Difference between revisions of "Team:UrbanTundra Edmonton/Results"

 
(6 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
{{NAIT_Edmonton/CSS6}}
+
{{UrbanTundra_Edmonton/Main-CSS}}
 +
{{UrbanTundra_Edmonton/Header}}
 +
 
 
<html>
 
<html>
  
−
<head>
+
<div id="ute-services-section">
 +
<div class="container">
 +
                    <div class="row">
  
  
−
<title>Team NAIT 2015</title>
 
  
−
<link href='http://fonts.googleapis.com/css?family=Source+Sans+Pro' rel='stylesheet' type='text/css'>
 
−
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.6.2/jquery.min.js"></script>
 
−
<script type="text/javascript" src="https://2015.igem.org/Team:NAIT_Edmonton/Results/PrefixTree.js?action=raw&amp;ctype=text/javascript"></script>
 
  
  
−
<!-----------https://static.igem.org/mediawiki/2015/d/d8/El_Capitan_.ttf------------------->
+
<!--NAV LINKS-->
  
  
−
<script type="text/javascript">
+
                        <div class="col-md-3 side-nav">
−
$(document).ready(function() {
+
  <div class="side-nav-container">
−
// grab the initial top offset of the navigation
+
    <ul style="list-style-type: none;">
−
  var stickyNavTop = $('.nav').offset().top;
+
      <li class="side-nav-toplink">TEAM</li>
−
 
+
        <ul class="sublist">
−
  // our function that decides weather the navigation bar should have "fixed" css position or not.
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Our_Story">Our Story</a></li>
−
  var stickyNav = function(){
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Team">Team</a></li>
−
    var scrollTop = $(window).scrollTop(); // our current vertical position from the top
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Collaborations">Collaborations</a></li>
−
       
+
        </ul>
−
    // if we've scrolled more than the navigation, change its position to fixed to stick to top,
+
      <li class="side-nav-toplink">PROJECT</li>
−
    // otherwise change it back to relative
+
        <ul class="sublist">
−
    if (scrollTop > stickyNavTop) {
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Description">Background</a></li>
−
        $('.nav').addClass('sticky');
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Overview">Overview</a></li>
−
    } else {
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Design">Gene Design</a></li>
−
        $('.nav').removeClass('sticky');
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Experiments">Experimental</a></li>
−
    }
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Proof">Bio Reaction</a></li>
−
};
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Demonstrate">O<sub>2</sub></a></li>
−
 
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Results">Results</a></li>
−
stickyNav();
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Notebook">Notebook</a></li>
−
// and run it again every time you scroll
+
        </ul>
−
$(window).scroll(function() {
+
      <li class="side-nav-toplink">PARTS</li>
−
stickyNav();
+
        <ul class="sublist">
−
});
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Parts">BioBrick</a></li>
−
});
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Composite_Part">CLD-</a></li>
−
</script>
+
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Part_Collection">Collection</a></li>
−
 
+
        </ul>
−
<script type="text/javascript" src="https://2015.igem.org/Team:NAIT_Edmonton/StickyMenu?action=raw&amp;ctype=text/javascript"></script>
+
      <li  class="side-nav-toplink">SAFETY</li>
 +
        <ul class="sublist">
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Lab_Safety">Lab Safety</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Protocals">Protocols</a></li>
 +
        </ul>
 +
      <li class="side-nav-toplink">ATTRIBUTIONS</li>
 +
        <ul class="sublist">
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Teamwork">Teamwork</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Support">Support</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/FullCitations">Citations</a></li>
 +
        </ul>
 +
      <li class="side-nav-toplink">HUMAN PRACTICES</li>
 +
        <ul class="sublist">
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Integrated_Practices">Integrated Practices</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/BroaderApplications">Broader Applications</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/Engagement">Outreach</a></li>
 +
        </ul>
 +
      <li class="side-nav-toplink">ACHIEVEMENTS</li>
 +
        <ul class="sublist">
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/aGEM">aGEM</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/HP/Silver">Silver</a></li>
 +
          <li><a href="https://2016.igem.org/Team:UrbanTundra_Edmonton/HP/Gold">Gold</a></li>
 +
        </ul>
 +
    </ul>
 +
  </div>
  
−
 
−
</head>
 
−
 
−
<body>
 
−
 
−
<div class="header">
 
−
<div class="header_c">
 
−
<a href="https://2015.igem.org/Team:NAIT_Edmonton"><img style="margin-top:15px;" src="https://static.igem.org/mediawiki/2015/2/2f/NAIT_Imagine.png" height="95px"></a>
 
−
</div>
 
 
</div>
 
</div>
  
  
  
−
<div class="nav">
 
  
−
<div tabindex="0" class="onclick-menu">
 
−
    <ul class="onclick-menu-content" style="list-style:none;">
 
−
        <li><a href="https://2015.igem.org/Team:NAIT_Edmonton">home</a></li>
 
−
        <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Team">team</a></li>
 
−
        <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Project">project</a></li>
 
−
        <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Human">human practices</a></li>
 
−
        <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Notebook">notebook</a></li>
 
−
    </ul>
 
−
</div>
 
  
  
−
<div class="navigation">
 
−
<ul>
 
  
  
−
                <li><a href="https://2015.igem.org/Team:NAIT_Edmonton"><img
 
−
                src="https://static.igem.org/mediawiki/2015/a/a9/NAIT_home.png" width="25px"></a></li>
 
  
−
                <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Team">team</a>
 
−
                    <ul>
 
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Bios">bios</a></li>
 
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Attributions">attributions</a></li>
 
−
                      <li><a href="https://igem.org/Team.cgi?id=1787">official team profile</a>
 
−
                    </ul>
 
−
                </li>
 
  
−
                <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Project">project</a>
+
<!-- THIS IS WHERE THE CONTENT GOES-->
−
                    <ul>
+
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Desc">description</a></li>
+
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Protocols">experiment and protocols</a></li>
+
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Results">parts and results</a></li>
+
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Modeling">modeling</a></li>
+
−
                    </ul>
+
−
                </li>
+
  
−
                <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Human">human practices</a>
 
−
                <ul>
 
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Outreach">community outreach</a></li>
 
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Practices">policy and practices</a></li>
 
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Collaborations">collaborations</a></li>
 
−
                     
 
−
                    </ul>
 
−
                </li>
 
  
−
                <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Notebook">notebook</a>
+
<div class="col-md-9 content-area">
−
                <ul>
+
<div class="content-container">
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Safety">lab safety</a></li>
+
<h1>Our Results</h1>
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Achievements">achievements</a></li>
+
−
                      <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Logbook">log book</a></li>
+
−
                </ul>
+
−
                </li>
+
  
−
            </ul>
+
<h5 style="font size: 24px">Supplemental</h5>
  
−
</div>
+
<h5 style="font size: 18px">Perchlorate and Chlorite Toxicity</h5>
  
−
</div>
+
<h5 style="font size: 18px">Perchlorate Extraction</h5>
  
 +
<h5 style="font size: 18px">LB Broth Replacement</h5>
  
 +
<h5 style="font size: 24px">Future Experimentation</h5>
  
−
</style>
+
<h5 style="font size: 18px">Puriciation of Synthesized Chlorite Dismutase</h5>
−
 
+
−
<div id="wrap">
+
  
 +
<h5 style="font size: 24px">Synthesis of Perchlorate Reductase Enzyme</h5>
  
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
  
−
<style type="text/css">
 
  
−
.top_slogan {text-align:center; font-family: 'Source Sans Pro', sans-serif; color:#0D4D8C; font-size:30px; padding: 40px 0px 40px 0px; font-style:strong; line-height:40px;}
+
</html>
  
 +
{{UrbanTundra_Edmonton/Footer}}
  
−
</style>
 
  
−
<center><div class="top_slogan">Parts and Results</div></center>
 
  
−
<div class="main_content">
 
  
−
<center>
 
−
<h2> Check out the new parts we made for the registry:</h2>
 
  
−
<a style="color:blue" href="http://parts.igem.org/Part:BBa_K1787001">BBa_K1787001 - MBL</a> <br>
 
−
<a style="color:blue" href="http://parts.igem.org/Part:BBa_K1787000">Bba_K1787000 - Cys-Thr</a>
 
  
−
</center>
 
  
−
<br><br>
 
  
−
<center><h1>Data Analysis</h1></center><br>
 
  
  
−
<center><img src="https://static.igem.org/mediawiki/2015/6/61/NAIT_p5.png" width="500px"></center> <br>
 
  
−
<p>The sequences that were ordered had a design flaw on them. The restriction sites were not on the correct place and were incompatible with pSB1C3. In order to fix them, we decided to create primers that would insert a point mutation in the restriction sites and, at the same time, add the correct iGEM prefix and suffix to the sequences.</p><br>
 
  
−
<p><img src="https://static.igem.org/mediawiki/2015/1/17/NAIT_p2.png" width="400px">A gradient PCR was conducted in order to determine the best annealing temperature (Ta) for the primers. It was observed that Ta=61ºC was optimum. A new PCR comprising all our sequences was done and, after using a PCR Purification kit, an agarose gel showed that out of 23 sequences, we were able to purify 18 (see Figure 2). Nonetheless, one of the sequences contained an illegal restriction site within itself and it was discarded.</p><br>
 
  
−
<p>The sequences, now containing an iGEM compatible prefix and suffix, needed a vector and a host organism so as to be expressed. T7 expression systems can produce a high copy of a Protein of Interest (POI), provided that the DNA sequence that encodes for the polypeptide is next to a T7 promoter. With regards to the vector, it was noted that BioBrick K1321338 (BBa_ K1321338), found on the iGEM 2015 Kit Plate #5, contained a T7 promoter and a Ribosome Binding Site. And pertaining the host organism, BL21 (DE3), a T7 E.coli expression strain was chosen as the system to synthesize our POIs</p><br>
 
  
−
<center><img src="https://static.igem.org/mediawiki/2015/e/e7/NAIT_p3.png" width="500px"></center><br>
 
  
−
<p>After transforming cells with BBa_K1321338, obtaining the plasmid (i.e., pSB1C3 with the BioBrick. Note: pSB1C3 contains a chloramphenicol resistant gene) via a MiniPrep Kit, and confirming its presence by running a sample in an agarose gel, a digestion with SpeI and PstI, and subsequent dephosphorylation was conducted so as to linearize the plasmid and prepare it for ligation to the sequences. Simultaneously, the sequences were digested with XbaI and PstI (see Figure 3).</p>
 
  
  
−
<center><img src="https://static.igem.org/mediawiki/2015/4/43/NAIT_p4.png" width="500px"></center><br>
 
  
  
−
<p>Ligation was performed using T4 DNA Ligase; subsequently, E. coli BL21 (DE3) was transformed with the ligation products and plated in LB + chloramphenicol agar. 34 plates (two per sequence of interest) were left 24 hours at 37ºC to ensure optimum growth of transformed cells. Grown colonies were accounted for and numbered (see Figure 4).</p><br>
 
  
−
<p>pSB1C3 Forward and Reverse Primers were used to confirm that the colonies actually contained the sequence. A gradient PCR showed that the optimum Ta was 57ºC, so a colony PCR was made following such parameter and an agarose gel was done to verify outcome of the PCR.</p><br>
 
  
−
<p>Data showed that, out of three hundred and two colonies, only five contained an insert (see Figure 5). Other colonies contained the plasmid without an insertion. This was concluded because the Forward and Reverse Primers amplify a fragment 339 bp long. The divergent colonies amplified longer fragments and, out of those six, only two had the size that was expected. These were sequences ‘Cys-Thr’ and ‘MLAB’ (see Figure 6, this figure only shows significant gels).</p><br>
 
  
  
 +
<!--{{UrbanTundra_Edmonton/ResearchPages}}
 +
<html>
  
−
<center><img src="https://static.igem.org/mediawiki/2015/9/97/NAIT_p6.png" width="500px"></center><br>
 
  
−
<p>These five positive colonies were cultured in 200mL of LB media with chloramphenicol and induced with IPTG to increase protein expression. The cells were pelleted and proteins were isolated using a NiNTA Kit.
+
<div class="column full_size" >
−
The samples were ran in a SDS-PAGE (see Figure 6). Only the sample containing the protein encoded by sequence ‘Cys-Thr’ showed bands. Additionally, the bands were ~19kDa in size, the expected size for this particular protein.
+
−
</p><br>
+
  
 +
<p>Here you can describe the results of your project and your future plans. </p>
  
−
<p>Preliminary data shows that this engineered protein is able to show a different colouration after silver staining (see Figure 8)</p><br>
+
<h5>What should this page contain?</h5>
 +
<ul>
 +
<li> Clearly and objectively describe the results of your work.</li>
 +
<li> Future plans for the project </li>
 +
<li> Considerations for replicating the experiments </li>
 +
</ul>
  
−
<center>
+
</div>
−
<img src="https://static.igem.org/mediawiki/2015/1/11/NAIT_p7.png" width="600px"></center> <br>
+
  
−
<center>
+
<div class="column half_size" >
  
−
<img src="https://static.igem.org/mediawiki/2015/8/8f/NAIT_p8.png" width="600px"></center><br>
 
  
−
<p>This preliminary data supports our original hypothesis that certain amino acid configurations within a protein alter band colouration post-silver staining.  We are currently looking into new combinations of amino acid motifs in the hopes of generating the colours blue, red, green, purple, orange, and shades of grey. </p><br>
+
<h5> Project Achievements </h5>
−
 
+
−
 
+
−
<div class="clear"></div>
+
−
 
+
−
 
+
−
</div>
+
  
 +
<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
  
 +
<ul>
 +
<li>A list of linked bullet points of the successful results during your project</li>
 +
<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
 +
</ul>
  
 
</div>
 
</div>
  
−
  <div class="clear"></div>
 
−
 
 
−
 
 
  
−
<div class="footer">
+
<div class="column half_size" >
−
        <div class="footer_content">
+
−
            <div class="footer_left">
+
−
                        <ul class="footer_menu">
+
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton">home</a></li>
+
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Team">team</a></li>
+
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Project">project</a></li>
+
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Human">human practices</a></li>
+
−
                    <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/Notebook">notebook</a></li>
+
−
                </ul>
+
−
            </div>
+
−
           
+
−
            <div class="footer_right">
+
−
                <ul class="social_icons">
+
−
                <li><a href="http://www.facebook.com/pages/IGEM-2015-NAIT-Edmonton/884025281659292"><img src="https://static.igem.org/mediawiki/2015/a/a3/NAIT_Icon_facebook.png" alt="" title="" /></a></li>
+
−
                <li><a href="http://www.twitter.com/TeamNAIT2015"><img src="https://static.igem.org/mediawiki/2015/6/64/NAIT_Icon_twitter.png" alt="" title="" /></a></li>
+
−
                <li><a href="https://2015.igem.org/Team:NAIT_Edmonton/ContactUs"><img src="https://static.igem.org/mediawiki/2015/2/29/NAIT_Icon_contact.png" width="20px" alt="" title="" /></a></li>
+
−
                </ul>
+
−
            </div>
+
−
          <div class="clear"></div>
+
−
          </div>
+
−
        </div>
+
  
 +
<h5>Inspiration</h5>
 +
<p>See how other teams presented their results.</p>
 +
<ul>
 +
<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
 +
<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
 +
<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
 +
</ul>
  
 +
</div>
  
−
</body>
 
  
−
</html>
+
 
 +
</html>-->

Latest revision as of 23:26, 19 October 2016


Urban Tundra | Intelligent Innovation

Our Results

Supplemental
Perchlorate and Chlorite Toxicity
Perchlorate Extraction
LB Broth Replacement
Future Experimentation
Puriciation of Synthesized Chlorite Dismutase
Synthesis of Perchlorate Reductase Enzyme

Explore With Us.