Team:EPF Lausanne/Microfluidics

{{CSS/EPFL_head}}
<html>
<style>
#contentSub, #footer-box, #catlinks, #search-controls, #p-logo, .printfooter, .firstHeading,.visualClear {display: none;} /*-- hides default wiki settings --*/
</style>

<!--  here ends the section that changes the default wiki template to a white full width background -->



<!-- MENU -->

<nav class="navbar navbar-default" role="navigation">
  <div class="container-fluid">
    <!-- Brand and toggle get grouped for better mobile display -->
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <a class="navbar-brand" href="https://2014.igem.org/Team:EPF_Lausanne"><img src="https://static.igem.org/mediawiki/2014/d/dc/LogoEPFL.png" alt="" /></a>
</a>
    </div>

    <!-- Collect the nav links, forms, and other content for toggling -->
    <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
      <ul class="nav navbar-nav navbar-right">
    <div class="nav-collapse">
      <ul class="nav">
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne">Home</a></li>
        <li class="dropdown">
          <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">
            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Overview">Overview</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>

        <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>
          <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/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/Safety">Safety</a></li>
          </ul>
        </li>

       <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>
          <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/Attributions">Attributions</a></li>
          </ul>
        </li>

      <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>
          <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/Parts">Parts</a></li>
          </ul>
        </li>
    </div>
      </ul>

    </div><!-- /.navbar-collapse -->
  </div><!-- /.container-fluid -->
</nav>

<!-- END MENU -->



<!-- ABSTRACT -->

<div class="whitebg">
<div class="container">


<ol class="breadcrumb">
  <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Designing">Designing a chip</a></li>
       <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>
</ol>




<h1 class="cntr">Microfluidics</h1>

<div class="cntr">
<img src="https://static.igem.org/mediawiki/2014/5/55/Chip_icon.png" alt="Chip icon" height="300" />
</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>-->

<h3>Microfluidics and synthetic biology</h3>

<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>


<p>The major benefits of using microfluidic chips are:</p>
<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>


<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>

<img src="https://static.igem.org/mediawiki/2014/0/03/Chip_sketch.png" alt="Chip sketch" class="cntr" width="100%" />

<br />
<br />
<br />
<ul>
	<li>a. Disassembled view of a microfluidic chip showing all the different components and the region where bacteria/yeasts are located</li>
	<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>
	<li>c. When pressure is retrieved, the ceiling elevates again, which opens the flow channel</li>
</ul>

<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>

<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>

<!-- END ABSTRACT -->
</html>
{{CSS/EPFL_bottom}}