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

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{{Jiangnan_China}}
 
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         <a class="nav-link py-2 d-none d-md-inline-block" href="#"><i class="fa fa-home"></i> Home</a>
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             <a class="dropdown-item" href="https://2018.igem.org/Team:Jiangnan_China/Results">Results</a>
 
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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/Parts">Basic Parts</a>
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     <main class="content-wrap">
 
     <main class="content-wrap">
       <img src="https://static.igem.org/mediawiki/2018/b/b2/T--jiangnan_china--interlab--1.jpg" width="100%">
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       <img src="https://static.igem.org/mediawiki/2018/9/99/T--jiangnan_china--demonstration--1.jpg" width="100%">
      <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>Overview</strong></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';">
 
    <div align="left" style="font-family: 'spr';font-size:40px;border-bottom:2px solid #584b4f;"><strong>Materials</strong></div>
 
    <br>
 
      96-spot well plates: clear plates from Corning<br>
 
      Bacteria strains: E.coli DH5α<br>
 
      Test devices: obtained from the distribution kit
 
      <br><br>
 
  
       <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 class="dcpt3" style="font-size:20px;line-height:1.5;font-family: 'spr';margin-top:-1px; ">
    <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 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>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>
 
     <br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;Because we use <span class="font-italic">nisA</span> as promoter to express our parts, 0.5 ng/mL of Nisin is required to induce cell expression in all the following steps.<br><br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;<strong><font size="5">Demonstration of <span class="font-italic">msmK</span> gene</font></strong><br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;Copy <span class="font-italic">msmK</span> gene from <span class="font-italic">Lactococcus lactis</span> NZ9000 gene group with PCR. Construct <span class="font-italic">msmK</span> overexpression strain <span class="font-italic">L.lactis</span> NZ3900/pNZ8149-<span class="font-italic">msmK</span> with electrotransformation. Take strains <span class="font-italic">L.lactis</span> NZ3900/pNZ8149-<span class="font-italic">msmK</span> and <span class="font-italic">L.lactis</span> NZ3900/pNZ8149 from glycerin tube kept under -80℃, dilute 1/25 in 2 x 10 ml fresh medium (30 °C). Grow until the OD600=0.4. Count their number of colonies per ml at pH 4.0 (More details can be seen in protocol).<br><br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;We can get the following results:<br>
 
     <div align="center">
 
     <div align="center">
       <img src="https://static.igem.org/mediawiki/2018/7/77/T--jiangnan_china--interlab--chart1.png" width="70%" >
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       <img src="https://static.igem.org/mediawiki/2018/6/68/T--jiangnan_china--wet--5.png" width="80%" >
 
     </div>
 
     </div>
    <br><br>
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     <div style="text-align:center;"><strong >Fig 3</strong> Number of colonies at acid stress (pH 4.0).</div>
 
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    <br>
     <div align="center"><strong><font size="5" color="#5B9BD5" >Particle Standard Curve (log scale)</font></strong></div>
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    <div align="center">
    <br>
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       <img src="https://static.igem.org/mediawiki/2018/0/0f/T--jiangnan_china--wet--6.png" width="60%" >
    <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>
 
     </div>
     <br><br>
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     <div style="text-align:center;"><strong >Fig 4</strong> Survival rate at acid stress (pH 4.0).</div><br>
 
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     &nbsp;&nbsp;&nbsp;&nbsp;The result shows that <span class="font-italic">msmK</span> is an effective anti-acid gene, which can make the recombinant strain has 213-fold higher survival rate than parent one.<br><br>
     <div align="center"><strong><font size="5" color="#5B9BD5" >Fluorescein Standard Curve</font></strong></div>
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    &nbsp;&nbsp;&nbsp;&nbsp;<strong><font size="5">Demonstration of composite part <span class="font-italic">msmK-cspD2</span></font></strong><br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;It has been reported that <span class="font-italic">cspD2</span> can effectively exert anti-freezing effect in the recipient bacteria. <span class="font-italic">CspD2</span> was ligated to the Pnz8149/<span class="font-italic">msmK</span> plasmid by one-step cloning (seamless ligation), and the recombinant plasmid was introduced into the constructed <span class="font-italic">L. lactis</span> NZ3900/pNZ8149-<span class="font-italic">msmk</span>-cspD2 strain using electroporation. <br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;The gfp gene was inserted as a marker gene, and cell viability was characterized by fluorescence intensity. The strain was tested for acid resistance and freezing resistance using a flow cytometer. The process of acid stress and cold stress is similar with the above demonstration process.<br><br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;<strong><font size="5">Acid stress </font></strong><br>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;Deal with the samples under pH 4.0 with nisin as an inducer.<br>
 
     <br>
 
     <br>
 
     <div align="center">
 
     <div align="center">
       <img src="https://static.igem.org/mediawiki/2018/3/31/T--jiangnan_china--interlab--chart3.png" width="70%" >
+
       <img src="https://static.igem.org/mediawiki/2018/6/62/T--jiangnan_china--wet--7.png" width="80%" >
 
     </div>
 
     </div>
    <br><br>
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     <div style="text-align:center;"><strong >Fig 5</strong> Number of colonies at acid stress (pH 4.0).<br><br></div>
 
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    <div align="center">
     <div align="center"><strong><font size="5" color="#5B9BD5" >Fluorescein Standard Curve (log scale)</font></strong></div>
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       <img src="https://static.igem.org/mediawiki/2018/7/71/T--jiangnan_china--wet--8.png" width="60%" >
    <br>
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    <div align="center">
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       <img src="https://static.igem.org/mediawiki/2018/f/f9/T--jiangnan_china--interlab--chart4.png" width="70%" >
+
 
     </div>
 
     </div>
    <br><br>
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     <div style="text-align:center;"><strong >Fig 6</strong> Survival rate at acid stress (pH4.0).<br><br></div>
 
+
    &nbsp;&nbsp;&nbsp;&nbsp;The result shows that composite part can make the recombinant strain has 243-fold higher survival rate than parent one under acid stress.<br>
     <div align="center"><strong><font size="5" color="#5B9BD5" >uM Fluorescein / OD</font></strong></div>
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    <div align="center">
    <br>
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       <img src="https://static.igem.org/mediawiki/2018/9/9f/T--jiangnan_china--wet--9.png" width="60%" >
    <div align="center">
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       <img src="https://static.igem.org/mediawiki/2018/5/55/T--jiangnan_china--interlab--chart5.png" width="70%" >
+
 
     </div>
 
     </div>
     <br><br>
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     <div style="text-align:center;"><strong >Fig 7</strong> Electron microscopy of <span class="font-italic">L.lactis</span> NZ3900/pNZ8149-<span class="font-italic">msmk-cspD2-gfp</span> and <span class="font-italic">L.lactis</span> NZ3900/pNZ8149 before and after acid stress.<br><br></div>
 
+
     &nbsp;&nbsp;&nbsp;&nbsp;Before the acid stress, the cell structure of the control strain and the recombinant strain remained intact. After 3 h of pH 4.0 stress, the cell membrane thickness became thinner and the surface became rough, and the cell membrane of some control strains ruptured. In comparison, the cell structure of the recombinant strain remains more intact, thereby effectively reducing the damage caused by acid stress on the cells.<br><br>
     <div align="center"><strong><font size="5" color="#5B9BD5" >Net Fluorescein a.u.</font></strong></div>
+
    &nbsp;&nbsp;&nbsp;&nbsp;<strong><font size="5">Cold stress </font></strong><br>
    <br>
+
    &nbsp;&nbsp;&nbsp;&nbsp;<span class="font-italic">L.lactis</span> NZ3900/pNZ8149-<span class="font-italic">msmk-cspD2-gfp</span> and <span class="font-italic">L.lactis</span> NZ3900/pNZ8149 strains were inoculated with 4% inoculation. When cultured at 30 °C for 2.5 h (OD=0.35), add 0, 0.5 ng/mL of Nisin, and then culture for 8 ∼ 10 h (OD=0.8), centrifuge at 4000 r/min. Resuspend them in the same volume of fresh M17 medium and count the number of colonies. Four freeze-thaw stimulations were performed on all samples by 1 mL of the sample after counting, and placed in a refrigerator at −20 °C to cool rapidly, frozen for 24 h, then slowly frozen at 4 min and 30 °C. Count separately and calculate the survival rate.<br><br>
    <div align="center">
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    <div align="center">
       <img src="https://static.igem.org/mediawiki/2018/a/a1/T--jiangnan_china--interlab--chart6.png" width="70%" >
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       <img src="https://static.igem.org/mediawiki/2018/f/fb/T--jiangnan_china--wet--10.jpg" width="50%" >
 
     </div>
 
     </div>
    <br><br>
+
     <div style="text-align:center;"><strong >Fig 8</strong> The Comparison curve of survival rate under cold stress.<br><br></div>
 
+
    &nbsp;&nbsp;&nbsp;&nbsp;After 4 consecutive repeated freeze-thaw tests, the recombinant strain was 47.5 times more viable than the control strain, indicating the antifreeze survival rate of the strain with increased overexpression of <span class="font-italic">cspD2</span>.<br><br>
     <div align="center"><strong><font size="5" color="#5B9BD5" >Net Abs 600</font></strong></div>
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    <div align="center">
    <br>
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       <img src="https://static.igem.org/mediawiki/2018/b/b7/T--jiangnan_china--wet--11.png" width="60%" >
    <div align="center">
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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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     </div>
 
     </div>
     <br><br>
+
     <div style="text-align:center;"><strong >Fig 9</strong> Electron microscopy before and after repeated freezing and thawing.<br><br></div>
 +
    &nbsp;&nbsp;&nbsp;&nbsp;Before freezing and thawing, the cell structure of the control strain and the recombinant strain remained intact. After repeated freezing and thawing for 4 times, the cell membrane of the cell became thin and rough, and some intracellular substances overflowed. In comparison, the cell structure of the recombinant strain remains more intact, and the damage of the cell membrane is alleviated, thereby effectively reducing the damage caused by freezing stress on the cells.<br>
  
    <div align="center"><strong><font size="5" color="#5B9BD5" >MEFL / particle</font></strong></div>
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 +
   
 
     <br>
 
     <br>
     <div align="center">
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     </div>
      <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>
 
  
      <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>Summery</strong></div>
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    <br>
+
 
      &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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      <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>Conclution</strong></div>
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    <br>
+
      <div>
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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.
+
      </div>
+
      <br>
+
      <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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      <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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      <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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Revision as of 11:44, 16 October 2018


    Because we use nisA as promoter to express our parts, 0.5 ng/mL of Nisin is required to induce cell expression in all the following steps.

    Demonstration of msmK gene
    Copy msmK gene from Lactococcus lactis NZ9000 gene group with PCR. Construct msmK overexpression strain L.lactis NZ3900/pNZ8149-msmK with electrotransformation. Take strains L.lactis NZ3900/pNZ8149-msmK and L.lactis NZ3900/pNZ8149 from glycerin tube kept under -80℃, dilute 1/25 in 2 x 10 ml fresh medium (30 °C). Grow until the OD600=0.4. Count their number of colonies per ml at pH 4.0 (More details can be seen in protocol).

    We can get the following results:
Fig 3 Number of colonies at acid stress (pH 4.0).

Fig 4 Survival rate at acid stress (pH 4.0).

    The result shows that msmK is an effective anti-acid gene, which can make the recombinant strain has 213-fold higher survival rate than parent one.

    Demonstration of composite part msmK-cspD2
    It has been reported that cspD2 can effectively exert anti-freezing effect in the recipient bacteria. CspD2 was ligated to the Pnz8149/msmK plasmid by one-step cloning (seamless ligation), and the recombinant plasmid was introduced into the constructed L. lactis NZ3900/pNZ8149-msmk-cspD2 strain using electroporation.
    The gfp gene was inserted as a marker gene, and cell viability was characterized by fluorescence intensity. The strain was tested for acid resistance and freezing resistance using a flow cytometer. The process of acid stress and cold stress is similar with the above demonstration process.

    Acid stress
    Deal with the samples under pH 4.0 with nisin as an inducer.

Fig 5 Number of colonies at acid stress (pH 4.0).

Fig 6 Survival rate at acid stress (pH4.0).

    The result shows that composite part can make the recombinant strain has 243-fold higher survival rate than parent one under acid stress.
Fig 7 Electron microscopy of L.lactis NZ3900/pNZ8149-msmk-cspD2-gfp and L.lactis NZ3900/pNZ8149 before and after acid stress.

    Before the acid stress, the cell structure of the control strain and the recombinant strain remained intact. After 3 h of pH 4.0 stress, the cell membrane thickness became thinner and the surface became rough, and the cell membrane of some control strains ruptured. In comparison, the cell structure of the recombinant strain remains more intact, thereby effectively reducing the damage caused by acid stress on the cells.

    Cold stress
    L.lactis NZ3900/pNZ8149-msmk-cspD2-gfp and L.lactis NZ3900/pNZ8149 strains were inoculated with 4% inoculation. When cultured at 30 °C for 2.5 h (OD=0.35), add 0, 0.5 ng/mL of Nisin, and then culture for 8 ∼ 10 h (OD=0.8), centrifuge at 4000 r/min. Resuspend them in the same volume of fresh M17 medium and count the number of colonies. Four freeze-thaw stimulations were performed on all samples by 1 mL of the sample after counting, and placed in a refrigerator at −20 °C to cool rapidly, frozen for 24 h, then slowly frozen at 4 min and 30 °C. Count separately and calculate the survival rate.

Fig 8 The Comparison curve of survival rate under cold stress.

    After 4 consecutive repeated freeze-thaw tests, the recombinant strain was 47.5 times more viable than the control strain, indicating the antifreeze survival rate of the strain with increased overexpression of cspD2.

Fig 9 Electron microscopy before and after repeated freezing and thawing.

    Before freezing and thawing, the cell structure of the control strain and the recombinant strain remained intact. After repeated freezing and thawing for 4 times, the cell membrane of the cell became thin and rough, and some intracellular substances overflowed. In comparison, the cell structure of the recombinant strain remains more intact, and the damage of the cell membrane is alleviated, thereby effectively reducing the damage caused by freezing stress on the cells.

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