Difference between revisions of "Team:Amsterdam"

 
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      Home
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  Home
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  <div class="site-wrapper">
 
  <div class="site-wrapper">
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     <div class="container-fluid">
 
     <div class="container-fluid">
 
       <div class="navbar-header">
 
       <div class="navbar-header">
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      <img src="https://static.igem.org/mediawiki/2017/8/86/TAmsterdam_pm_logo.png"/>
 
       <a class="navbar-brand nav-link" href="https://2017.igem.org/Team:Amsterdam">
 
       <a class="navbar-brand nav-link" href="https://2017.igem.org/Team:Amsterdam">
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         Cyanofactory
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         Photosynthetic Magic
 
       </a>
 
       </a>
 
       </div>
 
       </div>
 
       <ul class="list-inline nav navbar-right">
 
       <ul class="list-inline nav navbar-right">
 
       <li class="list-inline-item dropdown">
 
       <li class="list-inline-item dropdown">
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         <a class="nav-link" href="#">
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         <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Project">
 
         Project
 
         Project
 
         <span class="caret">
 
         <span class="caret">
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         <ul class="dropdown-menu">
 
         <ul class="dropdown-menu">
 
         <li>
 
         <li>
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           <a class="nav-link" href="#">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Project">
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           Modeling
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           Overview
 
           </a>
 
           </a>
 
         </li>
 
         </li>
 
         <li>
 
         <li>
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           <a class="nav-link" href="#">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Produce">
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           Glyoxylate Shunt
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           Production
 
           </a>
 
           </a>
 
         </li>
 
         </li>
 
         <li>
 
         <li>
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           <a class="nav-link" href="#">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Export">
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           Transport
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           Exportation
 
           </a>
 
           </a>
 
         </li>
 
         </li>
 
         <li>
 
         <li>
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           <a class="nav-link" href="#">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Detect">
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           Biosensor
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           Detection
 
           </a>
 
           </a>
 
         </li>
 
         </li>
 
         </ul>
 
         </ul>
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      </li>
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      <li class="list-inline-item">
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        <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Model">
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        Model
 +
        </a>
 
       </li>
 
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       <li class="list-inline-item dropdown">
 
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         <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Practices">
 
         Practices
 
         Practices
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Practices">
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          Overview
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          </a>
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        </li>
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        <li>
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          <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Carbon">
 
           Carbon Efficiency
 
           Carbon Efficiency
 
           </a>
 
           </a>
 
         </li>
 
         </li>
 
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         <li>
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           <a class="nav-link" href="#">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/HP/Silver">
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           Outreach
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           HP Silver
 
           </a>
 
           </a>
 
         </li>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/HP/Gold_Integrated">
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           Articles
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           HP Gold
 
           </a>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Engagement">
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           Entrepreneurship
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           Engagement
 
           </a>
 
           </a>
 
         </li>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Safety">
 
           Safety
 
           Safety
 
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         <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Lab">
 
         Lab
 
         Lab
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Lab">
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          Overview
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          </a>
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        </li>
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        <li>
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          <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Parts">
 
           Parts
 
           Parts
 
           </a>
 
           </a>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/interlab">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/InterLab">
 
           Interlab Study
 
           Interlab Study
 
           </a>
 
           </a>
 
         </li>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/LabJournal">
 
           Lab Journal
 
           Lab Journal
 
           </a>
 
           </a>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Protocol">
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           Protocol
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           Protocols
 
           </a>
 
           </a>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Methods">
 
           Methods
 
           Methods
 
           </a>
 
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         <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/team">
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         <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Team">
 
         Team
 
         Team
 
         <span class="caret">
 
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           <a class="nav-link" href="#">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Team">
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          Overview
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          </a>
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        </li>
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        <li>
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          <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Attributions">
 
           Attributions
 
           Attributions
 
           </a>
 
           </a>
 
         </li>
 
         </li>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Collaborations">
 
           Collaborations
 
           Collaborations
 
           </a>
 
           </a>
 
         </li>
 
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/sponsors">
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           <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Sponsors">
 
           Sponsors
 
           Sponsors
 
           </a>
 
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         <a class="nav-link" href="https://2017.igem.org/Team:Amsterdam/Achievements">
 
         Achievements
 
         Achievements
 
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       <video controls="" height="auto" poster="https://static.igem.org/mediawiki/2017/8/8f/Intro_poster.png" width="85%">
 
       <video controls="" height="auto" poster="https://static.igem.org/mediawiki/2017/8/8f/Intro_poster.png" width="85%">
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       <source src="https://static.igem.org/mediawiki/2017/c/c5/Intro.mp4" type="video/mp4">
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       <source src="https://static.igem.org/mediawiki/2017/4/4c/TAmsterdam_intro.mp4" type="video/mp4"/>
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     <div class="section-button-container">
 
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       <a class="section-button" href="#" id="Project">
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       <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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       <img alt="Project" src="https://static.igem.org/mediawiki/2017/9/9b/TAmsterdam_project.png">
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        Project
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        Project
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      </p>
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       </a>
 
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       <a class="section-button" href="#" id="Practices">
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       <a class="section-button" href="https://2017.igem.org/Team:Amsterdam/Practices" id="Practices">
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       <img alt="Practice logo" src="https://static.igem.org/mediawiki/2017/8/83/Practice_logo.png"/>
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       <img alt="Practices" src="https://static.igem.org/mediawiki/2017/6/66/TAmsterdam_practices.png"/>
 
       <p>
 
       <p>
 
         Practices
 
         Practices
 
       </p>
 
       </p>
 
       </a>
 
       </a>
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       <a class="section-button" href="#" id="Lab">
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       <a class="section-button" href="https://2017.igem.org/Team:Amsterdam/Lab" id="Lab">
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       <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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       <img alt="Lab" src="https://static.igem.org/mediawiki/2017/f/f3/TAmsterdam_lab.png"/>
 
       <p>
 
       <p>
 
         Lab
 
         Lab
 
       </p>
 
       </p>
 
       </a>
 
       </a>
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       <a class="section-button" href="#" id="Team">
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       <a class="section-button" href="https://2017.igem.org/Team:Amsterdam/Team" id="Team">
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       <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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       <img alt="Team" src="https://static.igem.org/mediawiki/2017/0/06/TAmsterdam_team.png"/>
 
       <p>
 
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         Team
 
         Team
 
       </p>
 
       </p>
 
       </a>
 
       </a>
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       <a class="section-button" href="#" id="Achievements">
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       <a class="section-button" href="https://2017.igem.org/Team:Amsterdam/Achievements" id="Achievements">
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       <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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       <img alt="Achievements" src="https://static.igem.org/mediawiki/2017/9/94/TAmsterdam_achievements.png"/>
 
       <p>
 
       <p>
 
         Achievements
 
         Achievements
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       </a>
 
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     </div>
 
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     <div class="home-spacer">
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     <div class="home-project-container-outer">
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      </img>
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      <div class="logo-spacer alternate">
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    </div>
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        <img src="https://static.igem.org/mediawiki/2017/1/1a/TAmsterdam_logo_line1.png"/>
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    <div class="summary-container">
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       </div>
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       <div class="summary-col-left">
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      <div class="line-connector-container">
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      </div>
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        <div class="line-connector" id="first">
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      <div class="summary-col-mid">
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         </div>
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      <p class="summary-text">
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        We are running out of oil and the climate is changing drastically due to the emission of polluting gases such as CO
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        <sub>
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        2
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        </sub>
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        . But what if CO
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        <sub>
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        2
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        </sub>
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        were a resource, rather than a wasteful pollutant; and might even replace oil? We aspire to create a bio-based economy – one that meets its energy and production demands by leveraging biotechnology [1]. We can genetically engineer bacteria to produce a compound we need. This is what we call a bacterial ‘cell factory’.
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Meet
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        <a class="in-text-link" href="#" style="font-size: 24px">
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        CYANOFACTORY
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        </a>
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        , a cyanobacterium that stably and efficiently produces fumarate.
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       </p>
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      </div>
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      <div class="summary-col-right">
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      <div class="vertical-text-container">
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        <p class="vertical-text">
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        OUR GOAL
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         </p>
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       </div>
 
       </div>
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      </div>
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      <div class="home-content-container">
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    </div>
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        <div class="home-intro-container" id="first">
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    <div class="home-spacer">
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        <img src="https://static.igem.org/mediawiki/2017/6/66/TAmsterdam_practices.png"/>
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      <img src="https://static.igem.org/mediawiki/2017/0/02/Design_thingy_1.png">
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        <p>
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      </img>
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          We are running out of oil and the climate is changing drastically due to the emission of greenhouse gases such as CO
−
    </div>
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          <sub>
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    <div class="summary-container">
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          2
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      <div class="summary-col-left">
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          </sub>
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       <img height="260px" src="https://static.igem.org/mediawiki/2017/7/7a/Erlenmeyer_flask.png" width="200px">
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          .
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      </img>
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        </p>
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      </div>
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        </div>
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      <div class="summary-col-mid">
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      </div>
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      <p class="summary-text">
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      <div class="home-content-container">
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         We use the cyanobacterium Synechocystis PCC6803, a photosynthetic model organism of which the genetic toolbox is rapidly expanding.
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        <div class="line-connector" id="second">
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         <br>
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        </div>
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         <br>
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        <div class="home-intro-container" id="second">
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           <a class="in-text-link" href="#">
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        <img src="https://static.igem.org/mediawiki/2017/e/ed/TAmsterdam_recycle.png"/>
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           Click here for a live feed with our Synechocystis cultivators.
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        <p>
 +
          But what if CO
 +
          <sub>
 +
          2
 +
          </sub>
 +
          were a resource, rather than a wasteful pollutant; and might even replace oil?
 +
        </p>
 +
        </div>
 +
      </div>
 +
      <div class="line-connector-container">
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        <div class="line-connector" id="third">
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        </div>
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       </div>
 +
      <div class="home-content-container">
 +
        <div class="home-intro-container" id="first">
 +
        <img src="https://static.igem.org/mediawiki/2017/8/8a/TAmsterdam_plants.png"/>
 +
        <p>
 +
          Early attempts to achieve this have focused on producing sugars with plants, which are then subsequently fermented by bacteria to produce liquid fuels and other chemicals.
 +
        </p>
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        </div>
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      </div>
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      <div class="home-content-container">
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        <div class="line-connector" id="second">
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         </div>
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         <div class="home-intro-container" id="second">
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         <img src="https://static.igem.org/mediawiki/2017/9/9b/TAmsterdam_project.png"/>
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        <p>
 +
          But there is a better way, where no arable land is needed and which is faster and more efficient.
 +
           <a class="in-text-link" href="https://2017.igem.org/Team:Amsterdam/Project" target="_blank">
 +
           This is the way
 
           </a>
 
           </a>
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         </br>
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          our team has chosen to go, using cyanobacteria to take up CO
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          <sub>
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          2
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          </sub>
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          and directly convert it into the valuable chemical
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          <span style="color: rgba(88, 190, 190, 1)">
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          FUMARATE
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          </span>
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         </p>
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         SYNECHOCYSTIS
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         PROJECT
 
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      <img height="202px" src="https://static.igem.org/mediawiki/2017/2/21/Fumarate.png" width="200px">
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       <p class="summary-text">
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         Fumarate is a multifaceted acid that is used as a plastic precursor, an additive for the food industry and a drug against multiple sclerosis and psoriasis.
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      </div>
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         <br>
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      <p>
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        <br>
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         <b>
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          <a class="in-text-link" href="#">
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        Fumarate
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          Click here to see what we did with Fumarate.
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        </b>
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          </a>
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        is used to make certain plastics, food additives, and medicine and is currently made from petroleum. The global market size of fumarate is
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         </br>
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         <a class="in-text-link" href="https://www.radiantinsights.com/press-release/global-fumaric-acid-market" target="_blank">
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         estimated
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         </a>
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        to exceed $760 million by 2020!
 
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      <div class="right-semi-circle">
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        FUMARATE
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        </p>
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          Biosensor
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          </h1>
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          A biosensor for fumarate is constructed in order to facilitate a high throughput screening of extracellular fumarate. This is essential for low measurement time and costs.
+
−
          <br>
+
−
            <a class="in-text-link" href="#">
+
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            &gt;&gt;read more
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          Transporter
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          In anticipation of high fumarate production, transport of fumarate out of the cell can be a limiting factor. This mechanism is largely unknown in Synechocystis and will therefore be -guided by bioinformatics- characterized by means of knock-out and over- expression experiments.
+
−
          <br>
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            &gt;&gt;read more
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           <h1>
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          Glyoxylate Shunt
+
           We are 6 students from Amsterdam with a passion for creating a more sustainable future.
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          </h1>
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        </p>
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          <p>
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        </div>
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          We will incorporate two enzymes (the glyoxylate shunt) in the Synechocystis genome, creating a shortcut in the TCA-cycle. Our modeling results show that if this shunt is only expressed at night, and the pentose phosphate pathway is blocked by knocking out the zwf gene, more fumarate will be produced. This means we will create a unique combination of growth- coupled and inducible production.
+
−
          <br>
+
−
            <a class="in-text-link" href="#">
+
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            &gt;&gt;read more
+
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+
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+
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+
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           <h1>
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          Stability
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        <img src="https://static.igem.org/mediawiki/2017/6/66/TAmsterdam_practices.png"/>
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          </h1>
+
         <p>
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          <p>
+
           We joined iGEM because we did not just wanted to ‘do science’ but we wanted to reach out to society, learn about communicating our research, and work on a shared vision in a small dynamic team.
−
          When an organism is genetically modified to create a product, it causes a decrease in growth rate. This means that a mutated - non- producing - organism will grow faster and take over the population. This problem is tackled by coupling fumarate production to growth. Given that evolution selects heavily on growth rate, we now have a way of naturally selecting for production rate [4]! Knocking out the fumarate degrading reaction in the TCA cycle causes fumarate to be produced in a growth coupled way.
+
        </p>
−
          <br>
+
        </div>
−
            <a class="in-text-link" href="#&gt;">
+
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            &gt;&gt;read more
+
−
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+
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+
 
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+
      </div>
−
         MODULES
+
      <div class="line-connector-container">
−
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+
        <div class="line-connector" id="seventh">
 +
        </div>
 +
      </div>
 +
       <div class="home-content-container">
 +
         <div class="home-intro-container" id="fifth">
 +
         <img src="https://static.igem.org/mediawiki/2017/9/9a/TAmsterdam_collaboration.png"/>
 +
        <p>
 +
          Guided by our fantastic supervisors, and owing to the generosity of our sponsors, we have managed to successfully conclude this challenging and incredibly rewarding project.
 +
        </p>
 +
         </div>
 +
      </div>
 +
      <div class="home-content-container">
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 +
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 +
        <img src="https://static.igem.org/mediawiki/2017/f/f3/TAmsterdam_lab.png"/>
 +
        <p>
 +
          We want to especially thank the Molecular Microbial Physiology group at the University of Amsterdam who have welcomed us in their lab for the past 7 months.
 +
        </p>
 +
        </div>
 +
      </div>
 +
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 +
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 +
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 +
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 +
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 +
    <!-- <div class="home-spacer">
 +
<img src='images/design_thingy_1.png'>
 +
</div>
 +
<div class="summary-container">
 +
<div class="summary-col-left">
 +
 +
</div>
 +
<div class="summary-col-mid">
 +
<p class="summary-text">We are running out of oil and the climate is changing drastically due to the emission of polluting gases such as CO<sub>2</sub>. But what if CO<sub>2</sub> were a resource, rather than a wasteful pollutant; and might even replace oil? We aspire to create a bio-based economy – one that meets its energy and production demands by leveraging biotechnology [1]. We can genetically engineer bacteria to produce a compound we need. This is what we call a bacterial ‘cell factory’.
 +
Meet <a class="in-text-link" href="#" style="font-size: 24px">CYANOFACTORY</a>, a cyanobacterium that stably and efficiently produces fumarate.</p>
 +
</div>
 +
<div class="summary-col-right">
 +
<div class="vertical-text-container">
 +
<p class='vertical-text'>OUR GOAL</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="home-spacer">
 +
<img src='images/design_thingy_1.png'>
 +
</div>
 +
<div class="summary-container">
 +
<div class="summary-col-left">
 +
<img src="images/erlenmeyer_flask.png" width="200px" height="260px">
 +
</div>
 +
<div class="summary-col-mid">
 +
<p class="summary-text">We use the cyanobacterium Synechocystis PCC6803, a photosynthetic model organism of which the genetic toolbox is rapidly expanding.<br><br>
 +
<a class="in-text-link" href="#">Click here for a live feed with our Synechocystis cultivators.</a></p>
 +
</div>
 +
<div class="summary-col-right">
 +
<div class="vertical-text-container">
 +
<p class='vertical-text'>SYNECHOCYSTIS</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="home-spacer">
 +
<img src='images/design_thingy_1.png'>
 +
</div>
 +
<div class="summary-container">
 +
<div class="summary-col-left">
 +
<img src="images/fumarate.png" width="200px" height="202px">
 +
</div>
 +
<div class="summary-col-mid">
 +
<p class="summary-text">Fumarate is a multifaceted acid that is used as a plastic precursor, an additive for the food industry and a drug against multiple sclerosis and psoriasis.<br><br>
 +
<a class="in-text-link" href="#">Click here to see what we did with Fumarate.</a></p>
 +
</div>
 +
<div class="summary-col-right">
 +
<div class="vertical-text-container">
 +
<p class='vertical-text'>FUMARATE</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div id="modules" class="summary-container">
 +
<div id="modules" class="home-spacer">
 +
<img src='images/design_thingy_1_long.png'>
 +
</div>
 +
<div class="summary-col-left">
 +
 +
</div>
 +
<div class="summary-col-mid">
 +
<div id='sensor' class="summary-modules-outer">
 +
<img class="animated-module-icon" src='images/sensor_icon.png'>
 +
<div class="modules-summary-text">
 +
<h1>Biosensor</h1>
 +
<p>A biosensor for fumarate is constructed in order to facilitate a high throughput screening of extracellular fumarate. This is essential for low measurement time and costs.
 +
<br><a class="in-text-link" href="#">>>read more</a></p>
 +
</div>
 +
</div>
 +
<div id="transporter" class="summary-modules-outer">
 +
<img class="animated-module-icon" src='images/transporter_icon.png'>
 +
<div class="modules-summary-text">
 +
<h1>Transporter</h1>
 +
<p>In anticipation of high fumarate production, transport of fumarate out of the cell can be a limiting factor. This mechanism is largely unknown in Synechocystis and will therefore be -guided by bioinformatics- characterized by means of knock-out and over- expression experiments.
 +
<br><a class="in-text-link" href="#">>>read more</a></p>
 +
</div>
 +
</div>
 +
<div id="shunt" class="summary-modules-outer">
 +
<img class="animated-module-icon" src='images/shunt_icon.png'>
 +
<div class="modules-summary-text">
 +
<h1>Glyoxylate Shunt</h1>
 +
<p>We will incorporate two enzymes (the glyoxylate shunt) in the Synechocystis genome, creating a shortcut in the TCA-cycle. Our modeling results show that if this shunt is only expressed at night, and the pentose phosphate pathway is blocked by knocking out the zwf gene, more fumarate will be produced. This means we will create a unique combination of growth- coupled and inducible production.
 +
<br><a class="in-text-link" href="#">>>read more</a></p>
 +
</div>
 +
</div>
 +
<div id="stability" class="summary-modules-outer">
 +
<img class="animated-module-icon" src='images/stability_icon.png'>
 +
<div class="modules-summary-text">
 +
<h1>Stability</h1>
 +
<p>When an organism is genetically modified to create a product, it causes a decrease in growth rate. This means that a mutated - non- producing - organism will grow faster and take over the population. This problem is tackled by coupling fumarate production to growth. Given that evolution selects heavily on growth rate, we now have a way of naturally selecting for production rate [4]! Knocking out the fumarate degrading reaction in the TCA cycle causes fumarate to be produced in a growth coupled way.
 +
<br><a class="in-text-link" href="#>">>>read more</a></p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="summary-col-right">
 +
<div class="vertical-text-container">
 +
<p class='vertical-text'>MODULES</p>
 +
</div>
 +
</div>
 +
</div>
 +
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 +
 +
-->
 
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Latest revision as of 11:25, 23 November 2017

Home

Project

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Achievements

Achievements

We are running out of oil and the climate is changing drastically due to the emission of greenhouse gases such as CO 2 .

But what if CO 2 were a resource, rather than a wasteful pollutant; and might even replace oil?

Early attempts to achieve this have focused on producing sugars with plants, which are then subsequently fermented by bacteria to produce liquid fuels and other chemicals.

But there is a better way, where no arable land is needed and which is faster and more efficient. This is the way our team has chosen to go, using cyanobacteria to take up CO 2 and directly convert it into the valuable chemical FUMARATE

PROJECT

Fumarate is used to make certain plastics, food additives, and medicine and is currently made from petroleum. The global market size of fumarate is estimated to exceed $760 million by 2020!

We are 6 students from Amsterdam with a passion for creating a more sustainable future.

We joined iGEM because we did not just wanted to ‘do science’ but we wanted to reach out to society, learn about communicating our research, and work on a shared vision in a small dynamic team.

Guided by our fantastic supervisors, and owing to the generosity of our sponsors, we have managed to successfully conclude this challenging and incredibly rewarding project.

We want to especially thank the Molecular Microbial Physiology group at the University of Amsterdam who have welcomed us in their lab for the past 7 months.

Auf Gss Aimms1 Sciencepark Dsm Idt Matrix Merck Rivm Phenomenex Snapgene Sils United consumers Vu Vu fs Vu cs