vivo. Hence in our experiment, we firstly selected anaerobic condition as part of preparation step for the nitrogenase activity testing</p>
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                          <ul>
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                            <li><strong>Testing Media</strong>: Minimal M9</li>
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                            <li> <strong> Carbon Source:</strong> Glucose(1mM, 10mM, 100mM)</li>
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                            <li><strong> Nitrogen Source:</strong> Glutamine(1mM, 10mM, 100mM), Glutamate(1mM, 10mM, 100mM), NH4Cl(1mM, 10mM, 100mM)</li>
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                            <li><strong> Temperature:</strong> 30&#176;C, 37&#176;C, 40&#176;C</li>
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                            <li><strong>pH:</strong>6,7,8</li>
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                            <li><strong>O<sub>2</sub> level:</strong>Anaerobic or Aerobic </li>
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                            <li><strong>Strains of <em>e. Coli</em>:</strong> JM109, BL21(DE3), WM1788, Top 10 DH5&#913;</li>
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                            <tbody>
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                              <tr>
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                                <th>Target Strain</th>
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                                <th>JM109</th>
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                                <th>BL21(DE3)</th>
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                                <th>WM1788</th>
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                                <th>Top 10 </th>
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                                <th>DH5&#913;</th>
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                              </tr>
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                              <tr>
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                                <td>Experimental Plates <br>
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                                </td>
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                                <td>JM 109 strain w/ plasmid<br>
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                                  <br>
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                                  Antibiotic <br>
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                                </td>
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                                <td>BL21(DE3) strain w/ plasmid<br>
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                                  <br>
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                                  Antibiotic
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                                </td>
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                                <td>WM1788 strain w/ plasmid<br>
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                                  <br>
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                                  Antibiotic <br>
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                                </td>
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                                <td>Top 10 strain w/ plasmid<br>
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                                  <br>
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                                  Antibiotic<br>
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                                </td>
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                                <td>DH5α strain w/ plasmid<br>
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                                  <br>
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                                  Antibiotic
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                                </td>
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                              </tr>
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                              <tr>
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                                <td>Positive Control</td>
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                                <td>JM 109 strain w/o plasmid<br>
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                                  <br>
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                                  No antibiotic
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                                </td>
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                                <td>BL21(DE3) strain w/o plasmid<br>
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                                  <br>
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                                  No antibiotic
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                                </td>
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                                <td> WM1788 strain w/o plasmid<br>
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                                  <br>
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                                  No antibiotic
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                                </td>
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                                <td>Top 10 straing w/o plasmid<br>
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                                  <br>
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                                  No Antibiotic<br>
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                                </td>
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                                <td>DH5α strain w/o plasmid<br>
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                                  <br>
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                                  No antibiotic</td>
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                                </tr>
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                                <tr>
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                                  <td>Negative Control <br>
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                                  </td>
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                                  <td> JM 109 strain w/o plasmid<br>
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                                    <br>
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                                    Antibiotic
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                                  </td>
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                                  <td>BL21(DE3) strain w/o
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                                    plasmid <br>
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                                    <br>
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                                    Antibiotic
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                                  </td>
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                                  <td>WM1788 strain w/o plasmid<br>
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                                    <br>
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                                    Antibiotic
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                                  </td>
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                                  <td>Top 10 strain w/o plasmid<br>
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                                    <br>
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                                    Antibiotic<br>
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                                  </td>
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                                  <td>DH5α strain w/out plasmid<br>
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                                    <br>
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                                    Antibiotic
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                                  </td>
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                                </tr>
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                              </tbody>
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                            </table>
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                            <strong>Results</strong>
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                            <p>In the minimal M9 media, all possible combinations of parameters listed above were tested.
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                              None of the concentrations of glucose had any affect on the growth of E. coli. It was expected that as the concentration of glucose increased, the growth of E. coli also increased. However, the variation between the concentrations of glucose may have been too small for a noticeable increase in E. coli growth as the concentration of glucose increased. Also, even the maximum concentration of glucose tested, 100mM, may have been too low to affect the growth of E. coli to an observable extent. Eventually, 10mM was determined to be the optimal glucose concentration for the purpose of least interference possible in solution.
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                              NH4Cl as minimal nitrogen source was proven to be not suitable for E. coli growth at any concentration as the OD600 testing results showed that cell density didn’t change throughout the time. It was probably due to the permeability of cell membrane was limited for NH4+ and Cl- ions. Eventually Glutamate at concentration of 10mM supported cell growth the best and thus chosen as part of optimal environment condition.
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                              With CASAmino solution’s buffering utility, the pH was controlled little bit below 7 but close to 7.
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                              To protect the iron core of the nitrogenase, temperature of 30°C and Anaerobic were both determined not for cell growth but for nitrogenase activity testing, which is the next phase.
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                            </p>
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                            <h3>Phase 3: Measurign nitrogen fixation activity under determined optimal conditions in <em>E. Coli</em> Strains. </h3><em>-2014</em>
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                            <p>
+
                              We used  an Acetylene Reduction Assay to examine the nitrogenase activity for JM109, BL21(DE3), Top10, DH5α at different cell density referred by OD600 values.
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                              Acetylene (C2H2) has an triple bond similar to that of atmospheric nitrogen (N2). Because of this structural similarity, the nitrogenase enzyme can cleave the triple bond in acetylene just as it would cleave the triple bond in N2. Ethylene (C2H4) is produced from this enzymatic activity, so a gas chromatograph can be used to detect the presence of ethylene and, consequently, nitrogenase activity.
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                            </p>
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                            <strong>Results</strong>
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                            <ol>
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                              <li>Of the five E. coli strains tested, JM109 and WM1788 showed strongest nitrogenase activity.</li>
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                              <li>The linear relationship between nitrogen fixation activity and time matches that seen in nature. </li>
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                              <li>Optimal conditions determined:
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                                <ul>
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                                  <li>Glucose as carbon-source</li>
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                                  <li>glutamate as nitrogen source </li>
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                                  <li>LB as inoculating media </li>
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                                  <li>minimal M9 as testing media for GC assay</li>
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                                  <li>anaerobic enviornment</li>
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                                  <li> 30&#176;C during the overnight preperation</li>
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                                </ul>
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                              </li>
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                            </ol>
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                            <h3> Phase 4/5 Computationally Modelling an E. Coli system that has Nitrogen Fixation (Penn) and Targeting Nif genes for Overexpression and Silencing (WashU)</h3><em>-2015</em>
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                            <h4 class="text-muted section-heading"><a href="description.html">IGEM 2015 Project Description.</a></h4>
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                            <p>While last year’s team was able to take the nif cluster from a cyanobacteria and get it to function in E. coli, nitrogenase activity was minimal.  This year’s team is dedicated to increasing the nitrogenase activity of E. coli with the nif cluster from Cyanothece 51142. The team members at Pennsylvania State will use high level computational modeling to optimize metabolic pathways within E. Coli, which will relieve the strain of nitrogen fixation. The team members at Washington University will create a minimal nif cluster of only those genes necessary for nitrogenase production and activation. In addition, they will silence and overexpress several genes in order to maximize nitrogenase activity.</p>
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                            <p>In doing such, we hope to create a system for nitrogen fixation for transformation into a photosynthetic system. After we come to a greater understanding of how the system works and perfect it, we can move on to working in a more complex organism, such as a cyanobacteria like Synecosystisspp. 6803. </p>
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                            <p>The end goal is to create plants that can fix their own nitrogen by moving from the cyanobacteria into the chloroplast of the plant. Endosymbiotic theory postulates that cyanobacteria are the ancestors to chloroplasts, so this is the natural progression.     </p>
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                            <h2>The Big Picture</h2>
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                            <p class="item-intro text-muted">Haber-Bosch is so 1909</p>
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                            <img class="img-responsive img-centered" src="https://static.igem.org/mediawiki/2015/6/65/Fertilizer-Manufacturing-Important-for-the-Country.jpg" alt="">
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                            <h3>Why are we doing this project</h3>
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                            Synthetic biology is an exciting area of research that aims to genetically improve organisms to make them more efficient and hopefully more useful to us as well. The human population in 1950 was 2.5 billion, yet it is predicted to surpass 9 billion by 2050 <a  href="#" data-container="body" data-toggle="popover" data-placement="top" data-content="Rogers, Oldroyd. Journal of Experimental Botany March 2014 doi:10.1093/jxb/eru098" ><sup>[1]</sup></a>". Even with population growth slowing, increasing life spans and standards of living will soon tax our natural resources. One of the most concerning is our food supply. The agriculture industry needs a revolution in order to keep up with our expected growth rates. Currently about 80% of chemically fixated nitrogen is used as agricultural fertilizers, the majority in developed lands<a  href="#" data-container="body" data-toggle="popover" data-placement="top" data-content="Rogers, Oldroyd. Journal of Experimental Botany March 2014 doi:10.1093/jxb/eru098" ><sup>[1]</sup></a>. Intracellular nitrogen fixation in crops could help to sustain the burgeoning world population, especially in areas with less fertile soil without taxing the planet’s waterways. The exponential increase in nitrogen fertilizer has led to more runoff into rivers and oceans. Fertilizers then provide nutrition for algal blooms that result in hypoxia and form oceanic dead zones. These dead zones lead to the death of marine species and have potentially large economic consequences.
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                            The ramifications of nitrogen fertilizer runoff can be averted by genetically engineering plant crops to fix their own nitrogen. Some cyanobacteria fix nitrogen for nutritional needs, while most organisms can only acquire it from the food it consumes. Synthetic biology allows us to transfer this ability to fix nitrogen to a heterologous host that has many genetic tools, Escherichia coli, so that we can learn how to give single cell organisms, and eventually chloroplasts the ability to create their own nitrogen fertilizer.
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                            Diazotrophic (organisms that fix nitrogen) cyanobacteria such Nostoc Punctiforme or Anabaena use heterocysts (specialized nitrogen fixing cells) to create a mini-anaerobic environment to aid nitrogen fixation. However, Cyanothece 51142, a non-heterocyst, fixes nitrogen in the same cell as photosynthesis by relying on a circadian metabolic process, when there is less oxygen byproduct from photosynthesis. This process is both fascinating and necessary since the key enzyme in nitrogen fixation, nitrogenase, is poisoned by oxygen. Our goal this summer is to engineer the regulation of the proteins necessary for nitrogen fixation so that they are highly repressed when activated by broad spectrum light (such as the sun), and are highly active when there is no light around, mimicking the cycle where photosynthesis occurs during the day and nitrogen fixation occurs at night.
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                              <h2>Materials and Methods</h2>
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                              <p class="item-intro text-muted">How we did what we did</p>
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                              <img class="img-responsive img-centered" src="https://static.igem.org/mediawiki/2014/7/7c/WashU_Engineered_Strains.jpg" alt="">
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Latest revision as of 00:43, 18 September 2015

Washington University - Penn State iGEM

Welcome To Our Website!
WashU and Penn State   iGEM 2015
Project Description Let's Talk Apply for the 2016 iGEM Team!

Team

NitroGeniuses

Charlotte Bourg Picture

Charlotte Bourg

Biochemistry and Spanish @ Washington University

Hi, I’m Charlotte Bourg and I’m a rising senior (eek) at Wash U. I’m double majoring in biochemistry and Spanish. I’m working with David in the Zhang lab, doing a lot of cloning with the Cyanothece nif cluster in E. coli. Outside of lab, I enjoy running, reading, cooking, watching movies, and exploring the St. Louis area.

Mike Picture

Mike Toomey

Biomedical Engineering @ Washington University

Hello! My name is Mike Toomey and I’m a rising sophomore majoring in Biomedical Engineering at Washington University in Saint Louis. This summer, I’m working in Dr. Tae Sook Moon’s lab in the Department of Energy, Environmental, and Chemical Engineering trying to assess the minimal genes necessary for expression of the enzyme nitrogenase from the Cyanothece sp. 51142 nif cluster. Other than iGEM, I’m Professional Outreach Chair for WashU’s Biomedical Engineering Society, I write for WashU’s student newspaper, and I serve as a Washington University Student Associate. I enjoy reading, watching movies, and running in my free time.

Ba la ke Picture

Blake Actkinson

Biomedical Engineering @ Washington University

Hi, I’m Blake Actkinson, and I’m a rising junior from Houston, Texas. I study Biomedical Engineering in WashU’s School of Engineering and Applied Science. When I’m not in lab, I enjoy playing video games and listening to music. My interests largely revolve around engineering microorganisms to produce novel compounds.

David Picture

David Ayeke

Computer Engineering @ Washington University

Hi, I'm David Ayeke, and I'm a rising junior from St. Louis Missouri. Now you may be wondering what a computer scientist is doing among biologist, and the answer is very simple: making this website. I enjoy programming all sorts of stuff, and I usually spend my time reading computer science papers, and on personal projects. I love building novel systems, and it doesn't get more novel than biological machines.

Jessica Picture

Jessica O'Callaghan

Chemical Engineering @ Penn State

Hello! My name is Jessica O’Callaghan and I’m currently a rising sophomore majoring in chemical engineering with a minor in spanish. I’m working under Dr. Maranas studying various strains of Escherichia coli to maximize ATP production and produce excess microbial energy. This is my first major-specific internship, and I look forward to learning more about the sub-disciplines of my field, specifically biochemistry. On campus, I am involved in several organizations, including SHC student council and Engineers Without Borders (EWB). In my free time, I enjoy playing lacrosse and reading.

Laura Picture

Laura Beebe

Biochemistry and Molecular Biology @ Penn State

Hi! My name is Laura Beebe, and I am a rising junior at Penn State majoring in BMB (Biochemistry and Molecular Biology) and minoring in math. I am working with metabolic models of the bacterial strains used to optimize nitrogen fixation in the labs at Wash U. Through a computational approach, I can identify interesting and quantitative features of the strains to help experimentation go as well as possible. Outside of iGEM, I work in the Center for Eukaryotic Gene Regulation on campus, and I enjoy running, caving, reading, and watching movies on Netflix.

Caroline Picture

Caroline Focht

Chemistry and Biochemistry @ Washington University

Hello there! I'm Caroline, and I am a rising junior pursuing a major in chemistry with a biochemistry concentration and a minor in ancient studies. I was a member of the WashU_StLouis 2014 iGEM team, and this summer, I am working as the 2015 team’s undergraduate advisor while continuing my own research on light-regulated systems. Whenever I am not in the lab, I like to bake cookies, go out with friends, and binge watch shows on Netflix.

Advisors

Cheryl Picture

Cheryl Immethun

PhD candidate @ Washington University

Hi, I’m Cheryl, a PhD candidate in the Moon Research Group. I am developing synthetic biology tools for cyanobacteria, mainly utilizing transcriptional regulation. Through their millions of years of evolution, cyanobacteria have developed amazing capabilities that I would like to employ for societal needs. By unlocking the secrets of nitrogen fixation in a photosynthetic cell, we could one day transform agriculture to keep up with the demands of our ever expanding population. My passions are solving puzzles (in and out of the lab,) as well as exciting students about the mysteries of science and helping them develop the tools to become society’s problem solvers.

Thomas Picture

Thomas Mueller

Graduate Student @ Penn State

Hello, my name is Tom Mueller, I am a graduate student in chemical engineering working for Dr. Costas D. Maranas at Penn State University. I work in computational modeling of both metabolic and regulatory networks, focusing predominantly on cyanobacteria. I spend much of my free time volunteering for the Penn State Dance Marathon.

Graduate Student Mentors

Andrea Picture

Andrea Balassy

Graduate Student @ Washington University

Zhang Lab

Carlos  Picture

Carlos Barba

Visiting Scholar @ Washington University

Zhang Lab

Yi  Picture

Yi Xiao

Postdoc @ Washington University

Zhang Lab

Ray Bourg Picture

Ray Henson

Graduate Student @ Washington University

Moon Lab

Ryan Bourg Picture

Young Je Lee

Graduate Student @ Washington University

Moon Lab

Sponsors

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