Team:EPF Lausanne/Microfluidics

From 2014.igem.org

(Difference between revisions)
Line 6: Line 6:
<!--  here ends the section that changes the default wiki template to a white full width background -->
<!--  here ends the section that changes the default wiki template to a white full width background -->
 +
Line 11: Line 12:
<!-- MENU -->
<!-- MENU -->
-
<nav class="navbar navbar-default" role="navigation">
+
<nav class="navbar navbar-default navbar_alt" role="navigation">
   <div class="container-fluid">
   <div class="container-fluid">
     <!-- Brand and toggle get grouped for better mobile display -->
     <!-- Brand and toggle get grouped for better mobile display -->
Line 30: Line 31:
     <div class="nav-collapse">
     <div class="nav-collapse">
       <ul class="nav">
       <ul class="nav">
-
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne">Home</a></li>
+
        <li><a href="https://2014.igem.org/Team:EPF_Lausanne">Home</a></li>
         <li class="dropdown">
         <li class="dropdown">
           <a href="https://2014.igem.org/Team:EPF_Lausanne" class="dropdown-toggle" data-toggle="dropdown">Project <span class="caret"></span></a>
           <a href="https://2014.igem.org/Team:EPF_Lausanne" class="dropdown-toggle" data-toggle="dropdown">Project <span class="caret"></span></a>
           <ul class="dropdown-menu" role="menu">
           <ul class="dropdown-menu" role="menu">
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Overview">Overview</a></li>
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Overview">Overview</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Envelope_stress_responsive_bacteria">Stress Responsive</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Yeast">Osmo Responsive</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics">Microfluidics</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Hardware">Hardware</a></li>
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Applications">Applications</a></li>
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Applications">Applications</a></li>
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/HumanPractice">Human Practices</a></li>
+
 
-
          </ul>
+
 
 +
<!--             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/HumanPractice">Human Practices</a></li>
 +
-->          </ul>
         </li>
         </li>
-
        <li class="dropdown">
+
 
-
           <a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook" class="dropdown-toggle active" data-toggle="dropdown">Notebook <span class="caret"></span></a>
+
      <li class="dropdown">
 +
           <a href="#" class="dropdown-toggle active" data-toggle="dropdown">Achievements <span class="caret"></span></a>
           <ul class="dropdown-menu" role="menu">
           <ul class="dropdown-menu" role="menu">
-
            <li class="active"><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook">Timeline</a></li>
+
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Results">Results</a></li>
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Protocol">Protocol</a></li>
+
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Data">Data</a></li>
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Data">Data</a></li>
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Safety">Safety</a></li>
+
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Judging">Judging</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Parts" class="active">Parts</a></li>
           </ul>
           </ul>
 +
        </li>
 +
 +
        <li class="dropdown">
 +
          <a href="#" class="dropdown-toggle" data-toggle="dropdown">Policy &amp; Practice <span class="caret"></span></a>
 +
          <ul class="dropdown-menu" role="menu">
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/HumanPractice">Human Practice</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Safety">Bio Safety</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/PolicyPractice">Policy &amp; Practice</a></li>
 +
 +
<!--            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/HumanPractice">Human Practices</a></li>
 +
-->          </ul>
         </li>
         </li>
       <li class="dropdown">
       <li class="dropdown">
-
           <a href="https://2014.igem.org/Team:EPF_Lausanne/Team" class="dropdown-toggle" data-toggle="dropdown">Team <span class="caret"></span></a>
+
           <a href="#" class="dropdown-toggle" data-toggle="dropdown">Notebook <span class="caret"></span></a>
           <ul class="dropdown-menu" role="menu">
           <ul class="dropdown-menu" role="menu">
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Team">Meet us!</a></li>
+
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Bacteria">Bacteria</a></li>
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Attributions">Attributions</a></li>
+
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Microfluidics">Microfluidics</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Yeast">Yeast</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/I.T">I.T</a></li>
 +
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Protocol">Protocol</a></li>
           </ul>
           </ul>
         </li>
         </li>
       <li class="dropdown">
       <li class="dropdown">
-
           <a href="https://2014.igem.org/Team:EPF_Lausanne/Team" class="dropdown-toggle" data-toggle="dropdown">Achievements <span class="caret"></span></a>
+
           <a href="#" class="dropdown-toggle" data-toggle="dropdown">Team <span class="caret"></span></a>
           <ul class="dropdown-menu" role="menu">
           <ul class="dropdown-menu" role="menu">
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Judging">Judging</a></li>
+
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook">Timeline</a></li>
-
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Parts">Parts</a></li>
+
             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Team">Meet us!</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Attributions">Attributions</a></li>
 +
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Acknowledgments">Acknowledgments</a></li>
           </ul>
           </ul>
         </li>
         </li>
Line 71: Line 95:
   </div><!-- /.container-fluid -->
   </div><!-- /.container-fluid -->
</nav>
</nav>
 +
<!-- END MENU -->
<!-- END MENU -->
-
 
<!-- ABSTRACT -->
<!-- ABSTRACT -->
-
<div class="whitebg">
 
<div class="container">
<div class="container">
 +
<div class="box" id="boxbread">
-
<ul class="list-unstyled">
+
<ol class="breadcrumb breadcrumb-arrow">
 +
                  <li><a href="https://2014.igem.org/Team:EPF_Lausanne"><i class="glyphicon glyphicon-home"></i> Home</a></li>
 +
                  <li class="dropdown"><a href="#"><i class="glyphicon glyphicon-star"></i> Achievements</a> <b class="caret"></b>
 +
                    <ul class="dropdown-menu">
 +
                      <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Making/PartI">Part I</a></li>
 +
                      <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Making/PartII">Part II</a></li>
 +
                    </ul>
 +
                  </li>
 +
                  <li class="active"><span><i class="glyphicon glyphicon-th-list"></i> Parts</span></li>
 +
                </ol>
 +
</div>
-
  <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Designing">Designing a chip</a></li>
+
<div class="row">
-
      <li class="dropdown">
+
-
            <a href="#" class="dropdown-toggle" data-toggle="dropdown">
+
-
                Making a chip <b class="caret"></b>
+
-
            </a>
+
-
            <ul class="dropdown-menu">
+
-
                <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Making/PartI">Part I</a></li>
+
-
                <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Making/PartII">Part II</a></li>
+
-
            </ul>
+
-
        </li>
+
-
</ul>
+
 +
<div class="col col-md-9">
 +
<div class="whitebg box">
-
<h1 class="cntr">Microfluidics</h1>
 
-
<br/>
+
<!-- PARTS -->
-
<div class="cntr">
 
-
<a href="https://static.igem.org/mediawiki/2014/d/d8/EPFLmicrofluidics.JPG" data-lightbox="image-1" data-title="EPFL microfluidic chips"><img src="https://static.igem.org/mediawiki/2014/d/d8/EPFLmicrofluidics.JPG" width="80%"></a>
 
-
</div>
 
-
<!--<p class="lead">Our Biopad is implemented in a microfluidic chip. This tool allows all kinds of analytical experiments and is increasingly used in biological research. From fabrication to applications, find out more about this awesome device here!</p>-->
+
<div id="parts">
 +
<div class="align-left">
-
<h3>Microfluidics and synthetic biology</h3>
+
<h1 class="cntr">PARTS</h1>
-
<p>Microfluidics is an efficient tool for biological experiments. Its fields of applications go from gene regulatory network analysis to antibody screening. Several laboratory techniques can be adapted to these devices, such as DNA amplification, protein separation or cell sorting.</p>
 
-
<p>The chips are generally fabricated from elastomeric materials, such as polydimethylsiloxane (PDMS) and contain micron-sized channels with integrated micromechanical tools (mixer, valve, pump…). This allows massive parallelisation as well as great modularity of the experiments.</p>
 
-
<p>Most soluble reagents can be used, including DNA, proteins and small molecule libraries. As we focused our work on E.coli and S. cerevisiae, most of our experiments included culture of these species on-chip during our experiments. We first used the MITOMI chip which was invented in the lab of our supervisor Prof. Maerkl. We then designed new chips that were more adapted to stress the cells by pressure, as needed to implement the final “BioPad”.</p>
 
 +
<section id="dna">
 +
<h3 class="section-heading">DNA parts submitted by the 2014 EPFL iGEM team</h3>
 +
<p class="lead">
 +
Our team submitted a total of 55 Biobricks (biobrick 51 does not exist).</p>
 +
<p class="lead">
 +
In addition, 4 microfluidic designs have also been submitted to the registry.</p>
 +
<table class="table table-striped table-hover" id="biobricks_list">
 +
  <tr>
 +
    <th>Biobrick</th>
 +
    <th>What it is</th>
 +
    <th>Function</th>
 +
    <th>Why do we use it?</th>
 +
    <th>Group</th>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486000</td>
 +
    <td>CpxR coding sequence</td>
 +
    <td>Transcription factor</td>
 +
    <td>To make most of our biobricks!</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486001</td>
 +
    <td>CpxR under arabinose promoter</td>
 +
    <td>Treanscription factor</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486002</td>
 +
    <td>PAra + sfGFP CpxR [Nterm]</td>
 +
    <td>Expresses fused protein</td>
 +
    <td>Test CpxR expression & Ara promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486003</td>
 +
    <td>Flexible linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486004</td>
 +
    <td>Flexible linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486005</td>
 +
    <td>PAra + CpxR sfGFP [Cterm]</td>
 +
    <td>Expresses fused protein</td>
 +
    <td>Test CpxR expression & Ara promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486006</td>
 +
    <td>IFP[1]</td>
 +
    <td>N terminus of split IFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486007</td>
 +
    <td>IFP[2]</td>
 +
    <td>C terminus of split IFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486008</td>
 +
    <td>CxpR & Split IFP1.4 [Cterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each C terminus attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486009</td>
 +
    <td>CxpR & Split IFP1.4 [Nterm + Nterm]</td>
 +
    <td>Two CpxR CDS, each N terminus attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486010</td>
 +
    <td>CxpR & Split IFP1.4 [Nterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486011</td>
 +
    <td>CxpR & Split IFP1.4 [Cterm + Nterm]</td>
 +
    <td>Two CpxR CDS, each attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486012</td>
 +
    <td>CpxR + IFP[1]</td>
 +
    <td>CpxR with the Nterm moiety of IFP attached at its C terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486013</td>
 +
    <td>CpxR + IFP[2]</td>
 +
    <td>CpxR with the Cterm moiety of IFP attached at its C terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486014</td>
 +
    <td>IFP[1] + CpxR</td>
 +
    <td>CpxR with the Nterm moiety of IFP attached at its N terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486015</td>
 +
    <td>IFP[2] + CpxR</td>
 +
    <td>CpxR with the Cterm moiety of IFP attached at its N terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486016</td>
 +
    <td>fLuc[1]</td>
 +
    <td>N terminus moiety of the firefly luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486017</td>
 +
    <td>fLuc[2]</td>
 +
    <td>C terminus moiety of the firefly luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486018</td>
 +
    <td>PAra + fLuc[1] + fLuc[2]</td>
 +
    <td>Split firefly luciferase under arabinose promoter</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486019</td>
 +
    <td>rLuc[1]</td>
 +
    <td>C terminus moiety of the renilla luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486020</td>
 +
    <td>rLuc[2]</td>
 +
    <td>N terminus moiety of the renilla luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486021</td>
 +
    <td>PAra + rLuc[1] + rLuc[2]</td>
 +
    <td>Split renilla luciferase under arabinose promoter</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486022</td>
 +
    <td>rLuc</td>
 +
    <td>Full renilla luciferase</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486023</td>
 +
    <td>Yeast sfGFP</td>
 +
    <td>Superfolder GFP for yeast cells</td>
 +
    <td>Reporter</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486024</td>
 +
    <td>Kan</td>
 +
    <td>Yeast kanamycin resistance gene</td>
 +
    <td>Selection marker</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486025</td>
 +
    <td>ADH1 terminator</td>
 +
    <td>Terminator</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486026</td>
 +
    <td>Yeast sfGFP + Kan</td>
 +
    <td>Yeast sfGFP attached to the yeast kanamycin resistance gene</td>
 +
    <td>Control the expression of pbs2</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486027</td>
 +
    <td>rLuc + Kan</td>
 +
    <td>Renilla luciferase attached to the kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486028</td>
 +
    <td>Yeast sfGFP[1]</td>
 +
    <td>N terminal moiety of split yeast sfGFP</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486029</td>
 +
    <td>sfGFP[1] + kan</td>
 +
    <td>Nterm moiety of split yeast sfGFP attached to yeast kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486030</td>
 +
    <td>rLuc[1] + kan</td>
 +
    <td>Nterm moiety of split renilla luciferase attached to yeast kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486031</td>
 +
    <td>Ura</td>
 +
    <td>CDS for Uracil (yeast selective purposes)</td>
 +
    <td>Confer resistance to Uracil-deprived medium</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486032</td>
 +
    <td>Yeast sfGFP + Ura</td>
 +
    <td>Yeast sfGFP attached to the Uracil CDS</td>
 +
    <td>Control the expression of hog1</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486033</td>
 +
    <td>rLuc + Ura</td>
 +
    <td>Renilla luciferase attached to the Uracil CDS</td>
 +
    <td>Control the expression of hog1</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486034</td>
 +
    <td>yeast sfGFP[2]</td>
 +
    <td>C terminal moiety of split the yeast sfGFP</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486035</td>
 +
    <td>yeast sfGFP[2] + Ura</td>
 +
    <td>Cterm moiety of split yeast sfGFP attached to the Uracil CDS</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486036</td>
 +
    <td>rLuc[2] + Ura</td>
 +
    <td>Cterm moiety of split renilla luciferase attached to the Uracil CDS</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486037</td>
 +
    <td>linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486038</td>
 +
    <td>sfGFP[1]</td>
 +
    <td>N terminus moiety of split superfolder GFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486039</td>
 +
    <td>sfGFP[2]</td>
 +
    <td>C terminus moiety of split superfolder GFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486040</td>
 +
    <td>sfGFP[1] + CpxR</td>
 +
    <td>N terminus moiety of split sfGFP attached to CpxR</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486041</td>
 +
    <td>sfGFP[2] + CpxR</td>
 +
    <td>C terminus moiety of split sfGFP attached to CpxR</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486042</td>
 +
    <td>LZip</td>
 +
    <td>Monomer of leucine zipper TF</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486043</td>
 +
    <td>LZip + split rLuc</td>
 +
    <td>Two Leucine Zipper monomers, each attached to a different split rLuc moiety</td>
 +
    <td>Control for split rLuc assays</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486044</td>
 +
    <td>mut IFP[1]</td>
 +
    <td>Biobrick-compatible IFP[1]</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486045</td>
 +
    <td>mut IFP[2]</td>
 +
    <td>Biobrick-compatible IFP[2]</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486046</td>
 +
    <td>CpxR promoter FW</td>
 +
    <td>CpxR binding-region in forward direction</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486047</td>
 +
    <td>CpxR promoter RV</td>
 +
    <td>CpxR binding-region in reverse direction</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486048</td>
 +
    <td>CpxR reporter</td>
 +
    <td>Calgary's CpxR reporter repaired (sequence was missing)</td>
 +
    <td>To see when CpxR is active</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486049</td>
 +
    <td>CpxR promoter FW + RFP</td>
 +
    <td>Reporter of CpxR</td>
 +
    <td>Test the direction of the complete CpxR promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486050</td>
 +
    <td>CpxR promoter RV + RFP</td>
 +
    <td>Reporter of CpxR</td>
 +
    <td>Test the direction of the complete CpxR promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486052</td>
 +
    <td>Spacer</td>
 +
    <td>40 bases placed between constructs</td>
 +
    <td>Separate two constructs in the same plasmid</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486053</td>
 +
    <td>Linker</td>
 +
    <td>10 amino-acid linker</td>
 +
    <td>Attach CheY/Z to split luciferases</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486054</td>
 +
    <td>CheY/CheZ rLuc</td>
 +
    <td>CheY and CheZ, each attached to a moiety of split renilla luciferase</td>
 +
    <td>Positive control for the split rLuc</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486055</td>
 +
    <td>CheY/CheZ fLuc</td>
 +
    <td>CheY and CheZ, each attached to a moiety of split firefly luciferase</td>
 +
    <td>Positive control for the split fLuc</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486056</td>
 +
    <td>CxpR & Split mut IFP1.4 [Cterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each C terminus attached to a moiety of the biobrick-compatible IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
</table>
-
<p>The major benefits of using microfluidic chips are:</p>
+
</section>
-
<ul>
+
-
<li>Low volume required (microliter range)</li>
+
-
<li>High-throughput</li>
+
-
<li>High precision and sensitive detection</li>
+
-
<li>Cheap</li>
+
-
<li>Wide range of applications</li>
+
-
<li>Safe, enclosed environment (for more information go to the safety page)</li>
+
-
</ul>
+
 +
<br /><br />
-
<p>Some examples of microfluidic experiments:</p>
 
-
<ul>
 
-
<li>Transcription factors – DNA interactions</li>
 
-
<li>Protein – protein interactions</li>
 
-
<li>On-chip gene synthesis: protein expression from coding DNA</li>
 
-
<li>On-chip chemostat chambers: can be used to trace the fate of a single bacterium or to grow bacteria/yeast</li>
 
-
<li>Antibody characterisation</li>
 
-
</ul>
 
-
<h3>How does it work ?</h3>
+
<section id="microfluidics">
 +
<h3 class="section-heading">Microfluidics parts (chips created)</h3>
 +
<p class="lead">
 +
Our team designed and made 4 microfluidic chips. At the beginning, we also used the <a target="_blank" href="http://link.springer.com/protocol/10.1007%2F978-1-61779-292-2_6">MITOMI chip</a>.</p>
 +
<p class="lead">When designing the chips, the team took into account the future users and the current iGEM classification of parts. We considered it best to construct our chips as composite microfluidic parts, so their sub-parts could be used and combined in multiple ways. The flow and control layers can be separated and reused, as well as all the basic structures (chamber + connecting channel), nodes, array parts,...</p>
-
<img src="https://static.igem.org/mediawiki/2014/0/03/Chip_sketch.png" alt="Chip sketch" class="cntr" width="100%" />
 
-
<br />
+
<!-- send all lines here: https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Designing -->
-
<br />
+
<table class="table table-striped table-hover" id="chips_list">
-
<br />
+
  <tr>
-
<ul>
+
    <th>Name</th>
-
<li>a. Disassembled view of a microfluidic chip showing all the different components and the region where bacteria/yeasts are located</li>
+
    <th>Main Function</th>
-
<li>b. Cross section of the chip showing how a valve works: when pressure is applied in the control channel, the ceiling of the flow layer is pushed against the glass slide, which closes the flow channel</li>
+
  </tr>
-
<li>c. When pressure is retrieved, the ceiling elevates again, which opens the flow channel</li>
+
  <tr>
-
</ul>
+
    <td>SmashColi</td>
 +
    <td>To be able to separate the chip in 4 different compartments and apply 4 different pressures on each row of chambers.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BioPad</td>
 +
    <td>A large and simple microfluidic chip containing 9600 chambers in which the cells are contained in. Each chamber acts as a pixel for the BioPad project.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>SafetyColi</td>
 +
    <td>As a result of our Safety page, we decided to create a chip that is able to seal the bacteria in the chip, preventing them to leave the chip.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>FilterColi</td>
 +
    <td>To successfully immerse cells in a certain solution, this chip was designed to flow in the new medium in the chambers instead of doing it by diffusion.</td>
 +
  </tr>
 +
</table>
 +
</section>
-
<br />
 
-
<br />
 
-
<p>A standard microfluidic chip is a grid of interconnected channels and chambers. It is usually composed of one or two PDMS layers placed on a glass slide. In our case we used two layers, the so called flow layer and control layer. The bacteria are enclosed between the flow layer and the glass slide. By its shape, the flow layer is responsible for the patterns of the chip. In our case, the pattern consists of several parallel rows of chambers. The control layer comes on top of the flow layer and allows to open or close valves by pressing or releasing water in the corresponding channels. Thus a mechanical pressure can be applied from the control layer on the flow layer, enabling a precise compartmentalization of the chip.</p>
+
<br /><br />
 +
</div>
 +
</div>
-
<p>Once the chip is ready to be used, small tubings of 0.35mm diameter are plugged in the inlets of the chip (see gif below). The tubings that are plugged in the control inlets are loaded with water and enable the opening or closing of valves. The tubings that are plugged into the flow inlets are used to flow bacteria/yeast or various solutions in the chambers. </p>
 
-
 
-
 
-
<p>Picture of the MITOMI Chip and our Smash-Coli chip</p>
 
-
 
-
<div class="row">
 
-
<div class="col col-md-6 cntr">
 
-
    <div class="thumbnail">
 
-
<a href="https://static.igem.org/mediawiki/2014/c/c6/Mitomi_che.PNG" data-lightbox="image-1" data-title="Mitomi"><img src="https://static.igem.org/mediawiki/2014/c/c6/Mitomi_che.PNG" alt="Mitomi" width="200" /></a>
 
-
      <div class="caption">
 
-
        <p>MITOMI chip filled with bacteria expressing GFP</p>
 
-
      </div>
 
-
    </div>
 
-
</div>
 
-
<div class="col col-md-6 cntr">
 
-
    <div class="thumbnail">
 
-
<a href="https://static.igem.org/mediawiki/2014/5/51/Killcoli.PNG" data-lightbox="image-1" data-title="Smash-coli"><img src="https://static.igem.org/mediawiki/2014/5/51/Killcoli.PNG" alt="Killcoli" width="200" /></a>
 
-
      <div class="caption">
 
-
        <p>“Smash-coli” chip, here with expression of RFP</p>
 
-
      </div>
 
-
    </div>
 
</div>
</div>
</div>
</div>
-
 
+
<div class="col col-md-3">
-
 
+
<nav id="affix-nav" class="sidebar hidden-sm hidden-xs">
-
 
+
    <ul class="nav sidenav box" data-spy="affix" data-offset-top="200" data-offset-bottom="400">
-
<ul  class="list-unstyled">
+
        <li class="active"><a href="#dna">DNA Parts</a></li>
-
 
+
        <li><a href="#microfluidics">Microfluidics Parts</a></li>
-
  <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Designing">Designing a chip</a></li>
+
    </ul>
-
      <li class="dropdown">
+
</nav>
-
            <a href="#" class="dropdown-toggle" data-toggle="dropdown">
+
-
                Making a chip <b class="caret"></b>
+
-
            </a>
+
-
            <ul class="dropdown-menu">
+
-
                <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Making/PartI">Part I</a></li>
+
-
                <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Making/PartII">Part II</a></li>
+
-
            </ul>
+
-
        </li>
+
-
</ul>
+
-
 
+
-
 
+
</div>
</div>
</div>
</div>
 +
</div>
 +
<!-- END ABSTRACT -->
-
 
+
<script type="text/javascript">
-
 
+
    $(document).ready(function() {
-
<!-- END ABSTRACT -->
+
      $('body').scrollspy({ target: '#affix-nav' });
 +
      $('#biobricks_list tr').click(function (e) {
 +
        text = $(this).children('td.biobrick_name').first().text();
 +
        if (text != '') {
 +
          return window.open('http://parts.igem.org/Part:' + text, '_blank');
 +
        }
 +
      });
 +
    });
 +
</script>
</html>
</html>
{{CSS/EPFL_bottom}}
{{CSS/EPFL_bottom}}

Revision as of 16:44, 14 October 2014

PARTS

DNA parts submitted by the 2014 EPFL iGEM team

Our team submitted a total of 55 Biobricks (biobrick 51 does not exist).

In addition, 4 microfluidic designs have also been submitted to the registry.

Biobrick What it is Function Why do we use it? Group
BBa_K1486000 CpxR coding sequence Transcription factor To make most of our biobricks! Bacteria
BBa_K1486001 CpxR under arabinose promoter Treanscription factor Bacteria
BBa_K1486002 PAra + sfGFP CpxR [Nterm] Expresses fused protein Test CpxR expression & Ara promoter Bacteria
BBa_K1486003 Flexible linker Attaches two proteins together Bacteria
BBa_K1486004 Flexible linker Attaches two proteins together Bacteria
BBa_K1486005 PAra + CpxR sfGFP [Cterm] Expresses fused protein Test CpxR expression & Ara promoter Bacteria
BBa_K1486006 IFP[1] N terminus of split IFP Bacteria
BBa_K1486007 IFP[2] C terminus of split IFP Bacteria
BBa_K1486008 CxpR & Split IFP1.4 [Cterm + Cterm] Two CpxR CDS, each C terminus attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486009 CxpR & Split IFP1.4 [Nterm + Nterm] Two CpxR CDS, each N terminus attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486010 CxpR & Split IFP1.4 [Nterm + Cterm] Two CpxR CDS, each attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486011 CxpR & Split IFP1.4 [Cterm + Nterm] Two CpxR CDS, each attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486012 CpxR + IFP[1] CpxR with the Nterm moiety of IFP attached at its C terminus Intermediate & control Bacteria
BBa_K1486013 CpxR + IFP[2] CpxR with the Cterm moiety of IFP attached at its C terminus Intermediate & control Bacteria
BBa_K1486014 IFP[1] + CpxR CpxR with the Nterm moiety of IFP attached at its N terminus Intermediate & control Bacteria
BBa_K1486015 IFP[2] + CpxR CpxR with the Cterm moiety of IFP attached at its N terminus Intermediate & control Bacteria
BBa_K1486016 fLuc[1] N terminus moiety of the firefly luciferase Bacteria
BBa_K1486017 fLuc[2] C terminus moiety of the firefly luciferase Bacteria
BBa_K1486018 PAra + fLuc[1] + fLuc[2] Split firefly luciferase under arabinose promoter Control Bacteria
BBa_K1486019 rLuc[1] C terminus moiety of the renilla luciferase Bacteria
BBa_K1486020 rLuc[2] N terminus moiety of the renilla luciferase Bacteria
BBa_K1486021 PAra + rLuc[1] + rLuc[2] Split renilla luciferase under arabinose promoter Control Bacteria
BBa_K1486022 rLuc Full renilla luciferase Control Bacteria
BBa_K1486023 Yeast sfGFP Superfolder GFP for yeast cells Reporter Yeast
BBa_K1486024 Kan Yeast kanamycin resistance gene Selection marker Yeast
BBa_K1486025 ADH1 terminator Terminator Yeast
BBa_K1486026 Yeast sfGFP + Kan Yeast sfGFP attached to the yeast kanamycin resistance gene Control the expression of pbs2 Yeast
BBa_K1486027 rLuc + Kan Renilla luciferase attached to the kanamycin resistance gene Yeast
BBa_K1486028 Yeast sfGFP[1] N terminal moiety of split yeast sfGFP Yeast
BBa_K1486029 sfGFP[1] + kan Nterm moiety of split yeast sfGFP attached to yeast kanamycin resistance gene Yeast
BBa_K1486030 rLuc[1] + kan Nterm moiety of split renilla luciferase attached to yeast kanamycin resistance gene Yeast
BBa_K1486031 Ura CDS for Uracil (yeast selective purposes) Confer resistance to Uracil-deprived medium Yeast
BBa_K1486032 Yeast sfGFP + Ura Yeast sfGFP attached to the Uracil CDS Control the expression of hog1 Yeast
BBa_K1486033 rLuc + Ura Renilla luciferase attached to the Uracil CDS Control the expression of hog1 Yeast
BBa_K1486034 yeast sfGFP[2] C terminal moiety of split the yeast sfGFP Yeast
BBa_K1486035 yeast sfGFP[2] + Ura Cterm moiety of split yeast sfGFP attached to the Uracil CDS Yeast
BBa_K1486036 rLuc[2] + Ura Cterm moiety of split renilla luciferase attached to the Uracil CDS Yeast
BBa_K1486037 linker Attaches two proteins together Yeast
BBa_K1486038 sfGFP[1] N terminus moiety of split superfolder GFP Bacteria
BBa_K1486039 sfGFP[2] C terminus moiety of split superfolder GFP Bacteria
BBa_K1486040 sfGFP[1] + CpxR N terminus moiety of split sfGFP attached to CpxR Bacteria
BBa_K1486041 sfGFP[2] + CpxR C terminus moiety of split sfGFP attached to CpxR Bacteria
BBa_K1486042 LZip Monomer of leucine zipper TF Bacteria
BBa_K1486043 LZip + split rLuc Two Leucine Zipper monomers, each attached to a different split rLuc moiety Control for split rLuc assays Bacteria
BBa_K1486044 mut IFP[1] Biobrick-compatible IFP[1] Bacteria
BBa_K1486045 mut IFP[2] Biobrick-compatible IFP[2] Bacteria
BBa_K1486046 CpxR promoter FW CpxR binding-region in forward direction Bacteria
BBa_K1486047 CpxR promoter RV CpxR binding-region in reverse direction Bacteria
BBa_K1486048 CpxR reporter Calgary's CpxR reporter repaired (sequence was missing) To see when CpxR is active Bacteria
BBa_K1486049 CpxR promoter FW + RFP Reporter of CpxR Test the direction of the complete CpxR promoter Bacteria
BBa_K1486050 CpxR promoter RV + RFP Reporter of CpxR Test the direction of the complete CpxR promoter Bacteria
BBa_K1486052 Spacer 40 bases placed between constructs Separate two constructs in the same plasmid Bacteria
BBa_K1486053 Linker 10 amino-acid linker Attach CheY/Z to split luciferases Bacteria
BBa_K1486054 CheY/CheZ rLuc CheY and CheZ, each attached to a moiety of split renilla luciferase Positive control for the split rLuc Bacteria
BBa_K1486055 CheY/CheZ fLuc CheY and CheZ, each attached to a moiety of split firefly luciferase Positive control for the split fLuc Bacteria
BBa_K1486056 CxpR & Split mut IFP1.4 [Cterm + Cterm] Two CpxR CDS, each C terminus attached to a moiety of the biobrick-compatible IFP Characterize CpxR dimerization Bacteria


Microfluidics parts (chips created)

Our team designed and made 4 microfluidic chips. At the beginning, we also used the MITOMI chip.

When designing the chips, the team took into account the future users and the current iGEM classification of parts. We considered it best to construct our chips as composite microfluidic parts, so their sub-parts could be used and combined in multiple ways. The flow and control layers can be separated and reused, as well as all the basic structures (chamber + connecting channel), nodes, array parts,...

Name Main Function
SmashColi To be able to separate the chip in 4 different compartments and apply 4 different pressures on each row of chambers.
BioPad A large and simple microfluidic chip containing 9600 chambers in which the cells are contained in. Each chamber acts as a pixel for the BioPad project.
SafetyColi As a result of our Safety page, we decided to create a chip that is able to seal the bacteria in the chip, preventing them to leave the chip.
FilterColi To successfully immerse cells in a certain solution, this chip was designed to flow in the new medium in the chambers instead of doing it by diffusion.


Sponsors

Copyright © iGEM EPFL 2014. All Rights Reserved

Retrieved from "http://2014.igem.org/Team:EPF_Lausanne/Microfluidics"