Difference between revisions of "Team:DTU-Denmark/Journal"

 
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             <i class="fa fa-bars"></i>
 
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           </button>
 
           </button>
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           <a class="navbar-brand navimg" href="#"><img src="/wiki/images/b/b7/DTU-Denmark_dtulogo.png"></a>
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         </div>
 
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         <!-- Collect the nav links, forms, and other content for toggling -->
 
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           <ul class="nav navbar-nav">
 
           <ul class="nav navbar-nav">
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<li class="dropdown">
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                <li >
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<a href="/Team:DTU-Denmark"
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                <a href="/Team:DTU-Denmark"
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  >Home
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                  >Home
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                                          </a></li>
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                  </a></li>
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<li class="dropdown">
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                <li  
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<a href="/Team:DTU-Denmark"
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  class="dropdown-toggle"
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  data-toggle="dropdown"
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  aria-expanded="false">Team and Attributions
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                                          <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
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                >
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<li class="dropdown">
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                <a href=""
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<a href="/Team:DTU-Denmark/Team"
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                  class="dropdown-toggle"
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  >Team
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                  data-toggle="dropdown"
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                                          </a></li>
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                  role="button"
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<li class="dropdown">
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                  aria-expanded="false">Team and Attributions
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<a href="/Team:DTU-Denmark/Attributions"
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                  <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
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  >Attributions
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                <li >
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                                          </a></li></ul></li>
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                <a href="/Team:DTU-Denmark/Team"
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<li class="dropdown">
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                  >Team
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<a href="/Team:DTU-Denmark"
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                  </a></li>
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  class="dropdown-toggle"
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                <li >
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  data-toggle="dropdown"
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                <a href="/Team:DTU-Denmark/Attributions"
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  role="button"
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                  >Attributions
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  aria-expanded="false">Project
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                  </a></li></ul></li>
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                                          <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
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                <li  
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<li class="dropdown">
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<a href="/Team:DTU-Denmark/Project/Overview"
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  >Overview
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                                          </a></li>
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<li class="dropdown">
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<a href="/Team:DTU-Denmark/Project/Background"
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  >Background
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                                          </a></li>
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−
<li class="dropdown">
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<a href="/Team:DTU-Denmark/Project/MAGE"
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  >MAGE Subtilis
+
               
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                                          </a></li>
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<li class="dropdown">
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<a href="/Team:DTU-Denmark/Project/Surfactin"
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  >Surfactin
+
               
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                                          </a></li>
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                >
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<li class="dropdown">
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                <a href=""
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<a href="/Team:DTU-Denmark/Project/Tyrocidine"
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                  class="dropdown-toggle"
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  >Tyrocidine
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                  data-toggle="dropdown"
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                                          </a></li>
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                  role="button"
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<li class="dropdown">
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                  aria-expanded="false">Project
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<a href="/Team:DTU-Denmark/Project/Chip"
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                  <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
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  >Lab-on-a-disc
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                <li >
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                                          </a></li>
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                <a href="/Team:DTU-Denmark/Project/Overview"
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<li class="dropdown">
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                  >Overview
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<a href="/Team:DTU-Denmark/Project/Intein"
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                  </a></li>
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  >Intein
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                <li >
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                                          </a></li>
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                <a href="/Team:DTU-Denmark/Project/Background"
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<li class="dropdown">
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                  >Background
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<a href="/Team:DTU-Denmark/Project/Detection"
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                  </a></li>
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  >Detection of NRP
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                <li >
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                                          </a></li></ul></li>
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                <a href="/Team:DTU-Denmark/Project/MAGE"
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<li class="dropdown">
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                  >MAGE subtilis
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<a href="/Team:DTU-Denmark/Practices"
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                  </a></li>
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  >Human Practices
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                <li >
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                                          </a></li>
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                <a href="/Team:DTU-Denmark/Project/Tyrocidine"
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<li class="dropdown">
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                  >Tyrocidine
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<a href="/Team:DTU-Denmark/Part_Collection"
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                  </a></li>
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  >Parts
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                <li >
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                                          </a></li>
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                <a href="/Team:DTU-Denmark/Project/Chip"
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<li class="dropdown active">
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                  >Lab-on-a-disc
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<a href="/Team:DTU-Denmark/Journal"
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                  </a></li>
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  >Journal
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                <li >
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                <a href="/Team:DTU-Denmark/Project/Inteins"
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<li class="dropdown">
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                  >Inteins
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<a href="/Team:DTU-Denmark/Software"
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                  </a></li>
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  >Software
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                <li >
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                <a href="/Team:DTU-Denmark/Project/Detection"
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<li class="dropdown">
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                  >Detection of NRP
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<a href="/Team:DTU-Denmark"
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                  </a></li></ul></li>
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  class="dropdown-toggle"
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                <li >
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  data-toggle="dropdown"
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                <a href="/Team:DTU-Denmark/Practices"
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  role="button"
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                  >Human Practices
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  aria-expanded="false">Achievements
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                  </a></li>
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                                          <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
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<li class="dropdown">
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<a href="/Team:DTU-Denmark/Achievements"
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  >Overview of Achievements
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                                          </a></li>
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<a href="/Team:DTU-Denmark/Collaborations"
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                >
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  >Collaborations
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                <a href=""
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                  class="dropdown-toggle"
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<li class="dropdown">
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                  data-toggle="dropdown"
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<a href="/Team:DTU-Denmark/Judging%20Form"
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                  role="button"
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  >Judging Form
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                  aria-expanded="false">Parts Collection
−
                                          </a></li></ul></li>
+
                  <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
 +
                <li >
 +
                <a href="/Team:DTU-Denmark/Parts"
 +
                  >Parts
 +
                  </a></li>
 +
                <li >
 +
                <a href="/Team:DTU-Denmark/Description"
 +
                  >Characterisation of xylR
 +
                  </a></li></ul></li>
 +
                <li class="active">
 +
                <a href="/Team:DTU-Denmark/Journal"
 +
                  >Journal
 +
                  </a></li>
 +
                <li >
 +
                <a href="/Team:DTU-Denmark/Software"
 +
                  >Software
 +
                  </a></li>
 +
                <li  
 +
               
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 +
                >
 +
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 +
                  class="dropdown-toggle"
 +
                  data-toggle="dropdown"
 +
                  role="button"
 +
                  aria-expanded="false">Achievements
 +
                  <span class="caret"></span></a><ul class="dropdown-menu" role="menu">
 +
                <li >
 +
                <a href="/Team:DTU-Denmark/Achievements"
 +
                  >Key Achievements
 +
                  </a></li>
 +
                <li >
 +
                <a href="/Team:DTU-Denmark/Collaborations"
 +
                  >Collaborations
 +
                  </a></li>
 +
                <li >
 +
                <a href="/Team:DTU-Denmark/Judging_Form"
 +
                  >Judging Form
 +
                  </a></li></ul></li>
 
             <li class="hidden-xs">
 
             <li class="hidden-xs">
 
               <a href="http://facebook.com/dtubiobuilders" data-toggle="tooltip" data-placement="bottom" title="Follow us on Facebook">
 
               <a href="http://facebook.com/dtubiobuilders" data-toggle="tooltip" data-placement="bottom" title="Follow us on Facebook">
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             <li class="hidden-lg">
 
               <a href="https://igem.org" target="_blank" class="navimg">
 
               <a href="https://igem.org" target="_blank" class="navimg">
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                 <img src="/wiki/images/a/af/DTU-Denmark_igemlogo.png">
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       </div>
 
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     </nav>
 
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    <nav class="navbar navbar-default extrabar hidden-xs hidden" data-spy="affix">
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      <div class="container-fluid" id="scrollspy">
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<nav class="navbar navbar-default extrabar hidden-xs hidden" data-spy="affix">
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          <li><a class="page-scroll" href="#Summary">Summary</a></li><li><a class="page-scroll" href="#Protocols">Protocols</a></li><li><a class="page-scroll" href="#Timeline">Timeline</a></li><li><a class="page-scroll" href="#References">References</a></li>
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  <div class="container-fluid" id="scrollspy">
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    <ul class="nav navbar-nav">
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      </div>
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      <li><a class="page-scroll" href="#Protocols">Protocols</a></li><li><a class="page-scroll" href="#LabNotebook">Lab Notebook </a></li><li><a class="page-scroll" href="#Timeline">Timeline</a></li>
−
    </nav>
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    <div class="jumbotron hero bg-hero">
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           <img src="/wiki/images/a/af/DTU-Denmark_igemlogo.png">
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           <div class="col-md-12">
 
              
 
              
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            <h3><br></h3>
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<h3><br></h3>
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            <h1>Journal</h1>
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<h1>Journal</h1>
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               <li>
 
               <li>
 
                 <a id="Timeline-submenu" class="btn btn-default btn-transparent btn-lg page-scroll" href="#Timeline">Timeline</a>
 
                 <a id="Timeline-submenu" class="btn btn-default btn-transparent btn-lg page-scroll" href="#Timeline">Timeline</a>
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              </li>
 
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              <li>
 
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                <a id="References-submenu" class="btn btn-default btn-transparent btn-lg page-scroll" href="#References">References</a>
 
 
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                 <a id="Summary-submenu" class="page-scroll" href="#Summary">Summary</a>
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                 <a id="Protocols-submenu" class="page-scroll" href="#Protocols">Protocols</a>
 
               </li>
 
               </li>
 
                
 
                
 
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                 <a id="Protocols-submenu" class="page-scroll" href="#Protocols">Protocols</a>
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                 <a id="LabNotebook-submenu" class="page-scroll" href="#LabNotebook">Lab Notebook </a>
 
               </li>
 
               </li>
 
                
 
                
 
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                 <a id="Timeline-submenu" class="page-scroll" href="#Timeline">Timeline</a>
 
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      <p>For OGRE (Oligo Recombineering) to be effective there is two genetic improvements that can be done. The first and most important is that the organism need to express a recombinase protein such as the beta protein derived from the lambda RED E. coli phage. The second improvement is to destroy/inhibit the mismatch repair system [1]. In B. subtilis the genes mutS and mutL are taking care of the mismatch repair [2]. For proof of concept purposes deleting the mismatch repair system will be adequate. According to (REF) the protein encoded by mutL will not be functional without a functional mutS, this is why deletion of only mutS will be sufficient to take out the mismatch repair system. With respect to recombinase we will test two different recombinases: lambda-beta (codon optimized for <em>B. subtilis 168</em>) and gp35 (a recombinase from the B. subtilis phage SPP1) [3]. For duing proof of concept of OGRE in <em>B. subtilis</em> four different strains was producere via genetic recombineering. All derived from <em>Bacillus subtilis 168</em>:</p>
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<ul>
+
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<li>∆<em>amyE::beta-neo<sup>R</sup></em></li>
+
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<li>∆<em>amyE::GP35-neo<sup>R</sup></em></li>
+
−
<li>∆<em>mutS::beta-neo<sup>R</sup></em></li>
+
−
<li>∆<em>mutS::GP35-neo<sup>R</sup></em></li>
+
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+
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<p>The four different strains where compared to each other to get compare there transformation efficienc in MAGE.</p>
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         Protocols
 
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<div class="panel-body">Needed materials: 100 ml. TAE buffer. 1gr. agarose. ethidium bromide</div>
+
<div class="panel-body">Needed materials: 100 ml&nbsp;TAE buffer,&nbsp;1gr. agarose,&nbsp;ethidium bromide.</div>
  
−
<div class="panel-body">Mix 100 ml. TAE buffer with 1 gr. agarose powder, heat in microwave till the agarose is disolved, let it cool till it can be handled with bare hands, add 10 &micro;l&nbsp;ethidium bromide. pour into mold containing slots for wells, and let cool.</div>
+
<div class="panel-body">Mix 100 ml. TAE buffer with 1 gr. agarose powder, heat in microwave till the agarose is disolved, let it cool till it can be handled with bare hands, add 10 &micro;l&nbsp;ethidium bromide. Then&nbsp;pour the mixture&nbsp;into a mold containing slots for wells, and let cool.</div>
 
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<div class="panel-body">Needed materials: 100 ml. TAE buffer. 1gr. agarose. ethidium bromide</div>
+
<div class="panel-body">Set gel into electrophoresis chamber filled with 1X TAE buffer so the wells are covered.&nbsp;<br />
−
 
+
Mix 5 &micro;l of&nbsp;your PCR reactions/sample with 1&nbsp;&micro;l 6X loading buffer.<br />
−
<p aria-controls="ui-id-36" aria-expanded="true" aria-selected="false" role="tab" tabindex="0">set gel into&nbsp;Electrophoresis chamber filled with 1X TAE buffer so the wells are covered.&nbsp;<br />
+
Pipette 5&nbsp;&micro;l into each well,&nbsp;pour 2-3&nbsp;&micro;l ladder in some so the size can be seen.<br />
−
mix 5 &micro;l of&nbsp;your PCR reactions/sample with 1&nbsp;&micro;l 6X loading buffer.<br />
+
Run at 140 V, for 30-40 min.</div>
−
pipette 5&nbsp;&micro;l into each well, pour 2-3&nbsp;&micro;l ladder in some so the size can be seen.<br />
+
−
run at 140 V, for 30-40 min</p>
+
 
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<div class="panel-body">Chemo competens is a way of getting E. coli to be able to take up new DNA, since this cant be done naturally like B. subtilis, then chemocompetent cells have to be made.</div>
 
<div class="panel-body">Chemo competens is a way of getting E. coli to be able to take up new DNA, since this cant be done naturally like B. subtilis, then chemocompetent cells have to be made.</div>
  
−
<div class="panel-body">Protocol can be found&nbsp;<a href="/wiki/images/c/cd/DTU-Denmark_Chemocompetentcells_protocol.pdf" target="_blank">here</a></div>
+
<div class="panel-body">Protocol can be found&nbsp;<a href="https://static.igem.org/mediawiki/2015/c/cd/DTU-Denmark_Chemocompetentcells_protocol.pdf" target="_blank">here</a></div>
 
</div>
 
</div>
 
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<div class="panel-body">
 
<div class="panel-body">
−
<div class="panel-body">Needed materials: a 40% glycerol solution, bacteria of your choice, cryo tubes</div>
+
<div class="panel-body">Needed materials: a 40% glycerol solution, bacteria of your choice, cryo tubes.</div>
  
−
<div class="panel-body">mix glycerol and bacteria 50/50 in a cryo tube and place in a -80 frezzer till needed</div>
+
<div class="panel-body">Mix glycerol and bacteria 50/50 in a cryo tube and place in a -80 frezzer till needed.</div>
 
</div>
 
</div>
 
</div>
 
</div>
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<p>A lot of lab work requires plates in order to produce results, and often you need a special concentration, a unique antibiotic mixed into the plates or a different composition than what is available at the lab you are in. If that is the case, the plate needs to be made from scratch, or somewhat along the way.</p>
 
<p>A lot of lab work requires plates in order to produce results, and often you need a special concentration, a unique antibiotic mixed into the plates or a different composition than what is available at the lab you are in. If that is the case, the plate needs to be made from scratch, or somewhat along the way.</p>
  
−
<p>Protocol can be found <a href="/wiki/images/e/e2/DTU-Denmark_making_plates_protocol.pdf" target="_blank">her</a></p>
+
<p>Protocol can be found <a href="https://static.igem.org/mediawiki/2015/e/e2/DTU-Denmark_making_plates_protocol.pdf" target="_blank">here</a>.</p>
 
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<div class="panel-body">
 
<div class="panel-body">
−
<div class="panel-body">For our experiments we have used minimal media designed for B. subtilis. The plates have been made by following this protocol (for 1 liter)</div>
+
<div class="panel-body">For the&nbsp;experiments a minimal media designed for <em>B. subtilis</em> has been used. The plates have been made by following this protocol (for 1 liter).</div>
  
−
<div class="panel-body">Protocolcan be found <a href="/wiki/images/5/52/DTU-Denmark_Minimal_media_protocol.pdf" target="_blank">here</a></div>
+
<div class="panel-body">Protocol can be found <a href="https://static.igem.org/mediawiki/2015/5/52/DTU-Denmark_Minimal_media_protocol.pdf" target="_blank">here</a>.</div>
 
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<div class="panel-body">
 
<div class="panel-body">
−
<div class="panel-body">in order to work with plasmids, then they needs to be purified, and condensed, this is done bu minipreping the bacteria, and afterwards the concentration can be investigating using&nbsp;NanoDrop&trade;.</div>
+
<div class="panel-body">In order to work with plasmids, then they needs to be purified&nbsp;and condensed, this is done bu minipreping the bacteria, and afterwards the concentration can be investigating using&nbsp;NanoDrop&trade;.</div>
  
−
<div class="panel-body">Protocol <a href="/wiki/images/4/48/DTU-Denmark_Miniprep_protocol.pdf" target="_blank">here</a>.</div>
+
<div class="panel-body">Protocol can be found <a href="https://static.igem.org/mediawiki/2015/4/48/DTU-Denmark_Miniprep_protocol.pdf" target="_blank">here</a>.</div>
 
</div>
 
</div>
 
</div>
 
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<div class="panel-body">
 
<div class="panel-body">
−
<div class="panel-body">Bacillus can be made Competent which makes it easy to alter the genome, so wanted mutaions can be inserted, this is a unique way of investigateing new pathways.</div>
+
<div class="panel-body">Bacillus can be made competent allowing an&nbsp;easy alteration of&nbsp;the genome and&nbsp;so wanted mutaions can be inserted, this is a unique way of investigateing new pathways.</div>
  
−
<div class="panel-body">Protocol can be found&nbsp;<a href="/wiki/images/2/29/DTU-Denmark_natural_competent_subtilis_protocol.pdf" target="_blank">here</a></div>
+
<div class="panel-body">Protocol can be found&nbsp;<a href="https://static.igem.org/mediawiki/2015/2/29/DTU-Denmark_natural_competent_subtilis_protocol.pdf" target="_blank">here</a>.</div>
 
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<div class="panel-heading" id="headingNine" role="tab">
−
<h4 class="panel-title"><a aria-controls="collapseNine" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseNine" role="button">OGRE</a></h4>
+
<h4 class="panel-title"><a aria-controls="collapseNine" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseNine" role="button">MAGE in Bacillus</a></h4>
 
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</div>
  
 
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<div aria-labelledby="headingNine" class="panel-collapse collapse" id="collapseNine" role="tabpanel">
 
<div class="panel-body">
 
<div class="panel-body">
−
<div class="panel-body">Electrotoration of&nbsp;bacteria is used in order to introduce mutations in the lagging strand of the strain, we have chosen to name this&nbsp;OGRE, this technique&nbsp;are used in order to incorporate wanted mutations in a strain of&nbsp;Bacillus subtilis 168.</div>
+
<div class="panel-body">Electrotoration of&nbsp;bacteria is used in order to introduce mutations in the lagging strand of the strain, this technique&nbsp;are used in order to incorporate wanted mutations in a strain of&nbsp;Bacillus subtilis 168.</div>
  
−
<div class="panel-body">Protocol can be found&nbsp;<a href="/wiki/images/0/02/DTU-Denmark_OGRE_protocol.pdf" target="_blank">here</a></div>
+
<div class="panel-body">Protocol can be found&nbsp;<a href="https://static.igem.org/mediawiki/2015/0/0e/DTU-Denmark_MAGE_in_baccilus.pdf" target="_blank">here</a>.</div>
 
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<div class="panel-heading" id="headingTen" role="tab">
−
<h4 class="panel-title"><a aria-controls="collapseTen" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseTen" role="button">Preperation of Electro Competent &nbsp;Bacillus subtilis 168</a></h4>
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<h4 class="panel-title"><a aria-controls="collapseTen" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseTen" role="button">Preperation of Electro Competent&nbsp;Bacillus subtilis 168</a></h4>
 
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</div>
  
 
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<div class="panel-body">
 
<div class="panel-body">
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<div class="panel-body">Electro competent cells are used in our OGRE part of the project, so a batch of cells was prepared using the following protocol.</div>
+
<div class="panel-body">Electro competent cells are used in our MAGE part of the project, so a batch of cells was prepared using the following protocol.</div>
  
−
<div class="panel-body">Protocol can be found&nbsp;<a href="/wiki/images/2/2e/DTU-Denmark_Electro_competent_protocol.pdf" target="_blank">here</a></div>
+
<div class="panel-body">Protocol can be found&nbsp;<a href="https://static.igem.org/mediawiki/2015/2/2e/DTU-Denmark_Electro_competent_protocol.pdf" target="_blank">here</a></div>
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        Lab Notebook
 +
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 +
<h4 class="panel-title"><a aria-controls="collapseTwentyone" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseTwentyone" role="button">Expression of Tyrocidine</a></h4>
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<div class="panel-body">The lab book for expression of tyrocidine&nbsp;can be found <a href="https://static.igem.org/mediawiki/2015/c/cf/DTU-Denmark_Tyrocidine_labnotebook.pdf" onclick="window.open(this.href, '', 'resizable=no,status=no,location=no,toolbar=no,menubar=no,fullscreen=no,scrollbars=no,dependent=no'); return false;">here</a>.&nbsp;</div>
 
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<h4 class="panel-title"><a aria-controls="collapseEleven" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseEleven" role="button">Collapsible Group Item #11</a></h4>
+
<h4 class="panel-title"><a aria-controls="collapseTwentytwo" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseTwentytwo" role="button">Generation&nbsp;of oligo-competent <em>B.subtilis</em> strains</a></h4>
 
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<div class="panel-body">000.</div>
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<div class="panel-body">
 +
<div class="panel-body">The lab book for the generation of oligo-competent strains can be found <a href="https://static.igem.org/mediawiki/2015/7/75/DTU-Denmark_straingeneration.pdf">here</a>.</div>
 
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 +
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 +
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 +
<h4 class="panel-title"><a aria-controls="collapseTwentythree" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseTwentythree" role="button">Blood cell lysis</a></h4>
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<div class="panel-body">To approve a lab-on-a-disc concept as a screening device, the UV-vis abasobancee were measured&nbsp;<a href="https://static.igem.org/mediawiki/2015/6/62/DTU-Denmark_bloodcell_lysis.pdf">here</a>.&nbsp;</div>
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 +
<h4 class="panel-title"><a aria-controls="collapseTwentyfour" aria-expanded="false" class="collapsed" data-parent="#accordion" data-toggle="collapse" href="#collapseTwentyfour" role="button">MAGE&nbsp;proof of concept</a></h4>
 +
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 +
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<div class="panel-body">
 +
<div class="panel-body">See our labnotebook <a href="https://static.igem.org/mediawiki/2015/1/10/DTU-Denmark_labnote_MAGE_proof.pdf">here.</a></div>
 +
</div>
 +
</div>
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</div>
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             <p style="text-align: justify;"><img alt="" src="/wiki/images/c/c5/DTU-Denmark_timeline_novoamb.png" style="height: 158px; width: 250px; float: left;" />Our team member Pernille spent an afternoon giving a presentation on cell factories and synthetic biology to 30 highschool students. She says: &quot;Synthetic biology is all about being creative and use your imagination&nbsp;to design bio-solutions that can impact the world. For that exact reason, it is neccesary to discuss which ethical values tat should drive research&quot;. The highschool students had lots of questions and opinion for the discussion about ethics.</p>
+
             <p style="text-align: justify;"><img alt="" src="https://static.igem.org/mediawiki/2015/c/c5/DTU-Denmark_timeline_novoamb.png" style="height: 158px; width: 250px; float: left;" />Our team member Pernille spent an afternoon giving a presentation on cell factories and synthetic biology to 30 highschool students. She says: &quot;Synthetic biology is all about being creative and use your imagination&nbsp;to design bio-solutions that can impact the world. For that exact reason, it is neccesary to discuss which ethical values tat should drive research&quot;. The highschool students had lots of questions and opinion for the discussion about ethics.</p>
  
 
<p style="text-align: justify;">&nbsp;</p>
 
<p style="text-align: justify;">&nbsp;</p>
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             <p>We are happy to announce that the VWR&nbsp;is contributing our team with&nbsp;their awesome products!</p>
 
             <p>We are happy to announce that the VWR&nbsp;is contributing our team with&nbsp;their awesome products!</p>
  
−
<p><img alt="" src="None" style="width: 400px; height: 533px;" /></p>
+
<p><img alt="" src="https://static.igem.org/mediawiki/2015/3/37/DTU-Denmark_VWR_lab.jpg" style="width: 400px; height: 533px;" /></p>
  
 
<p>&nbsp;</p>
 
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             <p>Today we had a visit by&nbsp;Susanne Basse from&nbsp;Fisher Scientific. She&nbsp;came by our office with a wagon full of items, Thanks!&nbsp;</p>
 
             <p>Today we had a visit by&nbsp;Susanne Basse from&nbsp;Fisher Scientific. She&nbsp;came by our office with a wagon full of items, Thanks!&nbsp;</p>
  
−
<p><img alt="" src="/wiki/images/c/c7/DTU-Denmark_Fisher_Scientific_visit.png" style="width: 300px; height: 280px;" /></p>
+
<p><img alt="" src="/files/Fisher%20Scientific%20visit.png" style="width: 300px; height: 280px;" /></p>
  
 
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             <p>We are pleased&nbsp;to announce that Macrogen is sponsoring our team with sequencing!</p>
 
             <p>We are pleased&nbsp;to announce that Macrogen is sponsoring our team with sequencing!</p>
  
−
<p><a href="http://www.macrogen.com/" target="_blank"><img alt="" src="/wiki/images/1/11/DTU-Denmark_Marcogen.jpg" style="width: 300px; height: 199px;" /></a></p>
+
<p><a href="http://www.macrogen.com/" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/1/11/DTU-Denmark_Marcogen.jpg" style="width: 300px; height: 199px;" /></a></p>
  
 
           </div>
 
           </div>
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             <p>We are happy to announce that AKG Acoustics is sponsoring our team with headphones for presentations in Boston!&nbsp;</p>
 
             <p>We are happy to announce that AKG Acoustics is sponsoring our team with headphones for presentations in Boston!&nbsp;</p>
  
−
<p><a href="http://us.akg.com/akg-homepage-us.html" target="_blank"><img alt="" src="/wiki/images/9/9d/DTU-Denmark_AKG.png" style="width: 400px; height: 121px;" /></a></p>
+
<p><a href="http://us.akg.com/akg-homepage-us.html" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/9/9d/DTU-Denmark_AKG.png" style="width: 400px; height: 121px;" /></a></p>
  
 
           </div>
 
           </div>
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           <div class="timeline-heading">
 
           <div class="timeline-heading">
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             <h4 class="timeline-title">Contributions from VWR - Bie & Berntsen A/S</h4>
+
             <h4 class="timeline-title">Contributions from VWR - Bie &amp; Berntsen A/S</h4>
 
             <p><small class="text-muted"><i class="glyphicon glyphicon-time"></i> 2015-08-11</small></p>
 
             <p><small class="text-muted"><i class="glyphicon glyphicon-time"></i> 2015-08-11</small></p>
 
           </div>
 
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             <p>We are happy to announce that VWR - Bie &amp; Berntsen A/S is sponsoring our team with lab consumeables!</p>
 
             <p>We are happy to announce that VWR - Bie &amp; Berntsen A/S is sponsoring our team with lab consumeables!</p>
  
−
<p><a href="dk.vwr.com" target="_blank"><img alt="" src="/wiki/images/e/ea/DTU-Denmark_VWR.jpg" style="width: 400px; height: 76px;" /></a></p>
+
<p><a href="dk.vwr.com" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/e/ea/DTU-Denmark_VWR.jpg" style="width: 400px; height: 76px;" /></a></p>
  
 
           </div>
 
           </div>
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             <p>We are happy to announce that Fisher Scientific&nbsp;is sponsoring our team with lab materials!&nbsp;</p>
 
             <p>We are happy to announce that Fisher Scientific&nbsp;is sponsoring our team with lab materials!&nbsp;</p>
  
−
<p><a href="https://dk.fishersci.com/dk/" target="_blank"><img alt="" src="/wiki/images/b/b4/DTU-Denmark_Fisher_Scientific.jpg" style="width: 400px; height: 123px;" /></a></p>
+
<p><a href="https://dk.fishersci.com/dk/" target="_blank"><img alt="" src="/files/Fisher%20Scientific.jpg" style="width: 400px; height: 123px;" /></a></p>
  
 
           </div>
 
           </div>
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             <p>Today we took a day off from lab to go canoeing, followed by a barbeque at Chris&#39; place.</p>
 
             <p>Today we took a day off from lab to go canoeing, followed by a barbeque at Chris&#39; place.</p>
  
−
<p><img alt="" src="/wiki/images/6/6a/DTU-Denmark_Teambuilding.jpg" /></p>
+
<p><img alt="" src="https://static.igem.org/mediawiki/2015/6/6a/DTU-Denmark_Teambuilding.jpg" /></p>
  
 
           </div>
 
           </div>
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             <p>We are happy to announce that the SnapGene&nbsp;is contributing&nbsp;our team with lisences to their awesome product!</p>
 
             <p>We are happy to announce that the SnapGene&nbsp;is contributing&nbsp;our team with lisences to their awesome product!</p>
  
−
<p><a href="http://www.snapgene.com/" target="_blank"><img alt="" src="/wiki/images/5/58/DTU-Denmark_Snapgene.png" style="width: 400px; height: 113px;" /></a></p>
+
<p><a href="http://www.snapgene.com/" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/5/58/DTU-Denmark_Snapgene.png" style="width: 400px; height: 113px;" /></a></p>
  
 
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           </div>
 
           <div class="timeline-body">
 
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             <p>3 high school students;&nbsp;Simran, Noor, and Charlotte, joined us and Biotech Academy for 5 days to make biosensors that changes color, when water is poluted. Read more at <span style="color:#000000;"><span style="background-color:#FFFF00;">ADD</span></span> and <a href="http://biotechacademy.dk">http://biotechacademy.dk</a>.</p>
+
             <p>3 high school students;&nbsp;Simran, Noor, and Charlotte, joined us and Biotech Academy for 5 days to make biosensors that changes color, when water is poluted. Read more at&nbsp;the <a href="/Team:DTU-Denmark/Practices" target="_blank">Human Practice</a>&nbsp;and <a href="http://biotechacademy.dk">http://biotechacademy.dk</a>.</p>
  
−
<p style="text-align: center;"><img alt="" src="/wiki/images/b/b8/DTU-Denmark_highschool_biotechacademy.jpg" style="width: 350px; height: 197px;" /></p>
+
<p style="text-align: center;"><img alt="" src="https://static.igem.org/mediawiki/2015/b/b8/DTU-Denmark_highschool_biotechacademy.jpg" style="width: 350px; height: 197px;" /></p>
  
 
           </div>
 
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             <p>We are happy to announce that the Lundbeck Foundation is contributing&nbsp;financially to our team!</p>
 
             <p>We are happy to announce that the Lundbeck Foundation is contributing&nbsp;financially to our team!</p>
  
−
<p><a href="http://www.lundbeckfoundation.com/" target="_blank"><img alt="" src="/wiki/images/e/e2/DTU-Denmark_Lundbeckfonden.jpg" style="width: 348px; height: 96px;" /></a></p>
+
<p><a href="http://www.lundbeckfoundation.com/" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/e/e2/DTU-Denmark_Lundbeckfonden.jpg" style="width: 348px; height: 96px;" /></a></p>
  
 
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             <p>We are happy to announce that In Vitro A/S is sponsoring our team with lab consumeables!&nbsp;</p>
 
             <p>We are happy to announce that In Vitro A/S is sponsoring our team with lab consumeables!&nbsp;</p>
  
−
<p><a href="in-vitro.dk" target="_top"><img alt="" src="/wiki/images/7/7c/DTU-Denmark_In_Vitro.jpg" style="width: 400px; height: 156px;" /></a></p>
+
<p><a href="in-vitro.dk" target="_top"><img alt="" src="/files/In%20Vitro.jpg" style="width: 400px; height: 156px;" /></a></p>
  
 
           </div>
 
           </div>
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             <p>We are happy to announce that Frisnette is sponsoring our team with lab consumeables!&nbsp;</p>
 
             <p>We are happy to announce that Frisnette is sponsoring our team with lab consumeables!&nbsp;</p>
  
−
<p><a href="http://frisenette.dk/" target="_blank"><img alt="" src="/wiki/images/c/c8/DTU-Denmark_Frisenette.jpg" style="width: 330px; height: 85px;" /></a></p>
+
<p><a href="http://frisenette.dk/" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/c/c8/DTU-Denmark_Frisenette.jpg" style="width: 330px; height: 85px;" /></a></p>
  
 
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−
             <div class="pull-left"><img alt="" src="/wiki/images/e/e1/DTU-Denmark_timeline_W168.jpg" style="width: 120px; height: 160px;" /></div>
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             <div class="pull-left"><img alt="" src="https://static.igem.org/mediawiki/2015/e/e1/DTU-Denmark_timeline_W168.jpg" style="width: 120px; height: 160px;" /></div>
  
 
<div class="pull-left">
 
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           </div>
 
           <div class="timeline-body">
 
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             <p style="text-align: center;"><img alt="" src="/wiki/images/f/fe/DTU-Denmark_timeline_biobrickworkshop.jpg" style="width: 350px; height: 198px;" /></p>
+
             <p style="text-align: center;"><img alt="" src="https://static.igem.org/mediawiki/2015/f/fe/DTU-Denmark_timeline_biobrickworkshop.jpg" style="width: 350px; height: 198px;" /></p>
  
 
<p>Southern University of&nbsp;Denmark and University of Copenhagen joined us for a three-day BioBrick tutorial, where we spent three days in the laboratory cloning, learning about iGEM, wiki design, and getting to know each other through social activities.</p>
 
<p>Southern University of&nbsp;Denmark and University of Copenhagen joined us for a three-day BioBrick tutorial, where we spent three days in the laboratory cloning, learning about iGEM, wiki design, and getting to know each other through social activities.</p>
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             <p>We are happy to announce that the Otto M&oslash;nsted Fonden&nbsp;is contributing&nbsp;financially to our team!</p>
 
             <p>We are happy to announce that the Otto M&oslash;nsted Fonden&nbsp;is contributing&nbsp;financially to our team!</p>
  
−
<p><a href="http://www.ottomoensted.dk/" target="_blank"><img alt="" src="/wiki/images/3/35/DTU-Denmark_Ottomoensted.png" style="width: 400px; height: 85px;" /></a></p>
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<p><a href="http://www.ottomoensted.dk/" target="_blank"><img alt="" src="https://static.igem.org/mediawiki/2015/3/35/DTU-Denmark_Ottomoensted.png" style="width: 400px; height: 85px;" /></a></p>
  
 
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        References
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          <li>Carr, P. A., Wang, H. H., Sterling, B., Isaacs, F. J., Lajoie, M. J., Xu, G., … Jacobson, J. M. (2012). Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Research, 40(17). doi:10.1093/nar/gks455</li>
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          <li>Ginetti, F., Perego, M., Albertini, A. M., &amp; Galizzi, A. (1996). Bacillus subtilis mutS mutL operon: Identification, nucleotide sequence and mutagenesis. Microbiology, 142(8), 2021–2029. doi:10.1099/13500872-142-8-2021</li>
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          <li>Sun, Z., Deng, A., Hu, T., Wu, J., Sun, Q., Bai, H., … Wen, T. (2015). A high-efficiency recombineering system with PCR-based ssDNA in Bacillus subtilis mediated by the native phage recombinase GP35. Applied Microbiology and Biotechnology, 99(12), 5151–5162. <a href="http://dx.doi.org/10.1007/s00253-015-6485-5" target="_blank">doi:10.1007/s00253-015-6485-5</a></li>
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               <img src="/wiki/images/a/af/DTU-Denmark_igemlogo.png" height="90px">
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               <img src="/wiki/images/5/5c/DTU-Denmark_NovoNordiskFonden_logo.png">
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Latest revision as of 15:12, 9 November 2015


Journal

Scroll down for more

Protocols

Needed materials: 100 ml TAE buffer, 1gr. agarose, ethidium bromide.
Mix 100 ml. TAE buffer with 1 gr. agarose powder, heat in microwave till the agarose is disolved, let it cool till it can be handled with bare hands, add 10 µl ethidium bromide. Then pour the mixture into a mold containing slots for wells, and let cool.
Set gel into electrophoresis chamber filled with 1X TAE buffer so the wells are covered. 
Mix 5 µl of your PCR reactions/sample with 1 µl 6X loading buffer.
Pipette 5 µl into each well, pour 2-3 µl ladder in some so the size can be seen.
Run at 140 V, for 30-40 min.
Chemo competens is a way of getting E. coli to be able to take up new DNA, since this cant be done naturally like B. subtilis, then chemocompetent cells have to be made.
Protocol can be found here
Needed materials: a 40% glycerol solution, bacteria of your choice, cryo tubes.
Mix glycerol and bacteria 50/50 in a cryo tube and place in a -80 frezzer till needed.

A lot of lab work requires plates in order to produce results, and often you need a special concentration, a unique antibiotic mixed into the plates or a different composition than what is available at the lab you are in. If that is the case, the plate needs to be made from scratch, or somewhat along the way.

Protocol can be found here.

For the experiments a minimal media designed for B. subtilis has been used. The plates have been made by following this protocol (for 1 liter).
Protocol can be found here.
In order to work with plasmids, then they needs to be purified and condensed, this is done bu minipreping the bacteria, and afterwards the concentration can be investigating using NanoDrop™.
Protocol can be found here.
Bacillus can be made competent allowing an easy alteration of the genome and so wanted mutaions can be inserted, this is a unique way of investigateing new pathways.
Protocol can be found here.
Electrotoration of bacteria is used in order to introduce mutations in the lagging strand of the strain, this technique are used in order to incorporate wanted mutations in a strain of Bacillus subtilis 168.
Protocol can be found here.
Electro competent cells are used in our MAGE part of the project, so a batch of cells was prepared using the following protocol.
Protocol can be found here

Lab Notebook

The lab book for expression of tyrocidine can be found here. 
The lab book for the generation of oligo-competent strains can be found here.
To approve a lab-on-a-disc concept as a screening device, the UV-vis abasobancee were measured here. 
See our labnotebook here.

Timeline

  • Biology of the Future

    2015-09-14

    Our team member Pernille spent an afternoon giving a presentation on cell factories and synthetic biology to 30 highschool students. She says: "Synthetic biology is all about being creative and use your imagination to design bio-solutions that can impact the world. For that exact reason, it is neccesary to discuss which ethical values tat should drive research". The highschool students had lots of questions and opinion for the discussion about ethics.

     

  • VWR to the rescue!

    2015-09-01

    We are happy to announce that the VWR is contributing our team with their awesome products!

     

  • Visit from Fisher Scientific!

    2015-08-26

    Today we had a visit by Susanne Basse from Fisher Scientific. She came by our office with a wagon full of items, Thanks! 

  • Contribution from Macrogen!

    2015-08-20

    We are pleased to announce that Macrogen is sponsoring our team with sequencing!

  • Contributions from AKG!

    2015-08-19

    We are happy to announce that AKG Acoustics is sponsoring our team with headphones for presentations in Boston! 

  • Contributions from VWR - Bie & Berntsen A/S

    2015-08-11

    We are happy to announce that VWR - Bie & Berntsen A/S is sponsoring our team with lab consumeables!

  • Contributions from Fisher Scientific

    2015-08-11

    We are happy to announce that Fisher Scientific is sponsoring our team with lab materials! 

  • Canoeing

    2015-08-07

    Today we took a day off from lab to go canoeing, followed by a barbeque at Chris' place.

  • Contribution from SnapGene

    2015-08-03

    We are happy to announce that the SnapGene is contributing our team with lisences to their awesome product!

  • Wiki Wizard

    2015-07-30

    We have uploaded the first beta version of the Wiki Wizard to GitHub

  • First BioBrick cloned into B. subtilis

    2015-07-30

    An expression cassette with lambda beta recombinase was sucesfully transformed into Bacillus subtilis. First step towards establishing MAGE in Bacillus subtilis completed!

  • BioBrick High School Project

    2015-07-23

    3 high school students; Simran, Noor, and Charlotte, joined us and Biotech Academy for 5 days to make biosensors that changes color, when water is poluted. Read more at the Human Practice and http://biotechacademy.dk.

  • First sequencing results

    2015-07-22

    We received our first sequencing results. One step closer to our first BioBrick!

  • Brevibacillus parabrevis arrives

    2015-07-16

    Brevibacillus parabrevis produces a lot of different antibiotics including tyrocidine. We will transfer the tyrocidine operon to our chassis Bacillus subtilis.

  • Contribution from the Lundbeck Foundation!

    2015-07-15

    We are happy to announce that the Lundbeck Foundation is contributing financially to our team!

  • Contributions from In Vitro!

    2015-05-06

    We are happy to announce that In Vitro A/S is sponsoring our team with lab consumeables! 

  • Contributions from Frisnette

    2015-04-30

    We are happy to announce that Frisnette is sponsoring our team with lab consumeables! 

  • We get our strain

    2015-04-28

    We get a plate of our chassis strain Bacillus subtilis W168.
    We can now begin the work in the laboratory.

  • BioBrick Workshop

    2015-04-24

    Southern University of Denmark and University of Copenhagen joined us for a three-day BioBrick tutorial, where we spent three days in the laboratory cloning, learning about iGEM, wiki design, and getting to know each other through social activities.

  • Contribution from the Otto Mønsted Fonden!

    2015-03-08

    We are happy to announce that the Otto Mønsted Fonden is contributing financially to our team!

  • First official team meeting

    2015-01-14

    Today we had our first official team meeting. We talked about the project and got to know each other.

  • Introductory meeting

    2014-11-25

    This day, last years team held an introductory session about iGEM for interested people.

Technical University of Denmark
Department of Systems Biology
Søltofts Plads 221
2800 Kgs. Lyngby
Denmark
P: +45 45 25 25 25
M: dtu-igem-2015@googlegroups.com