Difference between revisions of "Team:York/Notebook"

 
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<!DOCTYPE html>
 
<{{:Team:York/Templates/NavigationBar}}>
 
<{{:Team:York/Templates/NavigationBar}}>
 
<html>
 
<html>
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   <script type="text/javascript">
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   <body>
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      $(window).load(function() {
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      $('li.notebook').addClass('active');
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<div>
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      $('li.n_over').addClass('active');
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    <!-- Header -->
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  <div class="cam-container">
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      $(".affix").css("width", $("#parent").width());
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    <header class="intro-header" style="background: url(//2017.igem.org/wiki/images/2/27/TeamYork-TemporaryBackground.png); background-size: 100% 100%; background-position:0px 20px;">
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      });
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        <div class="container">
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            <div class="intro-message text-center container">
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      $(window).scroll(function() {
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                <br style = “line-height:20px;”><br>
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      $(".affix").css("width", $("#parent").width());
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                <h1 style="-webkit-text-stroke: 2px black; color:#fff;">Notebook</h1>
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      });
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                <h1 style="-webkit-text-stroke: 2px black; color:#fff;">Tracking Our Progress</h1>
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            </div>
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      $(window).resize(function() {
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        </div>
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      $(".affix").css("width", $("#parent").width());
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    </header>
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      });
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  </div>
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  </script>
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</div>
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  <body data-spy="scroll" data-target="#myScrollspy" data-offset="20">
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       <div class="container">
 
       <div class="container">
 
         <h2 style="padding: 0px; margin-bottom: 0px;">Notebook</h2>
 
         <h2 style="padding: 0px; margin-bottom: 0px;">Notebook</h2>
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       </div>
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       <style>
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       <!----------------------------- Week 1 -------------------------------------------->
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          body {
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       <h3 id="week1">Week 1 (19 June - 25 June)</h3>
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      position: relative;
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       <hr>
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  }
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       <ul class="media-list">
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        }
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        .vertical-menu a {
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        background-color: #eee;
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        color: black;
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        display: block;
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        padding: 12 em;
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        text-decoration: none;
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        }
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        .vertical-menu a:hover {
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        }
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      </style>
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       <div class="vertical-menu" id="myScrollspy">
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        <a href="#week1">Week 1</a>
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        <a href="#week2">Week 2</a>
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        <a href="#week3">Week 3</a>
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        <a href="#week4">Week 4</a>
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        <a href="#week5">Week 5</a>
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        <a href="#week6">Week 6</a>
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        <a href="#week7">Week 7</a>
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        <a href="#week8">Week 8</a>
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        <a href="#week9">Week 9</a>
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        <a href="#week10">Week 10</a>
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        <a href="#week11">Week 11</a>
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        <a href="#week12">Week 12</a>
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        <a href="#week13">Week 13</a>
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        <a href="#week14">Week 14</a>
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        <a href="#week15">Week 15</a>
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        <a href="#week16">Week 16</a>
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        <a href="#week17">Week 17</a>
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        <a href="#week18">Week 18</a>
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        <a href="#week19">Week 19</a>
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        <a href="#week20">Week 20</a>
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       </div>
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       <div class="container">
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      <!-- Wet Lab Overview
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         <li class="media">
 
         <li class="media">
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        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
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            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" />
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        <div class="media-body">
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            <div class="media-body">
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        <h4 class="media heading">Wet Lab Overview</h4>
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              <h4 class="media heading">Biology Division</h4>
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        <p>
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              <p>
−
        Our main goals were to 1) clone the three metal transport proteins and pea metallothionein,
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                  First week detailed experementation plan and lab supplies ordering. We have several candidates for a co-culture.
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        2) assemble the transport proteins and metallothionein to make our composite constructs,
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              </p>
−
        and 3) monitor sequestration efficiency in our <i>in vivo</i> model using <i>E. coli</i>.
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            </div>
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        </p>
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        </div>
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         </li>
 
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        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/2/28/Cornell-nb-dry.png">
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            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
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        <div class="media-body">
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            <div class="media-body">
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        <h4 class="media heading">Dry Lab Overview</h4>
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              <h4 class="media heading">Microscopy Division</h4>
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        <p>
+
              <p>
−
        Text goes here.
+
                  Had the first meeting of the division. Discussed timeline and the components we have available. For now, we will order only camera. Figured out that Biology Labs do not have any lasers and optical benches.  
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        </p>
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              </p>
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        </div>
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            </div>
 
         </li>
 
         </li>
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        -->
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      </ul>
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       <!-- nested template
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      <br><br>
 +
      <!----------------------------- Week 2 -------------------------------------------->
 +
       <h3 id="week2">Week 2 (26 June - 2 July)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 
         <li class="media">
 
         <li class="media">
−
        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
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            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" />
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        <div class="media-body">
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            <div class="media-body">
−
        <h4 class="media heading">Wet Lab Overview</h4>
+
            <h4 class="media heading">Biology Division</h4>
−
        <p>
+
            <p>
−
        Text
+
              In the end of a last weeek, we decided to work with algae and bacteria. Biology Lab Safety talk for all team members. Prepared LB media for <i>E.coli</i> and pored it into plates. Freezig <i>E.coli</i> cells for an emergency. Checking plates for algae and liquid culture for transformation. Prepared for plasmid extraction via electrophoresis.
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        </p>
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            </p>
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+
        <li class="media dry">
−
        <div class="media">
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            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
−
        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/2/28/Pb_small.png">
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            <div class="media-body">
−
        <div class="media-body">
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              <h4 class="media heading">Microscopy Division</h4>
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        <h4 class="media heading">Lead Subteam</h4>
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              <p>
−
        <p>
+
                  We were given access to Physics Labs. It will be our home for the next weeks. We watched laser safety video and started taking pictures with freshly arrived Raspberry Pi V2 Camera. Made prototype of the DIHM. How easy was that?!
−
        Text
+
              </p>
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        </p>
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            </div>
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        </div>
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        </div>
+
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+
−
        <div class="media">
+
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        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/a/a9/Hg_small.png">
+
−
        <div class="media-body">
+
−
        <h4 class="media heading">Mercury Subteam</h4>
+
−
        <p>
+
−
        Text
+
−
        </p>
+
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        </div>
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+
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        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/d/dd/Ni_small.png">
+
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        <div class="media-body">
+
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        <h4 class="media heading">Nickel Subteam</h4>
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        <p>
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        Text
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        </p>
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+
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        <div class="media">
+
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        <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/4/40/Cornell_reporters.jpg">
+
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        <div class="media-body">
+
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        <h4 class="media heading">Reporters Subteam</h4>
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        <p>
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        Text
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        </p>
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        </div>
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        </div>
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         </li>
 
         </li>
−
        -->
+
      </ul>
−
       <!----------------------------- Week 1 -------------------------------------------->
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      <br><br>
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       <h3 id="week1">Week 1</h3>
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       <!----------------------------- Week 3 -------------------------------------------->
 +
       <h3 id="week3">Week 3 (3 July - 9 July)</h3>
 
       <hr>
 
       <hr>
 
       <ul class="media-list">
 
       <ul class="media-list">
 
         <li class="media">
 
         <li class="media">
−
             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Digested and extracted pLM005. Prepared TAP media plates for algae. Performed colony PCR for ACA3.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 
             <div class="media-body">
 
             <div class="media-body">
−
               <h4 class="media heading">Wet Lab Overview</h4>
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               <h4 class="media heading">Microscopy Division</h4>
 
               <p>
 
               <p>
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                   Flower shape leaves pictures were obtained by shining laser on camera. Problem might be in IR filter on the lens of the camera. We ordered Raspberry Pi V2 NoIR camera which does not have IR filter. While waiting for a new camera, we were trying to make Rapsberry Pi to sent pictures automatically to desktop computer.
 
               </p>
 
               </p>
 
             </div>
 
             </div>
 
         </li>
 
         </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
<!----------------------------- Week 4 -------------------------------------------->
 +
      <h3 id="week4">Week 4 (10 July - 16 July)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Nanodroped and extracted PCR products. Re-streaked algae. Did cell counts through Optical Density and took pictures of Chlamydomonas. Currently we are devising growth experiments for algae and bacteria.
 +
            </p>
 
         <li class="media dry">
 
         <li class="media dry">
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/2/28/Cornell-nb-dry.png">
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 
             <div class="media-body">
 
             <div class="media-body">
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               <h4 class="media heading">Dry Lab Overview</h4>
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               <h4 class="media heading">Microscopy Division</h4>
 
               <p>
 
               <p>
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                   Received NoIR camera. Leaves shape pattern solved. We were trying to observe diffraction from single slit experiment with a laser. Intensity of a laser was lowered with polarisation filter to avoid overexposure of camera. We used converging lens available in the lab to focus diffraction pattern on CMOS. Unfortunately, it was hard to setup to capture clear image. We are thinking to acquire lens with small focal distance to make setup as compact as possible.
 
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       </ul>
 
       </ul>
 
       <br><br>
 
       <br><br>
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       <!----------------------------- Week 2 -------------------------------------------->
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       <h3 id="week2">Week 2</h3>
+
        </li>
 +
      </ul>
 +
      <br><br>
 +
 
 +
<!----------------------------- Week 5 -------------------------------------------->
 +
       <h3 id="week5">Week 5 (17 July - 23 July)</h3>
 
       <hr>
 
       <hr>
 
       <ul class="media-list">
 
       <ul class="media-list">
 
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" />
 
             <div class="media-body">
 
             <div class="media-body">
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             <h4 class="media heading">Wet Lab Overview</h4>
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             <h4 class="media heading">Biology Division</h4>
 
             <p>
 
             <p>
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               Obtaied bacteria growth curve in 96 well plate. Ethanol toxicity growth test should be run next week for <i>E.coli</i>. Some new plates were made. Performed Alkaline lysis,
 
             </p>
 
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 
             <div class="media-body">
 
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               <h4 class="media heading">Dry Lab Overview</h4>
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               <h4 class="media heading">Microscopy Division</h4>
 
               <p>
 
               <p>
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+
                   Removed lens from camera which was done easily. Now, light is shinning directly on CMOS. Still we have problems with alignment of laser, slits and camera. Moreover, single slit was too bright for naked CMOS. Now, we are using double slit experiment to observe interference in best tradition of Thomas Young.
 
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       </ul>
 
       </ul>
 
       <br><br>
 
       <br><br>
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       <!----------------------------- Week 3 -------------------------------------------->
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−
       <h3 id="week3">Week 3</h3>
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<!----------------------------- Week 6 -------------------------------------------->
 +
       <h3 id="week6">Week 6 (24 July - 30 July)</h3>
 
       <hr>
 
       <hr>
 
       <ul class="media-list">
 
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" />
 
             <div class="media-body">
 
             <div class="media-body">
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             <h4 class="media heading">Wet Lab Overview</h4>
+
             <h4 class="media heading">Biology Division</h4>
 
             <p>
 
             <p>
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+
               Growth tests are continuing. We are getting curve for bacteria. Repeating PCR using Polymerase Q5 for MEX1.
 
             </p>
 
             </p>
 
         <li class="media dry">
 
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             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 
             <div class="media-body">
 
             <div class="media-body">
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               <h4 class="media heading">Dry Lab Overview</h4>
+
               <h4 class="media heading">Microscopy Division</h4>
 
               <p>
 
               <p>
−
                   Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.
+
                   After imaging double slit interference pattern we are moving to object imaging comperable with microorganisms size - microbeads. In parallel, we are translating software code for image reconstruction from LabVIEW to MATLAB. We received laser from TU Darmstadt team which is iterested in building DIHM, too.
 
               </p>
 
               </p>
 
             </div>
 
             </div>
Line 211: Line 165:
 
       </ul>
 
       </ul>
 
       <br><br>
 
       <br><br>
−
       <!----------------------------- Week 4 -------------------------------------------->
+
        
−
       <h3 id="week4">Week 4</h3>
+
        </li>
 +
      </ul>
 +
      <br><br>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
 
 +
<!----------------------------- Week 7 -------------------------------------------->
 +
       <h3 id="week7">Week 7 (31 July - 6 August)</h3>
 
       <hr>
 
       <hr>
 
       <ul class="media-list">
 
       <ul class="media-list">
 
         <li class="media">
 
         <li class="media">
−
             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/6/6f/Cornell-nb-wet.png">
+
             <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png" style="max-height: 100px; max-width: 100px;" />
 
             <div class="media-body">
 
             <div class="media-body">
−
               <h4 class="media heading">Wet Lab Overview</h4>
+
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Started <i>E.coli</i> transformation. Designing growth test with 24 well plate for algae. 96 wels plate well's are too small for algae. Set-up co-culture with untransformed microorganisms.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
               <h4 class="media heading">Microscopy Division</h4>
 
               <p>
 
               <p>
−
                   Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.
+
                   We were able to see single microbeads with our setup. Now, we have to be technical and measure precisely distances need for fully working DIHM. Also, we met with Dr Wilson to discuss our progress so far.
 
               </p>
 
               </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
 +
<!----------------------------- Week 8 -------------------------------------------->
 +
      <h3 id="week8">Week 8 (7 August - 13 August)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Performed PCR for MEX1, again. Experimenting on our 'frankenstein' media for a co-culture. Co-culture testing in traditional media.
 +
            </p>
 
         <li class="media dry">
 
         <li class="media dry">
−
         <img class="media object pull-left" src="https://static.igem.org/mediawiki/2014/2/28/Cornell-nb-dry.png">
+
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
−
         <div class="media-body">
+
            <div class="media-body">
−
         <h4 class="media heading">Dry Lab Overview</h4>
+
              <h4 class="media heading">Microscopy Division</h4>
−
         <p>
+
              <p>
−
         Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.
+
                  Looks like we will have to make image analysis in Python for a beginning. We still see the noise on captured images.
−
         </p>
+
              </p>
−
         </div>
+
            </div>
 +
         </li>
 +
      </ul>
 +
      <br><br>
 +
 
 +
      <!----------------------------- Week 9 -------------------------------------------->
 +
      <h3 id="week9">Week 9 (14 August - 20 August)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Obtained algae growth curve. Next is algae ethanol tolerance test. Still adjusting new media for co-culture.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png" style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Last week we ordered a new laser and quality of the image changed drastically. Laser that we were using in the lab was inappropriate for Digital Holography as we have figured that out.
 +
              </p>
 +
            </div>
 +
         </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
    <!----------------------------- Week 10 -------------------------------------------->
 +
      <h3 id="week10">Week 10 (21 August - 27 August)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Finally, we start transforming algae! In parallel, we run algae-bacteria depedence tests to find relationship between them.
 +
            </p>
 +
         <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Image recostruction software is almost ready. We are thinking about the design of DIHM and seeking for inspiration around the campus. Teflon mold was made for us this week which we will use to cast PDMS.
 +
              </p>
 +
            </div>
 +
         </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
<!----------------------------- Week 11 -------------------------------------------->
 +
      <h3 id="week11">Week 11 (28 August - 3 September)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              We have run initial transformation screening adn identified individual colonies containing assembled constructs.
 +
            </p>
 +
         <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  We find difficult to attach PDMS chamber to a glass slide. We met with plasma researcher in your university to discuss plasma bonding options. Whereas, UI for image capturing and analysis is rapidly developed.  
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
<!----------------------------- Week 12 -------------------------------------------->
 +
      <h3 id="week12">Week 12 (4 September - 10 September)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Ordered BioBrick for <i>E.coli</i> that increases it's motility. Transformation did not proceed correctly.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  We abandoned idea of using PDMS as a material for imaging chamber. Aluminium case for our microscope is ready. We hope to get all parts by next week.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
<!----------------------------- Week 13 -------------------------------------------->
 +
      <h3 id="week13">Week 13 (11 September - 17 September)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              It look like we will not be able to fix problem with algae transformation. It was ambitious task which was not possible to be done in such short period of time for us, but we still have the microscope.
 +
            </p>
 +
         <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Solution for imaging chamber was found by using acryl sheets and laser cutting. Desktop does not want to communicate with Raspberry Pi, but we will reconcile them.
 +
              </p>
 +
            </div>
 +
         </li>
 +
      </ul>
 +
      <br><br>
 +
<!----------------------------- Week 14 -------------------------------------------->
 +
      <h3 id="week14">Week 14 (18 September - 24 September)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Offered sacrifice sample of algae and bacteria to Microscopy Division. Analysing data from growth tests for algae and bacteria.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  We have imaged <i>Chlamydomonas reinhardtii</i> and <i>E.coli</i> separately and together. We figured out that millichamber we have manufactured are too thick for your laser. Instead, we are using glass slide and coverslip. UI is completed.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
 +
<!----------------------------- Week 15 -------------------------------------------->
 +
      <h3 id="week15">Week 15 (25 September - 1 October)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Received BioBrick from iGEM HQ. We will transform <i>E.coli</i> to copmare motility of wild type and engineered organism.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  We compared results from last week imaging and automated cell counter. It looks like our setup is working and we are able to calculate concetration of the microorganisms. We will do imaging of yeast and other bacteria and algae.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
<!----------------------------- Week 16 -------------------------------------------->
 +
      <h3 id="week16">Week 16 (2 October - 8 October)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Transformed <i>E.coli</i>. If algae would be transformable so easily.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Ran high motility bacteria on your DIHM.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
     
 +
    <!----------------------------- Week 17 -------------------------------------------->
 +
      <h3 id="week16">Week 17 (9 October - 15 October)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Clenaing our lab space and helping to upload information to wiki.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Not much progress was done on laptop-microscope connection.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
 
 +
  <!----------------------------- Week 18 -------------------------------------------->
 +
      <h3 id="week18">Week 18 (16 October - 22 October)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Still clearing up the lab.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  All content is being uploaded to wiki.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
 
 +
  <!----------------------------- Week 19 -------------------------------------------->
 +
      <h3 id="week19">Week 19 (23 October - 29 October)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              Finished analysis of a growth curves and we are fully moved out of the lab. We will miss it.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Unfortunately, UI does not like computers other than were it was created.
 +
              </p>
 +
            </div>
 +
        </li>
 +
      </ul>
 +
      <br><br>
 +
 
 +
  <!----------------------------- Week 19.5 -------------------------------------------->
 +
      <h3 id="week19.5">Week 19.5 (29 October - 1 November)</h3>
 +
      <hr>
 +
      <ul class="media-list">
 +
        <li class="media">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/e/e9/IGEMYork_BiologyLogo.png"  style="max-height: 100px; max-width: 100px;" />
 +
            <div class="media-body">
 +
            <h4 class="media heading">Biology Division</h4>
 +
            <p>
 +
              We are working on wiki, poster and presentation preparation.
 +
            </p>
 +
        <li class="media dry">
 +
            <img class="media object pull-left" src="https://static.igem.org/mediawiki/2017/3/36/IGEMYork_MicroscopeLogo.png"  style="max-height: 100px; max-width: 100px; padding: 0px 17px 0px 17px;" />
 +
            <div class="media-body">
 +
              <h4 class="media heading">Microscopy Division</h4>
 +
              <p>
 +
                  Everybody is working hard on wiki and will do so until the deadline.
 +
              </p>
 +
            </div>
 
         </li>
 
         </li>
 
       </ul>
 
       </ul>

Latest revision as of 21:20, 31 October 2017

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Notebook

Tracking Our Progress

Notebook

Week 1 (19 June - 25 June)

  • Biology Division

    First week detailed experementation plan and lab supplies ordering. We have several candidates for a co-culture.

  • Microscopy Division

    Had the first meeting of the division. Discussed timeline and the components we have available. For now, we will order only camera. Figured out that Biology Labs do not have any lasers and optical benches.



Week 2 (26 June - 2 July)

  • Biology Division

    In the end of a last weeek, we decided to work with algae and bacteria. Biology Lab Safety talk for all team members. Prepared LB media for E.coli and pored it into plates. Freezig E.coli cells for an emergency. Checking plates for algae and liquid culture for transformation. Prepared for plasmid extraction via electrophoresis.

  • Microscopy Division

    We were given access to Physics Labs. It will be our home for the next weeks. We watched laser safety video and started taking pictures with freshly arrived Raspberry Pi V2 Camera. Made prototype of the DIHM. How easy was that?!



Week 3 (3 July - 9 July)

  • Biology Division

    Digested and extracted pLM005. Prepared TAP media plates for algae. Performed colony PCR for ACA3.

  • Microscopy Division

    Flower shape leaves pictures were obtained by shining laser on camera. Problem might be in IR filter on the lens of the camera. We ordered Raspberry Pi V2 NoIR camera which does not have IR filter. While waiting for a new camera, we were trying to make Rapsberry Pi to sent pictures automatically to desktop computer.





Week 4 (10 July - 16 July)

  • Biology Division

    Nanodroped and extracted PCR products. Re-streaked algae. Did cell counts through Optical Density and took pictures of Chlamydomonas. Currently we are devising growth experiments for algae and bacteria.

  • Microscopy Division

    Received NoIR camera. Leaves shape pattern solved. We were trying to observe diffraction from single slit experiment with a laser. Intensity of a laser was lowered with polarisation filter to avoid overexposure of camera. We used converging lens available in the lab to focus diffraction pattern on CMOS. Unfortunately, it was hard to setup to capture clear image. We are thinking to acquire lens with small focal distance to make setup as compact as possible.





Week 5 (17 July - 23 July)

  • Biology Division

    Obtaied bacteria growth curve in 96 well plate. Ethanol toxicity growth test should be run next week for E.coli. Some new plates were made. Performed Alkaline lysis,

  • Microscopy Division

    Removed lens from camera which was done easily. Now, light is shinning directly on CMOS. Still we have problems with alignment of laser, slits and camera. Moreover, single slit was too bright for naked CMOS. Now, we are using double slit experiment to observe interference in best tradition of Thomas Young.



Week 6 (24 July - 30 July)

  • Biology Division

    Growth tests are continuing. We are getting curve for bacteria. Repeating PCR using Polymerase Q5 for MEX1.

  • Microscopy Division

    After imaging double slit interference pattern we are moving to object imaging comperable with microorganisms size - microbeads. In parallel, we are translating software code for image reconstruction from LabVIEW to MATLAB. We received laser from TU Darmstadt team which is iterested in building DIHM, too.







Week 7 (31 July - 6 August)

  • Biology Division

    Started E.coli transformation. Designing growth test with 24 well plate for algae. 96 wels plate well's are too small for algae. Set-up co-culture with untransformed microorganisms.

  • Microscopy Division

    We were able to see single microbeads with our setup. Now, we have to be technical and measure precisely distances need for fully working DIHM. Also, we met with Dr Wilson to discuss our progress so far.





Week 8 (7 August - 13 August)

  • Biology Division

    Performed PCR for MEX1, again. Experimenting on our 'frankenstein' media for a co-culture. Co-culture testing in traditional media.

  • Microscopy Division

    Looks like we will have to make image analysis in Python for a beginning. We still see the noise on captured images.



Week 9 (14 August - 20 August)

  • Biology Division

    Obtained algae growth curve. Next is algae ethanol tolerance test. Still adjusting new media for co-culture.

  • Microscopy Division

    Last week we ordered a new laser and quality of the image changed drastically. Laser that we were using in the lab was inappropriate for Digital Holography as we have figured that out.



Week 10 (21 August - 27 August)

  • Biology Division

    Finally, we start transforming algae! In parallel, we run algae-bacteria depedence tests to find relationship between them.

  • Microscopy Division

    Image recostruction software is almost ready. We are thinking about the design of DIHM and seeking for inspiration around the campus. Teflon mold was made for us this week which we will use to cast PDMS.



Week 11 (28 August - 3 September)

  • Biology Division

    We have run initial transformation screening adn identified individual colonies containing assembled constructs.

  • Microscopy Division

    We find difficult to attach PDMS chamber to a glass slide. We met with plasma researcher in your university to discuss plasma bonding options. Whereas, UI for image capturing and analysis is rapidly developed.





Week 12 (4 September - 10 September)

  • Biology Division

    Ordered BioBrick for E.coli that increases it's motility. Transformation did not proceed correctly.

  • Microscopy Division

    We abandoned idea of using PDMS as a material for imaging chamber. Aluminium case for our microscope is ready. We hope to get all parts by next week.



Week 13 (11 September - 17 September)

  • Biology Division

    It look like we will not be able to fix problem with algae transformation. It was ambitious task which was not possible to be done in such short period of time for us, but we still have the microscope.

  • Microscopy Division

    Solution for imaging chamber was found by using acryl sheets and laser cutting. Desktop does not want to communicate with Raspberry Pi, but we will reconcile them.



Week 14 (18 September - 24 September)

  • Biology Division

    Offered sacrifice sample of algae and bacteria to Microscopy Division. Analysing data from growth tests for algae and bacteria.

  • Microscopy Division

    We have imaged Chlamydomonas reinhardtii and E.coli separately and together. We figured out that millichamber we have manufactured are too thick for your laser. Instead, we are using glass slide and coverslip. UI is completed.



Week 15 (25 September - 1 October)

  • Biology Division

    Received BioBrick from iGEM HQ. We will transform E.coli to copmare motility of wild type and engineered organism.

  • Microscopy Division

    We compared results from last week imaging and automated cell counter. It looks like our setup is working and we are able to calculate concetration of the microorganisms. We will do imaging of yeast and other bacteria and algae.



Week 16 (2 October - 8 October)

  • Biology Division

    Transformed E.coli. If algae would be transformable so easily.

  • Microscopy Division

    Ran high motility bacteria on your DIHM.



Week 17 (9 October - 15 October)

  • Biology Division

    Clenaing our lab space and helping to upload information to wiki.

  • Microscopy Division

    Not much progress was done on laptop-microscope connection.



Week 18 (16 October - 22 October)

  • Biology Division

    Still clearing up the lab.

  • Microscopy Division

    All content is being uploaded to wiki.



Week 19 (23 October - 29 October)

  • Biology Division

    Finished analysis of a growth curves and we are fully moved out of the lab. We will miss it.

  • Microscopy Division

    Unfortunately, UI does not like computers other than were it was created.



Week 19.5 (29 October - 1 November)

  • Biology Division

    We are working on wiki, poster and presentation preparation.

  • Microscopy Division

    Everybody is working hard on wiki and will do so until the deadline.



  • ABOUT US
  • We are an overgraduate team representing the University of York.
  • Our Quicker Way to Analyse Co-Cultures (QWACC) is our entry into the Hardware track for iGEM 2017.
    •