Difference between revisions of "Team:SYSU-Software/InterLab"

 
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<h1>InterLab</h1>
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      <a id="sdin-link" href="http://sdin.sysusoftware.info" target="_blank">
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<h3>Bronze Medal Criterion #4</h3>
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        <img id="sdin-icon" src="https://static.igem.org/mediawiki/2017/1/17/T--SYSU-Software--project_sdin-small.png" alt="logo">
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<p><b>Standard Tracks:</b> Participate in the Interlab Measurement Study and/or improve the characterization of an existing BioBrick Part or Device and enter this information on that part's Main Page in the Registry. The part that you are characterizing must NOT be from a 2017 part number range.
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<br><br>
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For teams participating in the <a href="https://2017.igem.org/Competition/InterLab_Study">InterLab study</a>, all work must be shown on this page.  
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        <a href="https://2017.igem.org/Team:SYSU-Software/Project" class="page-link">Project</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Project#description" class="item">Description</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Project#applied-design" class="item">Applied Design</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Project#wet-lab" class="item">Wet-Lab Validation</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Project#demonstrate" class="item">Demonstrate</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Model#overview" class="item">Overview</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Model#simulation" class="item">Simulation for General Genetic Circuits</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Model#references" class="item">References</a>
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        <a href="https://2017.igem.org/wiki/index.php?title=Team:SYSU-Software/HP" class="page-link">Human Practices</a>
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          <a href="https://2017.igem.org/wiki/index.php?title=Team:SYSU-Software/HP#overview_id" class="item">Overview</a>
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        <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations" class="page-link">Collaborations</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#overview" class="item">Overview</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#scut-china-a" class="item">SCUT-CHINA-A</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#nju-china" class="item">NJU-China</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#hkust" class="item">Hong_Kong_HKUST</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#sysu-china" class="item">SYSU-CHINA</a>
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        <a href="https://2017.igem.org/Team:SYSU-Software/InterLab" class="page-link">Interlab</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/InterLab#overview" class="item">Overview</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/InterLab#results" class="item">Results</a>
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        <a href="https://2017.igem.org/Team:SYSU-Software/Safety" class="page-link">Safety</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Safety#dry-lab" class="item">Biosafety in Dry Lab</a>
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        <a href="https://2017.igem.org/Team:SYSU-Software/Attributions" class="page-link">Attributions</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Attributions#overview" class="item">Overview</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Attributions#attribution-in-project" class="item">Attribution in Project</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Attributions#journey-planning" class="item">Journey Planning and Financing</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Attributions#acknowledgements" class="item">Acknowledgements</a>
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        <a href="https://2017.igem.org/Team:SYSU-Software/Team" class="page-link">Team</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Team#biology-group" class="item">Biology Group</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Medal#bronze" class="item">Bronze</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Medal#silver" class="item">Silver</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Medal#gold" class="item">Gold</a>
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        <a href="https://2017.igem.org/Team:SYSU-Software/Statements" class="page-link">Statements</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Statements#term-of-use" class="item">Term of Use</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Statements#bio-safety-alerts" class="item">Bio Safety Alerts</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Statements#privacy-policy" class="item">Privacy Policy</a>
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          <a href="https://2017.igem.org/Team:SYSU-Software/Statements#cookie-policy" class="item">Cookie Policy</a>
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    </div>
  
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    <div id="first-page">
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      <div id="ship-background"></div>
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      <h1 id="top-title">interlab</h1>
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      <h2 id="slogan">Synbio is just a S-Din away!</h2>
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      <h3 id="sysu-software-2017">SYSU-Software 2017</h3>
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      <!-- CONTENT OF FIRST PAGE -->
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      <div class="page-content overview">
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        <h2 id="overview">overview</h2>
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        <div class="overview-block">
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          <div id="o1">
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            <img class="blue-background" src="https://static.igem.org/mediawiki/2017/8/89/T--SYSU-Software--interlab_Untitled-2.png" alt="">
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            <p>
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              We are proud to be part of the interlab study. Although we are a Software Team, this never separate us from experiments and never extinguish our passions for contributing our efforts for iGEM and Synthetic biology community.
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            </p>
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          </div>
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          <div id="o2">
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            <img class="blue-background" src="https://static.igem.org/mediawiki/2017/9/92/T--SYSU-Software--interlab_Untitled-3.png" alt="">
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            <p>
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              This year, Interlab study provide detailed protocol to eliminate as much difference as they can, and find a way to make OD/FI measurement conducted by different machine comparable.
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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>
  
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    <!-- DEFINE PAGES CORRESPOINDING TO EACH TAB HERE -->
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    <section class="plain">
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      <h2 id="experiment-design">Experiment Design</h2>
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      <div class="epblk">
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        <p>
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          Eight different plasmids, Positive Control (BBa_I20270), Negative Control (BBa_R0040), Device 1 (BBa_J364000), Device 2 (BBa_J364001), Device 3 (BBa_J364002), Device 4 (BBa_J364003), Device 5 (BBa_J364004), Device 6 (BBa_J364005) were transformed into Escherichia coli DH5α, which were inoculated on LB plate with chloramphenicol (cmr). After an overnight cultivation, single colonies was picked to keep cultivating. After 6 hours cultivation, Colony PCR was conducted to test if the plasmids were transformed successfully. And the colonies were moved into liquid cultures (LB medium) and cultivated overnight. Liquid cultures were diluted with LB medium until the value of OD600 reached 0.02. Then we took out 500 μL samples from the cultures every 2 hour (t=0, 2, 4, 6h). At last, we measured OD600 and fluorescence of all samples.
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        </p>
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      </div>
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    </section>
  
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    <section class="plain">
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      <h2 id="material-and-methods">Materials and Methods</h2>
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      <div class="matblk">
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        <h4>Growth Conditions</h4>
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        <p>
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          The bacteria were cultivated in Lysogeny Broth(LB) plate with chloramphenicol added when doing transformation. The plates were kept at 37°C. Colonies we picked were grown in 5ml LB medium with chloramphenicol. Afterwards, they were kept at 37°C and 220 rpm shaking frequency. We used 5ml LB medium and chloramphenicol to target OD600 of 0.02.
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        </p>
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      </div>
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      <div class="matblk">
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        <h4>Strains &amp Devices Transformed</h4>
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        <p>
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          We used Escherichia coli strain DH5α cells for transformation. Three devices and two controls are all provided by iGEM HQ as follows:
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          <ul>
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            <li>Positive Control (BBa_I20270)</li>
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            <li>Negative Control (BBa_R0040)</li>
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            <li>Device 1 (BBa_J364000)</li>
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            <li>Device 2 (BBa_J364001)</li>
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            <li>Device 3 (BBa_J364002)</li>
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            <li>Device 4 (BBa_J364003)</li>
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            <li>Device 5 (BBa_J364004)</li>
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            <li>Device 6 (BBa_J364005)</li>
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          </ul>
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        </p>
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      </div>
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      <div class="matblk">
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        <h4>Colony PCR &amp Gel electrophoresis</h4>
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        <p>Primer designed by choose 15bp on VF2 primer site &amp VR primer site. PCR conducted by standard procedure. Gel electrophoresis were conducted after PCR, with standard procedure. Gel photo was captured by UV imagery system provided by SYSU school of life science.</p>
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        <img src="https://static.igem.org/mediawiki/2017/a/af/T--SYSU-Software--interlab_marker.png" alt="marker" class="center-img">
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        <img src="https://static.igem.org/mediawiki/2017/a/a5/T--SYSU-Software--interlab_round.png" alt="round" class="center-img">
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      </div>
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      <div class="matblk">
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        <h4>Generating FITC Fluorescence Standard Curve by Using Plate Reader</h4>
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        <p>We have used 96-well plates to do the plate reader’s measurement. A serial dilution was performed to generate a FITC fluorescence standard curve. When measuring fluorescence, the excitation wavelength we set was 480nm(9), and emission wavelength was set at 535nm(20).
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        </p>
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      </div>
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      <div class="matblk">
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        <h4>Using LUDOX-S40 as A Single Point Reference</h4>
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        <p>
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          We used LUDOX-S40 to transform our absorbance data into standard OD600 measurement. Volumes of LUDOX was 100μl. We prepared a column of 4 wells containing 100 μl LUDOX and 4 wells containing water. The samples were measured using plate reader.
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        </p>
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      </div>
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      <div class="matblk">
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        <h4>Measuring Fluorescence &amp OD600 by Using Plate Reader</h4>
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        <p>
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          Colonies with devices tested by us were picked from the plates, then were cultured overnight in 5ml LB medium with chloramphenicol. The liquid cultures were diluted to target OD600=0.02. The fluorescence and OD600 of samples at 0,2,4, 6 hours were measured by using 96-well plate. The volumes of samples were 100 μl LB medium with chloramphenicol were used as blank
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        </p>
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      </div>
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    </section>
  
 +
    <section class="full">
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      <h2 id="results">Results</h2>
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      <div class="result-block-outer blue">
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        <div class="resblk first">
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          <img src="https://static.igem.org/mediawiki/2017/d/d3/T--SYSU-Software--interlab_curve.png" alt="fig_1" class="center-img blue-shadowed">
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          <p class="img-ex">Fig 1. Fluorescien Standard Curve</p>
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        </div>
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      </div>
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      <div class="result-block-outer">
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        <div class="resblk img-left">
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          <div class="fig_exp">
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            <img class="blue-background" src="https://static.igem.org/mediawiki/2017/0/09/T--SYSU-Software--interlab_od.png" alt="fig_2">
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            <p class="img-ex">Fig 2. OD600 Measurement</p>
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          </div>
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          <p class="explanation">
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            OD600 This value represents the concentration of bacteria in the medium. Due to the amount of the samples, the 0h phare failed to synchronize at the same value, and at this point the bacteria might already enter log phase. (Fig 2.)
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          </p>
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        </div>
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      </div>
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      <div class="result-block-outer green">
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        <div class="resblk img-right">
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          <div class="fig_exp">
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            <img class="green-shadowed" src="https://static.igem.org/mediawiki/2017/5/59/T--SYSU-Software--interlab_measure.png" alt="fig_3">
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            <p class="img-ex">Fig 3. Fluorescence Measurement</p>
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          </div>
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          <p class="explanation">
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            Fluorescein The results are shown in the graph. The fluorescein level of Negative control, Device 1, 3, 5, 6 reach peak at the very beginning and then decrease remarkably in the next 2 hours. The positive control and Device 4 increase quit a lot at 2h but also decrease afterward. The Device 2 increase in a peace pace. (Fig 3.)
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          </p>
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        </div>
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      </div>
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      <div class="result-block-outer">
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        <div class="resblk img-left">
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          <div class="fig_exp">
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            <img class="blue-background" src="https://static.igem.org/mediawiki/2017/9/98/T--SYSU-Software--interlab_measure2.png" alt="fig_4">
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            <p class="img-ex">Fig 4. μM Fluorescein / OD600</p>
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          </div>
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          <p class="explanation">
 +
            Attribution: All our experiments were conducted in the professor Lu’s laboratory in School of life science, Sun Yat-sen University. They provided everything we need and answered every one of our doubts patiently. Here we present our appreciation.
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          </p>
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        </div>
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      </div>
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    </section>
  
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    <div id="contact">
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      <div id="contact-content">
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        <div class="contact-item">
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          <div class="contact-heading">contact</div>
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          <div class="contact-value">sysusoftware@126.com</div>
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        </div>
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        <div class="contact-item">
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          <div class="contact-heading">address</div>
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          <div class="contact-value">135# Xin'gang Rd(W.)<br>Sun Yat-sen University, Guangzhou, China</div>
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Latest revision as of 17:02, 1 November 2017

Interlab

interlab

Synbio is just a S-Din away!

SYSU-Software 2017

overview

We are proud to be part of the interlab study. Although we are a Software Team, this never separate us from experiments and never extinguish our passions for contributing our efforts for iGEM and Synthetic biology community.

This year, Interlab study provide detailed protocol to eliminate as much difference as they can, and find a way to make OD/FI measurement conducted by different machine comparable.

Experiment Design

Eight different plasmids, Positive Control (BBa_I20270), Negative Control (BBa_R0040), Device 1 (BBa_J364000), Device 2 (BBa_J364001), Device 3 (BBa_J364002), Device 4 (BBa_J364003), Device 5 (BBa_J364004), Device 6 (BBa_J364005) were transformed into Escherichia coli DH5α, which were inoculated on LB plate with chloramphenicol (cmr). After an overnight cultivation, single colonies was picked to keep cultivating. After 6 hours cultivation, Colony PCR was conducted to test if the plasmids were transformed successfully. And the colonies were moved into liquid cultures (LB medium) and cultivated overnight. Liquid cultures were diluted with LB medium until the value of OD600 reached 0.02. Then we took out 500 μL samples from the cultures every 2 hour (t=0, 2, 4, 6h). At last, we measured OD600 and fluorescence of all samples.

Materials and Methods

Growth Conditions

The bacteria were cultivated in Lysogeny Broth(LB) plate with chloramphenicol added when doing transformation. The plates were kept at 37°C. Colonies we picked were grown in 5ml LB medium with chloramphenicol. Afterwards, they were kept at 37°C and 220 rpm shaking frequency. We used 5ml LB medium and chloramphenicol to target OD600 of 0.02.

Strains &amp Devices Transformed

We used Escherichia coli strain DH5α cells for transformation. Three devices and two controls are all provided by iGEM HQ as follows:

  • Positive Control (BBa_I20270)
  • Negative Control (BBa_R0040)
  • Device 1 (BBa_J364000)
  • Device 2 (BBa_J364001)
  • Device 3 (BBa_J364002)
  • Device 4 (BBa_J364003)
  • Device 5 (BBa_J364004)
  • Device 6 (BBa_J364005)

Colony PCR &amp Gel electrophoresis

Primer designed by choose 15bp on VF2 primer site &amp VR primer site. PCR conducted by standard procedure. Gel electrophoresis were conducted after PCR, with standard procedure. Gel photo was captured by UV imagery system provided by SYSU school of life science.

marker round

Generating FITC Fluorescence Standard Curve by Using Plate Reader

We have used 96-well plates to do the plate reader’s measurement. A serial dilution was performed to generate a FITC fluorescence standard curve. When measuring fluorescence, the excitation wavelength we set was 480nm(9), and emission wavelength was set at 535nm(20).

Using LUDOX-S40 as A Single Point Reference

We used LUDOX-S40 to transform our absorbance data into standard OD600 measurement. Volumes of LUDOX was 100μl. We prepared a column of 4 wells containing 100 μl LUDOX and 4 wells containing water. The samples were measured using plate reader.

Measuring Fluorescence &amp OD600 by Using Plate Reader

Colonies with devices tested by us were picked from the plates, then were cultured overnight in 5ml LB medium with chloramphenicol. The liquid cultures were diluted to target OD600=0.02. The fluorescence and OD600 of samples at 0,2,4, 6 hours were measured by using 96-well plate. The volumes of samples were 100 μl LB medium with chloramphenicol were used as blank

Results

fig_1

Fig 1. Fluorescien Standard Curve

fig_2

Fig 2. OD600 Measurement

OD600 This value represents the concentration of bacteria in the medium. Due to the amount of the samples, the 0h phare failed to synchronize at the same value, and at this point the bacteria might already enter log phase. (Fig 2.)

fig_3

Fig 3. Fluorescence Measurement

Fluorescein The results are shown in the graph. The fluorescein level of Negative control, Device 1, 3, 5, 6 reach peak at the very beginning and then decrease remarkably in the next 2 hours. The positive control and Device 4 increase quit a lot at 2h but also decrease afterward. The Device 2 increase in a peace pace. (Fig 3.)

fig_4

Fig 4. μM Fluorescein / OD600

Attribution: All our experiments were conducted in the professor Lu’s laboratory in School of life science, Sun Yat-sen University. They provided everything we need and answered every one of our doubts patiently. Here we present our appreciation.

contact
sysusoftware@126.com
address
135# Xin'gang Rd(W.)
Sun Yat-sen University, Guangzhou, China
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