Difference between revisions of "Team:Jiangnan China/Model"

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            <i class="fa fa-part"></i> Parts
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            <a class="dropdown-item" href="https://2018.igem.org/Team:Jiangnan_China/BasicParts">Basic Parts</a>
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            <a class="dropdown-item" href="https://2018.igem.org/Team:Jiangnan_China/Compositeparts">Composite parts</a>
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          </div>
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        </div>
  
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        <a class="nav-link py-2 d-none d-md-inline-block" href="https://2018.igem.org/Team:Jiangnan_China/InterLab"><i class="fa fa-interlab" aria-hidden="true"></i> InterLab</a>
  
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      </div>
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    </nav>
  
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<div class="column full_size judges-will-not-evaluate">
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    <main class="content-wrap">
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<h3>★  ALERT! </h3>
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      <img src="https://static.igem.org/mediawiki/2018/b/b2/T--jiangnan_china--interlab--1.jpg" width="100%">
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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      <div class="dcpt3" style="font-size:20px;line-height:1.5;font-family: 'spr';">
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Overview</strong></div>
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</div>
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    <br>
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      &nbsp;&nbsp;&nbsp;&nbsp;In the last 4 years, the Measurement Committee has been developing a robust measurement procedure for green fluorescent protein (GFP) though the Interlab study, aiming to improve the measurement tools available to both the iGEM community and the synthetic biology community as a whole. And this year, we are delighted to join the study to know if we can reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD.
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      <br><br>
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      </div>
  
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      <div id="dcpt4" style="font-size:20px;line-height:1.5;font-family: 'spr';">
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    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Materials</strong></div>
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    <br>
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      96-spot well plates: clear plates from Corning<br>
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      Bacteria strains: E.coli DH5α<br>
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      Test devices: obtained from the distribution kit
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      <br><br>
  
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<div class="clear"></div>
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      <table class="table" id="HQ_page">
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        <thead>
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          <tr><th>Device</th>
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          <th>Part number</th>
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          <th>Location</th>
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        </tr></thead>
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        <tbody>
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          <tr>
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            <td><a text-decoration="underline">Position control </a></td>
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            <td>BBa_R0040</td>
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            <td>Well 2D</td>
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          </tr>
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          <tr>
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            <td><a text-decoration="underline">Negative control</a></td>
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            <td>BBa_I20270</td>
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            <td>Well 2B</td>
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          </tr>
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                <tr>
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            <td><a text-decoration="underline">Test Device 1</a></td>
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            <td>BBa_J364000</td>
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            <td>Well 2F</td>
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          </tr>
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          <tr>
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            <td><a text-decoration="underline">Test Device 2</a></td>
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            <td>BBa_J364001</td>
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            <td>Well 2H</td>
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          </tr>
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          <tr>
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            <td><a text-decoration="underline">Test Device 3</a></td>
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            <td>BBa_J364002</td>
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            <td>Well 2J</td>
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          </tr>
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          <tr>
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            <td><a text-decoration="underline">Test Device 4</a></td>
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            <td>BBa_J364007</td>
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            <td>Well 2L</td>
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          </tr>
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          <tr>
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            <td><a text-decoration="underline">Test Device 5</a></td>
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            <td>BBa_J364008</td>
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            <td>Well 2N</td>
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          </tr>
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          <tr>
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            <td><a text-decoration="underline">Test Device 6</a></td>
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            <td>BBa_J364009</td>
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            <td>Well 2P</td>
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          </tr>
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        </tbody>
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      </table>
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      </div>
  
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      <div class="dcpt3" style="font-size:20px;line-height:1.5;font-family: 'spr';">
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    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Protocols</strong></div>
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      <br><br>
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      <p style="text-align: center;"><a href="https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf" class="btn btn-info">Here is the link </a></p>
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      </div>
  
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<div class="column full_size">
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      <div id="dcpt4" style="font-size:20px;line-height:1.5;font-family: 'spr';">
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<h1> Modeling</h1>
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    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Results</strong></div>
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      <br><br>
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    <div align="center" ><strong><font size="5" color="#5B9BD5" >Particle Standard Curve</font></strong></div>
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    <br>
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    <div align="center">
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      <img src="https://static.igem.org/mediawiki/2018/7/77/T--jiangnan_china--interlab--chart1.png" width="70%" >
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    </div>
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    <br><br>
  
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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    <div align="center"><strong><font size="5" color="#5B9BD5" >Particle Standard Curve (log scale)</font></strong></div>
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    <br>
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    <div align="center">
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      <img src="https://static.igem.org/mediawiki/2018/4/4b/T--jiangnan_china--interlab--chart2.png" width="70%" >
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    </div>
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    <br><br>
  
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</div>
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    <div align="center"><strong><font size="5" color="#5B9BD5" >Fluorescein Standard Curve</font></strong></div>
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<div class="clear"></div>
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    <br>
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    <div align="center">
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      <img src="https://static.igem.org/mediawiki/2018/3/31/T--jiangnan_china--interlab--chart3.png" width="70%" >
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    </div>
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    <br><br>
  
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<div class="column full_size">
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    <div align="center"><strong><font size="5" color="#5B9BD5" >Fluorescein Standard Curve (log scale)</font></strong></div>
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<h3> Gold Medal Criterion #3</h3>
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    <br>
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<p>
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    <div align="center">
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.
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      <img src="https://static.igem.org/mediawiki/2018/f/f9/T--jiangnan_china--interlab--chart4.png" width="70%" >
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<br><br>
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    </div>
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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    <br><br>
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</p>
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<p>
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    <div align="center"><strong><font size="5" color="#5B9BD5" >uM Fluorescein / OD</font></strong></div>
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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    <br>
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Medals Page</a> for more information.
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    <div align="center">
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</p>
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      <img src="https://static.igem.org/mediawiki/2018/5/55/T--jiangnan_china--interlab--chart5.png" width="70%" >
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</div>
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    </div>
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    <br><br>
  
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<div class="column two_thirds_size">
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    <div align="center"><strong><font size="5" color="#5B9BD5" >Net Fluorescein a.u.</font></strong></div>
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<h3>Best Model Special Prize</h3>
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    <br>
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    <div align="center">
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      <img src="https://static.igem.org/mediawiki/2018/a/a1/T--jiangnan_china--interlab--chart6.png" width="70%" >
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    </div>
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    <br><br>
  
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<p>
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    <div align="center"><strong><font size="5" color="#5B9BD5" >Net Abs 600</font></strong></div>
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.
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    <br>
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<br><br>
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    <div align="center">
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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      <img src="https://static.igem.org/mediawiki/2018/d/d0/T--jiangnan_china--interlab--chart7.png" width="70%" >
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</p>
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    </div>
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    <br><br>
  
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</div>
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    <div align="center"><strong><font size="5" color="#5B9BD5" >MEFL / particle</font></strong></div>
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    <br>
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    <div align="center">
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      <img src="https://static.igem.org/mediawiki/2018/b/b0/T--jiangnan_china--interlab--chart8.png" width="70%" >
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    </div>
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    <br><br>
  
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      </div>
  
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<div class="column third_size">
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      <div class="dcpt3" style="font-size:20px;line-height:1.5;font-family: 'spr';">
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<div class="highlight decoration_A_full">
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    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Summery</strong></div>
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<h3> Inspiration </h3>
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    <br>
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<p>
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      &nbsp;&nbsp;&nbsp;&nbsp;We studied for a time before doing interlab, and spent one-two day preparing experimental materials, such as preparing E. coli DH5α and several culture media. After full preparation, we started the experiment. In the first experiment, our antibiotics failed, causing too much bacteria to colonize the plate.The second time we had a problem with the competent cells, so the bacteria did not grow after the plate was painted.The third time, we reprepared the competent cells and replaced the antibiotics, and the experiment went well.
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Here are a few examples from previous teams:
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      <br><br>
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</p>
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      </div>
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<ul>
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      <div id="dcpt4" style="font-size:20px;line-height:1.5;font-family: 'spr';">
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Conclution</strong></div>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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    <br>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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      <div>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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      &nbsp;&nbsp;&nbsp;&nbsp;We studied for a time before doing interlab, and spent one-two day preparing experimental materials, such as preparing E. coli DH5α and several culture media. After full preparation, we started the experiment. In the first experiment, our antibiotics failed, causing too much bacteria to colonize the plate.The second time we had a problem with the competent cells, so the bacteria did not grow after the plate was painted.The third time, we reprepared the competent cells and replaced the antibiotics, and the experiment went well.
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</ul>
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      </div>
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</div>
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      <br>
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</div>
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      <div>
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      <font size="5">1.</font> The final concentration of chloramphenicol is not clearly defined in the experimental protocol. Although we have made the experiment proceed smoothly based on experience, we believe that accurate antibiotic dosage requirements are still necessary;
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      </div>
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      <br>
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      <div>
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      <font size="5">2.</font> Regarding the use of the plate reader: although there are some descriptions in the experimental protocol that explain the experimental design and a simple explanation of the plate reader, we used the plate reader incorrectly at the beginning of the experiment, leading to a invalid data. So we still expect more instructions on the setup and use of the plate reader;
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      </div>
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      <br>
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      <div>
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      <font size="5">3.</font> Regarding the preservation of competent cells: we have transferred the competent cells position between buildings due to the change of the laboratory position, which took about 10 minutes. And in the transformation experiment, the competent cells stayed outside for too long. These improper storage of competent cells made the bacteria grow very unsatisfactorily after plating. Therefore, the preservation of competent cells is very important.
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      </div>
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      <br><br>
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        <a href="http://biotech.jiangnan.edu.cn/" title="江南大学生物工程学院"><img src="https://static.igem.org/mediawiki/2018/a/a6/T--jiangnan_china--shenggonglogo.png"></a>
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Revision as of 05:12, 12 October 2018

Overview

    In the last 4 years, the Measurement Committee has been developing a robust measurement procedure for green fluorescent protein (GFP) though the Interlab study, aiming to improve the measurement tools available to both the iGEM community and the synthetic biology community as a whole. And this year, we are delighted to join the study to know if we can reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD.

Materials

96-spot well plates: clear plates from Corning
Bacteria strains: E.coli DH5α
Test devices: obtained from the distribution kit

Device Part number Location
Position control BBa_R0040 Well 2D
Negative control BBa_I20270 Well 2B
Test Device 1 BBa_J364000 Well 2F
Test Device 2 BBa_J364001 Well 2H
Test Device 3 BBa_J364002 Well 2J
Test Device 4 BBa_J364007 Well 2L
Test Device 5 BBa_J364008 Well 2N
Test Device 6 BBa_J364009 Well 2P
Protocols


Here is the link

Results


Particle Standard Curve



Particle Standard Curve (log scale)



Fluorescein Standard Curve



Fluorescein Standard Curve (log scale)



uM Fluorescein / OD



Net Fluorescein a.u.



Net Abs 600



MEFL / particle



Summery

    We studied for a time before doing interlab, and spent one-two day preparing experimental materials, such as preparing E. coli DH5α and several culture media. After full preparation, we started the experiment. In the first experiment, our antibiotics failed, causing too much bacteria to colonize the plate.The second time we had a problem with the competent cells, so the bacteria did not grow after the plate was painted.The third time, we reprepared the competent cells and replaced the antibiotics, and the experiment went well.

Conclution

    We studied for a time before doing interlab, and spent one-two day preparing experimental materials, such as preparing E. coli DH5α and several culture media. After full preparation, we started the experiment. In the first experiment, our antibiotics failed, causing too much bacteria to colonize the plate.The second time we had a problem with the competent cells, so the bacteria did not grow after the plate was painted.The third time, we reprepared the competent cells and replaced the antibiotics, and the experiment went well.

1. The final concentration of chloramphenicol is not clearly defined in the experimental protocol. Although we have made the experiment proceed smoothly based on experience, we believe that accurate antibiotic dosage requirements are still necessary;

2. Regarding the use of the plate reader: although there are some descriptions in the experimental protocol that explain the experimental design and a simple explanation of the plate reader, we used the plate reader incorrectly at the beginning of the experiment, leading to a invalid data. So we still expect more instructions on the setup and use of the plate reader;

3. Regarding the preservation of competent cells: we have transferred the competent cells position between buildings due to the change of the laboratory position, which took about 10 minutes. And in the transformation experiment, the competent cells stayed outside for too long. These improper storage of competent cells made the bacteria grow very unsatisfactorily after plating. Therefore, the preservation of competent cells is very important.


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