Team:Tokyo Tech/Experiment/C4HSL-dependent 3OC12HSL production

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        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3OC12HSL production</a></li>
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3OC12HSL production</a></li>
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3OC12HSL-dependent C4HSL production</a></li>
        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3OC12HSL-dependent C4HSL production</a></li>
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        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Symbiosis confirmation by co-culture </a></li>
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        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Mutualism Confirmation ~Co-culture Assay~</a></li>
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        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Transporter_assay" style="width:400px; margin-left:-135px;">Transporter assay</a></li>
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  </ul>
  </ul>
</li>
</li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling">Modeling</a></li>
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<li><a href="#">Modeling</a>
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                          <ul>
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                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Overview"  style="width:400px; margin-left:-135px;">Overview</a></li>
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                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Growth Conditions For Company And Customer"  style="width:400px; margin-left:-135px;">Growth Conditions For Company And Customer</a></li>
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                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Analysis of C4HSL-dependent Switch" style="width:400px; margin-left:-135px;">Analysis of C4HSL-dependent Switch</a></li>
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                              <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Economic Wave"  style="width:400px; margin-left:-135px;">Economic Wave</a></li>
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                          </ul>
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                        </li>
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">Parts</a></li>
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">Parts</a></li>
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Policy_and_Practices" style="height:50px; padding-top:3px;">Policy and Practices</a></li>
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Policy_and_Practices" style="height:50px; padding-top:3px;">Policy and Practices</a></li>
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               <p>&nbsp;</p>
               <p>&nbsp;</p>
                 <div id="gototop"><a href="#"><img src="https://static.igem.org/mediawiki/2014/5/55/Tokyo_Tech_Go-to-top-icon.png" height="50" /></a></div>
                 <div id="gototop"><a href="#"><img src="https://static.igem.org/mediawiki/2014/5/55/Tokyo_Tech_Go-to-top-icon.png" height="50" /></a></div>
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              <p align="center"><span class="title-small">Contents</span></p>
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                <p align="left" class="info-24"><a href="#1">1. Introduction </a></p>  
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            <p align="left" class="info-24"><a href="#2">2. Summary of the Experiments </a></p>
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                                  <p align="left" class="info-18"><a href="#2.1">2.1 C4HSL-dependent CmR expression</a></p>
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                                  <p align="left" class="info-18"><a href="#2.2">2.2 C4HSL-dependent 3OC12HSL production </a></p>
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                      <p align="left" class="info-24"><a href="#3">3. Results </a></p>
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                      <p align="left" class="info-18"><a href="#3.1">3.1. C4HSL-Dependent  CmR Expression Assay</a></p>
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                      <p align="left" class="info-18"><a href="#3.2">3.2. C4HSL-Dependent 3OC12HSL  Production Assay</a></p>
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                      <p align="left" class="info-24"><a href="#4">4. Materials and Methods</a></p>
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  <p align="left" class="info-18"><a href="#4.1">4.1. Construction</a></p>
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  <p align="left" class="info-18"><a href="#4.2">4.2. Assay Protocol </a></p>
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  <p align="left" class="info" style="text-indent:40px;"><a href="#4.2.1">4.2.1. C4HSL-Dependent  CmR Expression Assay</a></p>
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  <p align="left" class="info" style="text-indent:40px;"><a href="#4.2.2">4.2.2. C4HSL-Dependent 3OC12HSL Production Assay</a></p>
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              <p align="left" class="info-24"><a href="#5">5. Reference</a></p>
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                      <div class="title" style="clear: both;">&nbsp;</div>
               <table width="900" border="0">
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                   <td width="890"><div align="center" class="title-small">C4HSL-dependent 3OC12HSL production module</div></td>
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                   <td colspan="2" class="entry-long"><a name="1" id="1"></td>
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                   <td>&nbsp;</td>
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                   <td colspan="2">&nbsp;</td>
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                   <td>&nbsp;</td>
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                   <td colspan="2"><h2>1. Introduction</h2></td>
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                   <td><h2>1. Summary of the experiment </h2></td>
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                   <td colspan="2"><p class="info-18">We designed signal-dependent signal production in our system by using signaling molecules and antibiotics resistance gene. In our bank story, we used signaling molecule C4HSL as money.</p></td>  
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                  <td colspan="2"><p class="info-18">For construction of the  C4HSL-dependent chloramphenicol resistance gene product(CmR) and 3OC12HSL production  module, we constructed a new part Prhl(RL)-CmR-LasI(<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>). Prhl(RL)-CmR-LasI cell is an engineered <i>E. coli</i> that contains  a C4HSL-dependent LasI generator and a constitutive RhlR generator. As a constitutive  RhlR generator, we used Ptet-RhlR. In our bank story, this part imitates the functions of Company. (Fig. 3-3-1-1) We confirmed the C4HSL-dependent growth by measuring optical density, and C4HSL-dependent 3OC12HSL production by using reporter cell. </p>                  </td>
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                   <td><p class="info-18">Construction of the C4HSL-dependent 3OC12HSL production and chloramphenicol resistance expression module.</p>                  </td>
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                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
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                   <td><p class="info-18">We created a symbiosis of Company E.coli and Customer E.coli for reproducing the situation in real economy. We used signaling molecules and antibiotics resistance gene ,and constructed signal-dependent signal production in our system.                   </p></td>
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                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-1-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/7/77/Tokyo_Tech_3-3-1-1.png/800px-Tokyo_Tech_3-3-1-1.png" width="400" /></a></div></td>
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                   <td><p class="info-18">For construction of the C4HSL-dependent chloramphenicol resistance (CmR) and 3OC12HSL production module, we constructed a new part Plux-CmR-lasI (BBa_). Plux-CmR-lasI cell is an engineered E.coli that contains a C4HSL-dependent lasI generator and a constitutive rhlR generator. We constructed a new Biobrick part Plux-CmR-lasI by combining Plux-CmR (BBa_K39562) and lasI (BBa_). As a constitutive rhlR generator, we used Pret-rhlR (BBa_S0319). In our bank story, this part is company.                  </p></td>
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                   <td colspan="2"><div align="center"><strong>Fig. 3-3-1-1.</strong> Genetic Circuit of Company <i>E. coli</i></div></td>
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                   <td><p class="head">1-1 C4HSL-dependent 3OC12HSL production </p></td>
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                   <td colspan="2">&nbsp;</td>
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                   <td><p class="info-18">First, we performed a reporter assay by using Lux reporter cell to characterize the function of C4HSL-dependent 3OC12HSL production. As the negative control of 3OC12HSL production, we prepared 3OC12HSL non-producer cell. 3OC12HSL non-producer cell contains Plux-CmR instead of Plux-CmR-lasI. The cell of negative control does not produce 3OC12HSL even in the presence of C4HSL.</p></td>
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                   <td colspan="2">&nbsp;</td>
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                  <td colspan="2" class="entry-long">&nbsp;<a name="2" id="2"></td>
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                  <td colspan="2">&nbsp;</td>
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                   <td>&nbsp;</td>
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                   <td colspan="2"><h2>2.  Summary of the experiments</h2></td>
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                   <td><p class="info-18">Sender</p></td>
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                   <td colspan="2"><h1>2-1. C4HSL-dependent CmR expression</h1></td>
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                   <td>&nbsp;</td>
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                   <td colspan="2">&nbsp;</td>
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                <td width="445"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-1-2.png"><img src="https://static.igem.org/mediawiki/2014/9/9a/Tokyo_Tech_3-3-1-2.png" width="500" /></a></div></td>
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                   <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td>
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                   <td><div align="center"><strong>Fig. 3-3-2-1.</strong> Flow chart of C4HSL-dependent CmR expression assay</div></td>
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                   <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td>
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                   <td colspan="2">&nbsp;</td>
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                  <td colspan="2"><p class="info-18"> We confirmed the function of C4HSL-dependent CmR expression by measuring optical density of the cultures containing chloramphenicol(Fig. 3-3-2-1). </a></td>
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                  <td colspan="2"><p class="info-18">In this experiment we prepared three plasmids, A, B and C. (See Fig. 3-3-2-2) Right after the C4HSL induction, we added chloramphenicol into the medium containing Company cell. We measured the optical density for about eight hours to estimate the concentration of the cell.</a>
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</p>                  </td>
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                  <td colspan="2">&nbsp;</td>
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      <tr><td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-2-2-1.png"><img src="https://static.igem.org/mediawiki/2014/9/9d/Tokyo_Tech_3-3-2-2-1.png" width="400" /></a></div></td>
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<td><div align="center"><strong>Fig. 3-3-2-2.</strong> Plasmids for the experiment of C4HSL-dependent CmR expression</div></td>
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                   <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td>
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                   <td colspan="2">&nbsp;</td>
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                   <td>&nbsp;</td>
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                   <td colspan="2"><h1>2-2. C4HSL-dependent 3OC12HSL production</h1></td>
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                   <td><p class="info-18">Repoter</p></td>
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                   <td colspan="2">&nbsp;</td>
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                   <td>&nbsp;</td>
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<td colspan="2"><p class="info-18">We performed a reporter assay by using reporter cells to characterize the function of C4HSL-dependent C4HSL production. Prhl(RL)-CmR-LasI cell containing constitutive RhlR generator expresses LasI and produces 3OC12HSL in the presence of C4HSL. Since 3OC12HSL is excreted to the culture, the supernatant of the sender cell contains 3OC12HSL when the part works as expected. </p></td>
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                  <td colspan="2"><p class="info-18"> Reporter cells are incubated in the supernatant of the culture of sender cells. When there are 3OC12HSL in the supernatant, reporter cell expresses GFP. We checked the fluorescence of reporter cells to confirm the expression of 3OC12HSL. The expression of the reporter cells were measured by flow cytometer.(See Fig.3-3-2-3)</p></td>
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                  <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td>
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                  <td width="445"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-1-3.png"><img src="https://static.igem.org/mediawiki/2014/4/45/Tokyo_Tech_3-3-1-3.png" width="500" /></a></div></td>
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                  <td><div align="center"><strong>Fig. 3-3-2-3. </strong>Flow chart of C4HSL-dependent 3OC12HSL production Assay  </div></td>
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                <tr><td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-2-2.png"><img src="https://static.igem.org/mediawiki/2014/2/2f/Tokyo_Tech_3-3-2-2.png" width="700" /></a></div></td>
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<td><div align="center"><strong>Fig. 3-3-2-4.</strong>Plasmids for the experiment of C4HSL-dependent 3OC12HSL production</div></td>
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                  <td colspan="2"><p class="info-18">We prepared the following conditions for the induction of reporter cells. (Plux-CmR cell was used as the negative control. See Fig. 3-3-2-4)</p></td>
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                   <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td>
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                   <td colspan="2"><p class="info-18">(1) Culture containing Prhl(RL)-CmR-lasI cell with C4HSL induction</p></td>
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                   <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td>
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                   <td colspan="2"><p class="info-18">(2) Culture containing Prhl(RL)-CmR-lasI cell without induction</p></td>
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                  <td colspan="2"><p class="info-18">(3) Culture containing Plux-CmR cell with C4HSL induction</p></td>
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                   <td>&nbsp;</td>
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                   <td colspan="2"><p class="info-18">(4) Culture containing Plux-CmR cell without induction</p></td>
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                  <td colspan="2"><p class="info-18">(5) 5 microM of synthetic C4HSL in LB medium </p></td>
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                  <td colspan="2"><p class="info-18">(6) DMSO in LB medium</p></td>
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                  <td colspan="2">&nbsp;</td>
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                   <td><p class="info-18">We prepared four culture conditions as follow.</p></td>
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                   <td colspan="2"><p class="info-18">Reporter</p></td>
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                   <td class="info-18">    A) Culture containing Plux-CmR-LasI cell with C4HSL induction</td>
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                   <td colspan="2" class="info-18">E) The cell containing constitutive LasR generator and Plas-GFP cell</td>
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                   <td class="info-18">    B) Culture containing Plux-CmR-LasI cell without C4HSL induction</td>
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                   <td colspan="2" class="info-18">F) The cell containing constitutive LuxR generator and PlacIq-GFP cell…Positive control</td>
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                   <td class="info-18">    C) Culture containing Plux-CmR cell with C4HSL induction</td>
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                   <td colspan="2" class="info-18">G) The cell containing constitutive LuxR generator and Promoter-less-GFP cell…Negative control </td>
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                 <tr>
-
                   <td class="info-18">    D) Culture containing Plux-CmR cell without C4HSL induction</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">The supernatants of this four different culture were used as the inducer in the reporter assay.</p></td>
+
                   <td colspan="2" class="entry-long">&nbsp;<a name="3" id="3"></td>
 +
                </tr>   
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>                 
 +
                <tr>
 +
                  <td colspan="2"><h2>3. Result</h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2">&nbsp;<a name="3.1" id="3.1"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">In the reporter assay, we used a Lux reporter strain that contains Ptet-luxR and Plux-GFP. Also, a reporter cell that expresses GFP constitutively and a reporter cell that does not express GFP were used as the positive control and the negative control, respectively.</p></td>
+
                   <td colspan="2"><h1>3-1. C4HSL-dependent CmR expression assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">We tested two types of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)</p></td>
 +
                  </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">Fig.3-3-3-1, Fig.3-3-3-2 shows the condition in the absence and presence of chloramphenicol, respectively. </p></td>
 +
                  </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">Fig 3-3-3-1. shows that every cell can grow in the absence of chloramphenicol.
 +
</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">1-2  C4HSL-dependent growth</p></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">The cell which contains Plux-CmR-lasI can grow in the medium containing chloramphenicol<br />
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-3-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/5/58/Tokyo_Tech_3-3-3-1.png/800px-Tokyo_Tech_3-3-3-1.png" width="500" /></a></div></td>
-
                  (Chloramphenicol is one of the antibiotics. )                  </p></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">After induction, we added chloramphenicol into the medium and measured optical density<br />
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-3-1.</strong> C4HSL-Dependent Company growth with no Cm addition</div></td>
-
                  after induction.</p></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><h2>2. Results</h2></td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-3-2.png"><img src="https://static.igem.org/mediawiki/2014/thumb/e/ed/Tokyo_Tech_3-3-3-2.png/800px-Tokyo_Tech_3-3-3-2.png" width="500" /></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-3-2.</strong> C4HSL-Dependent Company Growth in 100  microg/mL Cm</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">2-1  C4HSL-dependent 3OC12HSL production</p></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">We measured the expression of GFP in the reporter cell by flow cytometer.</p></td>
+
                   <td colspan="2"><p class="info-18">On the other hand, in the presence of chloramphenicol, the cell containing Prhl(RL)-CmR-LasI can grow only when induced by C4HSL. Without the induction of C4HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Prhl(RL)-CmR-LasI expressed CmR when induced by C4HSL as expected.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">2-2 C4HSL-dependent growth</p>                   </td>
+
                   <td colspan="2">&nbsp;<a name="3.2" id="3.2"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">After induction, optical density were measured to estimate the concentration of the cell.</p></td>
+
                   <td colspan="2"><h1>3-2. C4HSL-dependent 3OC12HSL Production Assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-1-1.png"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></a></div></td>
+
                   <td colspan="2"><p class="info-18">Fig. 3-3-3-3 shows the fluorescence intensities generated by the reporter cells. When the reporter cell E was incubated in the condition (1) (the culture of the induced Company cell), the fluorescence intensity of the reporter cell increased. Comparing the results of condition (1) and (2) reporter cell in the supernatant of (1) had 29-fold higher fluorescence intensity. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center">Fig. 3-1-1. </div></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">This result indicates that Company cell produced 3OC12HSL in response to C4HSL induction by the function of Prhl(RL)-CmR-LasI.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-1-2.png"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></a></div></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center">Fig. 3-1-2. </div></td>
+
                   <td colspan="2"><p class="info-18">From this experiment, we confirmed that a new part Prhl(RL)-CmR-LasI synthesized 3OC12HSL (LasI) as expected.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Customer excretes 3OC12HSL when C4HSL exists.png"><img src="https://static.igem.org/mediawiki/2014/0/07/Customer_excretes_3OC12HSL_when_C4HSL_exists.png" width="500" /></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">explanation?    </p>                   </td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-3-3.</strong> Company excretes 3OC12HSL when C4HSL exists</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td><h2>3.  Materials and methods</h2></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2" class="entry-long">&nbsp;<a name="4" id="4"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">3-1  Construction</p></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">-Strain</p></td>
+
                   <td colspan="2"><h2>4. Materials and methods</h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">All the samples were JM2.300 strain</p></td>
+
                   <td colspan="2">&nbsp;<a name="4.1" id="4.1"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">-Plasmids</p></td>
+
                   <td colspan="2"><h1>4-1 Construction</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td>&nbsp;</td>
+
                   <td colspan="2"><p class="head">-Strain</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">3-2 </p></td>
+
                   <td colspan="2"><p class="info-18">All  the samples were JM2.300 strain.</p>                   </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18" style="text-indent:0px;">3-2-1.  C4HSL-dependent 3OC12HSL production assay by using reporter assay</p></td>
+
                   <td colspan="2"><p class="head">-Plasmids</p></td>
 +
                </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">--C4HSL-dependent CmR expression</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">Prepare the supernatant of the sender cell</p></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">1. Grow the colony of sender cell in LB containing antibiotic O/N at 37°C.</td>
+
                   <td colspan="2" class="info-18"><div align="left">A. Ptet-GFP-Ptet-RhlR (pSB6A1),  Prhl(RL)-CmR-LasI(pSB3K3)</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37C until the observed OD590 reaches 0.5. </td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">3. Centrifuge 1mL of the sample at 5000g, RT for 1 minute.</td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/5/5e/Tokyo_Tech_3-3-4-1.png/800px-Tokyo_Tech_3-3-4-1.png" width="500" /></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">4. Suspend the pellet in<u> </u><u>1 mL of LB containing Ampicillin</u><u>(</u><u>50μg/mL</u><u>)</u><u>and Kanamycin(30μg/mL) .</u></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-4-1.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">5. Add 30&#181;L of suspension in the following medium.</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Add 30&#181;L of 500&#181;M C12HSL to 3mL LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">B. Ptet-GFP-Ptet-RhlR (pSB6A1), PlacIq-CmR (pSB3K3)…Positive control</td>
 +
                </tr
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Add 30&#181;L DMSO to 3mL of LB containing Amp and Kan                 </td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-2.png"><img src="https://static.igem.org/mediawiki/2014/thumb/4/41/Tokyo_Tech_3-3-4-2.png/800px-Tokyo_Tech_3-3-4-2.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-2.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR  (pSB3K3)… Negative control</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                 </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-3.png"><img src="https://static.igem.org/mediawiki/2014/thumb/d/de/Tokyo_Tech_3-3-4-3.png/800px-Tokyo_Tech_3-3-4-3.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-3.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">--C4HSL-dependent 3OC12HSL production</td>
 +
                </tr> 
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">Sender</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI (pSB3K3)  </td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/5/5e/Tokyo_Tech_3-3-4-1.png/800px-Tokyo_Tech_3-3-4-1.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-4.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)  </td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-4.png"><img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Tokyo_Tech_3-3-4-4.png/800px-Tokyo_Tech_3-3-4-4.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-5.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">Reporter</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">E. Ptrc-LasR (pSB6A1), Plas-GFP (pSB3K3) </td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-5.png"><img src="https://static.igem.org/mediawiki/2014/thumb/f/f4/Tokyo_Tech_3-3-4-5.png/800px-Tokyo_Tech_3-3-4-5.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-6.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">F. Ptet-LuxR (pSB6A1), PlacIq-GFP (pSB3K3)...Positive  control</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-6.png"><img src="https://static.igem.org/mediawiki/2014/thumb/1/1e/Tokyo_Tech_3-3-4-6.png/800px-Tokyo_Tech_3-3-4-6.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-7.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">G. Ptet-LuxR (pSB6A1), Promoter-less-GFP (pSB3K3)...Negative  control</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-7.png"><img src="https://static.igem.org/mediawiki/2014/thumb/8/8e/Tokyo_Tech_3-3-4-7.png/800px-Tokyo_Tech_3-3-4-7.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-8.</strong></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;<a name="4.2" id="4.2"></td>
 +
                </tr>               
 +
                <tr>
 +
                  <td colspan="2"><h1>4-2. Assay Protocol </h1><a name="4.2.1" id="4.2.1"></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p class="info-18" style="text-indent:0px;"><strong>4-2-1.  C4HSL-Dependent CmR Expression Assay</strong></p></td>
                 </tr>
                 </tr>
                  
                  
                 <tr>
                 <tr>
-
                   <td class="info-18">6. Grow the samples of sender cell at 37°C for 4 hours.</td>
+
                   <td colspan="2" class="info-18">1. Prepare overnight cultures for the sender cells in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12h.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">7. Measure optical density every hour.  (If optical density is over 1.0, dilute the cell medium.)</td>
+
                   <td colspan="2" class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containing  antibiotic and grow the cells at 37°C <br />
 +
          until the observed OD590 reaches 0.5.(→fresh culture) </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">8. Centrifuge sample at 9000g, 4°C for 1minute. Filter sterilize supernatant.</td>
+
                   <td colspan="2" class="info-18">3. Add 30  microL of suspension in the following medium.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">9. Use the supernatant in reporter assay.</td>
+
                   <td colspan="2" class="info-18">          1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 5 microM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2" class="info-18">          2) 3 mL  of LB containing Amp and Kan + 30 microL DMSO</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td><p class="info-18"><strong>Reporter Assay</strong></p></td>
+
                   <td colspan="2" class="info-18">          3) 3 mL  of LB containing Amp, Kan and Cm (final concentration is 100 microg/mL) <br />
 +
                                                      + 30  microL C4HSL (final concentration is 500 microM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">1. Grow the colony of Reporter cell(D~Fin LB containing antibiotic O/N at 37°C.</td>
+
                   <td colspan="2" class="info-18">          4) 3 mL of LB containing Amp, Kan and Cm (final concentration of Cm is 100 microg/mL) + 30  microL DMSO</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB+ antibiotic and grow the cells at 37°C until you reach an 0.5 OD590. (fresh culture).</td>
+
                   <td colspan="2" class="info-18">4. Grow the samples of sender cells at 37°C for more than 8 hours.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">5. Measure optical density every hour. (If the optical density is over 1.0, dilute the cell medium to 1/10.)</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;<a name="4.2.2" id="4.2.2"></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><p class="info-18" style="text-indent:0px;"><strong>4-2-2. C4HSL-Dependent 3OC12HSL Production Assay</strong></p></td>
 +
                </tr>
 +
               
 +
                <tr>
 +
                  <td colspan="2" class="info-18"> Prepare  the supernatant of the sender cell</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">3. Centrifuge  sample at 5000g, 25°C RT for 1 minute. Discard the supernatant.</td>
+
                   <td colspan="2" class="info-18">1. Prepare overnight cultures for the sender cells in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12h. </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">4. Suspended the sample in 3 mL of LB containing Ampicillin(50μg/mL) and Kanamycin(30μg/mL).</td>
+
                   <td colspan="2" class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C until the observed OD590  reaches 0.5.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">5. Add 30&#181;L of suspension in the following medium.</td>
+
                   <td colspan="2" class="info-18">3. Add 30 microL of the culture containing the cells in the following medium.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate of A①+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          a) Add 15 microL of 10 mM C4HSL to 3 mL LB containing Amp and Kan (final concentration is 50 microM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate of A②+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          b) Add 15 microL DMSO to 3 mL of LB containing Amp+Kan</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of B①+3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">4. Grow the samples of sender cell at 37°C for 8 hours.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of B②+3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">5. Measure the optical density every hour. (If the optical density is over 1.0, dilute the cell medium to 1/10.)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of C①+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">6. Centrifuge the sample at 9000x g, 4°C for 1 min. Filter sterilize the supernatant. (Pore size is 0.22 microm.)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">          Filtrate  of C②+3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">7. Use the supernatant in reporter assay.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">          3OC12HSL+3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">          DMSO +  3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Reporter Assay</strong></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">6. Grow  the samples of Reporter cell in incubator at 37°C for 4 hours.</td>
+
                   <td colspan="2" class="info-18">1. Prepare overnight cultures for the Reporter cell (E~G) in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12h.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">7. Start  preparing the flow cytometer 1 h before the end of incubation.</td>
+
                   <td colspan="2" class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB + antibiotic and grow the cells at 37°C until you reach an 0.5 in OD590 (fresh culture).</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">8. Take 200 microL of the sample, and centrifuge at 9000 Xg, 1 min, 4°C.</td>
+
                   <td colspan="2" class="info-18">3. Add 30 microL of suspension in the following medium.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">9. Remove  the supernatant by using P1000 pipette.</td>
+
                   <td colspan="2" class="info-18">          1) 2.7 mL filtrate of Aa +300 microL LB </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">10. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend.</td>
+
                   <td colspan="2" class="info-18">          2) 2.7 mL filtrate of Ab +300 microL LB</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">11. Dispense  all of each suspension into a disposable tube through a cell strainer.</td>
+
                   <td colspan="2" class="info-18">          3) 2.7 mL filtrate of Da +300 microL LB </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">12. Use  flow cytometer to measure the fluorescence  of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton,  Dickenson and Company).</td>
+
                   <td colspan="2" class="info-18">          4) 2.7 mL filtrate of Db +300 microL LB</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2" class="info-18">          5) 3 mL LB + 5 microM C12HSL 3 microL (Final concentration is 5 nM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="head"><p>3-2-2. C4HSL-depemdent CmR expression</p></td>
+
                   <td colspan="2" class="info-18">          6) 3 mL LB + DMSO 3 microL </td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td class="info-18">1. Grow the colony of sender cell in LB containing  antibiotic O/N at 37°C.</td>
+
                   <td colspan="2" class="info-18">4. Grow the samples of Reporter cell in incubator at 37°C for 4 h.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containig  antibiotic and grow the cells at 37°C until the observed OD590 reaches  0.5 (fresh culture).</td>
+
                   <td colspan="2" class="info-18">5. Start preparing the flow cytometer 1 h before the end of incubation.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">3. Centrifuge  1mL of the sample at 5000g, RT for 1 minute.</td>
+
                   <td colspan="2" class="info-18">6. After the incubation, take the sample, and centrifuge at 9000x g, 1 min., 4°C.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">4. Suspend the pellet in <u>1 mL of LB containing  Ampicillin(50 microg/mL)and Kanamycin(30 microg/mL)</u></td>
+
                   <td colspan="2" class="info-18">7. Remove the supernatant by using P1000 pipette.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">5. Add 30&#181;L of suspension in the following medium.</td>
+
                   <td colspan="2" class="info-18">8. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is  0.3.)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">         Add 3&#181;L of 5&#181;M C12HSL to 3mL LB containing Amp, Kan(concentration is described upper) and Cm(100 microg /mL).</td>
+
                   <td colspan="2" class="info-18">9. Dispense all of each suspension into a disposable tube through a cell strainer.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">         Add 3microL DMSO to 3mL of LB containing Amp and Kan.</td>
+
                   <td colspan="2" class="info-18">10. Use  flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton,  Dickenson and Company.)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">6. Grow  the samples of sender cell at 37°C for 4 hours.</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">7. Measure optical density every hour.  (If optical density is over 1.0, dilute the  cell medium.)</td>
+
                   <td colspan="2" class="entry-long">&nbsp;<a name="5" id="5"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><h2>4. Reference</h2></td>
+
                   <td colspan="2"><h2>5. Reference</h2></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td colspan="2" class="info-18">1. Bo Hu <em>et al.</em> (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5):  e10619</td>
                 </tr>
                 </tr>
               </table>
               </table>
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Latest revision as of 03:36, 18 October 2014

Tokyo_Tech

Experiment

C4HSL-dependent 3OC12HSL production

 

Contents

1. Introduction

2. Summary of the Experiments

2.1 C4HSL-dependent CmR expression

2.2 C4HSL-dependent 3OC12HSL production

3. Results

3.1. C4HSL-Dependent CmR Expression Assay

3.2. C4HSL-Dependent 3OC12HSL Production Assay

4. Materials and Methods

4.1. Construction

4.2. Assay Protocol

4.2.1. C4HSL-Dependent CmR Expression Assay

4.2.2. C4HSL-Dependent 3OC12HSL Production Assay

5. Reference

 
 
 

1. Introduction

We designed signal-dependent signal production in our system by using signaling molecules and antibiotics resistance gene. In our bank story, we used signaling molecule C4HSL as money.

For construction of the C4HSL-dependent chloramphenicol resistance gene product(CmR) and 3OC12HSL production module, we constructed a new part Prhl(RL)-CmR-LasI(BBa_K1529302). Prhl(RL)-CmR-LasI cell is an engineered E. coli that contains a C4HSL-dependent LasI generator and a constitutive RhlR generator. As a constitutive RhlR generator, we used Ptet-RhlR. In our bank story, this part imitates the functions of Company. (Fig. 3-3-1-1) We confirmed the C4HSL-dependent growth by measuring optical density, and C4HSL-dependent 3OC12HSL production by using reporter cell.

 
Fig. 3-3-1-1. Genetic Circuit of Company E. coli
 
 
 
 

2. Summary of the experiments

2-1. C4HSL-dependent CmR expression

 
Fig. 3-3-2-1. Flow chart of C4HSL-dependent CmR expression assay
 

We confirmed the function of C4HSL-dependent CmR expression by measuring optical density of the cultures containing chloramphenicol(Fig. 3-3-2-1).

In this experiment we prepared three plasmids, A, B and C. (See Fig. 3-3-2-2) Right after the C4HSL induction, we added chloramphenicol into the medium containing Company cell. We measured the optical density for about eight hours to estimate the concentration of the cell.

 
Fig. 3-3-2-2. Plasmids for the experiment of C4HSL-dependent CmR expression
 

2-2. C4HSL-dependent 3OC12HSL production

 

We performed a reporter assay by using reporter cells to characterize the function of C4HSL-dependent C4HSL production. Prhl(RL)-CmR-LasI cell containing constitutive RhlR generator expresses LasI and produces 3OC12HSL in the presence of C4HSL. Since 3OC12HSL is excreted to the culture, the supernatant of the sender cell contains 3OC12HSL when the part works as expected.

Reporter cells are incubated in the supernatant of the culture of sender cells. When there are 3OC12HSL in the supernatant, reporter cell expresses GFP. We checked the fluorescence of reporter cells to confirm the expression of 3OC12HSL. The expression of the reporter cells were measured by flow cytometer.(See Fig.3-3-2-3)

 
Fig. 3-3-2-3. Flow chart of C4HSL-dependent 3OC12HSL production Assay
Fig. 3-3-2-4.Plasmids for the experiment of C4HSL-dependent 3OC12HSL production

We prepared the following conditions for the induction of reporter cells. (Plux-CmR cell was used as the negative control. See Fig. 3-3-2-4)

(1) Culture containing Prhl(RL)-CmR-lasI cell with C4HSL induction

(2) Culture containing Prhl(RL)-CmR-lasI cell without induction

(3) Culture containing Plux-CmR cell with C4HSL induction

(4) Culture containing Plux-CmR cell without induction

(5) 5 microM of synthetic C4HSL in LB medium

(6) DMSO in LB medium

 

Reporter

E) The cell containing constitutive LasR generator and Plas-GFP cell
F) The cell containing constitutive LuxR generator and PlacIq-GFP cell…Positive control
G) The cell containing constitutive LuxR generator and Promoter-less-GFP cell…Negative control
 
 
 

3. Result

 

3-1. C4HSL-dependent CmR expression assay

We tested two types of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)

Fig.3-3-3-1, Fig.3-3-3-2 shows the condition in the absence and presence of chloramphenicol, respectively.

Fig 3-3-3-1. shows that every cell can grow in the absence of chloramphenicol.

 
Fig. 3-3-3-1. C4HSL-Dependent Company growth with no Cm addition
 
Fig. 3-3-3-2. C4HSL-Dependent Company Growth in 100 microg/mL Cm
 

On the other hand, in the presence of chloramphenicol, the cell containing Prhl(RL)-CmR-LasI can grow only when induced by C4HSL. Without the induction of C4HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Prhl(RL)-CmR-LasI expressed CmR when induced by C4HSL as expected.

 

3-2. C4HSL-dependent 3OC12HSL Production Assay

Fig. 3-3-3-3 shows the fluorescence intensities generated by the reporter cells. When the reporter cell E was incubated in the condition (1) (the culture of the induced Company cell), the fluorescence intensity of the reporter cell increased. Comparing the results of condition (1) and (2) reporter cell in the supernatant of (1) had 29-fold higher fluorescence intensity.

 

This result indicates that Company cell produced 3OC12HSL in response to C4HSL induction by the function of Prhl(RL)-CmR-LasI.

 

From this experiment, we confirmed that a new part Prhl(RL)-CmR-LasI synthesized 3OC12HSL (LasI) as expected.

Fig. 3-3-3-3. Company excretes 3OC12HSL when C4HSL exists
 
 
 
 

4. Materials and methods

 

4-1 Construction

-Strain

All the samples were JM2.300 strain.

-Plasmids

--C4HSL-dependent CmR expression

 
A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI(pSB3K3)
 
Fig. 3-3-4-1.
 
B. Ptet-GFP-Ptet-RhlR (pSB6A1), PlacIq-CmR (pSB3K3)…Positive control
 
Fig. 3-3-4-2.
 
C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR (pSB3K3)… Negative control
 
Fig. 3-3-4-3.
--C4HSL-dependent 3OC12HSL production
 
 
Sender
A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI (pSB3K3)
 
Fig. 3-3-4-4.
 
D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)
 
Fig. 3-3-4-5.
 
Reporter
 
E. Ptrc-LasR (pSB6A1), Plas-GFP (pSB3K3)
 
Fig. 3-3-4-6.
 
F. Ptet-LuxR (pSB6A1), PlacIq-GFP (pSB3K3)...Positive control
 
Fig. 3-3-4-7.
 
G. Ptet-LuxR (pSB6A1), Promoter-less-GFP (pSB3K3)...Negative control
 
Fig. 3-3-4-8.
 

4-2. Assay Protocol

4-2-1. C4HSL-Dependent CmR Expression Assay

1. Prepare overnight cultures for the sender cells in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C
          until the observed OD590 reaches 0.5.(→fresh culture)
3. Add 30 microL of suspension in the following medium.
          1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 5 microM)
          2) 3 mL of LB containing Amp and Kan + 30 microL DMSO
          3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100 microg/mL)
                   + 30 microL C4HSL (final concentration is 500 microM)
          4) 3 mL of LB containing Amp, Kan and Cm (final concentration of Cm is 100 microg/mL) + 30 microL DMSO
4. Grow the samples of sender cells at 37°C for more than 8 hours.
5. Measure optical density every hour. (If the optical density is over 1.0, dilute the cell medium to 1/10.)
 

4-2-2. C4HSL-Dependent 3OC12HSL Production Assay

Prepare the supernatant of the sender cell
1. Prepare overnight cultures for the sender cells in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C until the observed OD590 reaches 0.5.
3. Add 30 microL of the culture containing the cells in the following medium.
          a) Add 15 microL of 10 mM C4HSL to 3 mL LB containing Amp and Kan (final concentration is 50 microM)
          b) Add 15 microL DMSO to 3 mL of LB containing Amp+Kan
4. Grow the samples of sender cell at 37°C for 8 hours.
5. Measure the optical density every hour. (If the optical density is over 1.0, dilute the cell medium to 1/10.)
6. Centrifuge the sample at 9000x g, 4°C for 1 min. Filter sterilize the supernatant. (Pore size is 0.22 microm.)
7. Use the supernatant in reporter assay.
 
Reporter Assay
1. Prepare overnight cultures for the Reporter cell (E~G) in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB + antibiotic and grow the cells at 37°C until you reach an 0.5 in OD590 (fresh culture).
3. Add 30 microL of suspension in the following medium.
          1) 2.7 mL filtrate of Aa +300 microL LB
          2) 2.7 mL filtrate of Ab +300 microL LB
          3) 2.7 mL filtrate of Da +300 microL LB
          4) 2.7 mL filtrate of Db +300 microL LB
          5) 3 mL LB + 5 microM C12HSL 3 microL (Final concentration is 5 nM)
          6) 3 mL LB + DMSO 3 microL
4. Grow the samples of Reporter cell in incubator at 37°C for 4 h.
5. Start preparing the flow cytometer 1 h before the end of incubation.
6. After the incubation, take the sample, and centrifuge at 9000x g, 1 min., 4°C.
7. Remove the supernatant by using P1000 pipette.
8. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3.)
9. Dispense all of each suspension into a disposable tube through a cell strainer.
10. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)
 
 
 

5. Reference

1. Bo Hu et al. (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619