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>
         
         
  </ul>
  </ul>
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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 align="center"><span class="title-small">Content</span></p>
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               <p align="center"><span class="title-small">Contents</span></p>
                 <p align="left" class="info-24"><a href="#1">1. Introduction </a></p>    
                 <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-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>
                       <p align="left" class="info-24"><a href="#3">3. Results </a></p>
                       <p align="left" class="info-24"><a href="#3">3. Results </a></p>
                       <p align="left" class="info-18"><a href="#3.1">3.1. C4HSL-Dependent  CmR Expression Assay</a></p>
                       <p align="left" class="info-18"><a href="#3.1">3.1. C4HSL-Dependent  CmR Expression Assay</a></p>
                       <p align="left" class="info-18"><a href="#3.2">3.2. C4HSL-Dependent 3OC12HSL  Production Assay</a></p>
                       <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-24"><a href="#4">4. Materials and Methods</a></p>
  <p align="left" class="info-18"><a href="#4.1">4.1. Construction</a></p>
  <p align="left" class="info-18"><a href="#4.1">4.1. Construction</a></p>
  <p align="left" class="info-18"><a href="#4.2">4.2. Assay Protocol </a></p>
  <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="#3.2.4">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="#4.2.1">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="#3.2.4">4.2.2. C4HSL-Dependent 3OC12HSL Production 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>
              <p align="left" class="info-24"><a href="#5">5. Reference</a></p>
              <p align="left" class="info-24"><a href="#5">5. Reference</a></p>
                       <div class="title" style="clear: both;">&nbsp;</div>
                       <div class="title" style="clear: both;">&nbsp;</div>
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                   <td colspan="2"><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. In our bank story, we used signaling molecules C4HSL as money. For construction of the  C4HSL-dependent chloramphenicol resistance (CmR) and 3OC12HSL production  module, we designed 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 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 is Company. (Fig. 3-3-1-1.)</p>                  </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 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 colspan="2"><div align="center">Fig. 3-3-1-1 Company’s Genetic Circuit</div></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 colspan="2"><p class="info-18">In order to  confirm Company’s dependency on C4HSL, we measured the growth of Company cell and  expression of 3OC12HSL in the presence and absence of C4HSL. </p></td>
 
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                  <td><div align="center">Fig. 3-3-1-2. C4HSL-depemdent CmR expression Assay  Flow Chart</div></td>
 
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                  <td><div align="center">Fig. 3-3-1-3. C4HSL-dependent 3OC12HSL <br />
 
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                  production Assay  Flow Chart</div></td>
 
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                   <td colspan="2"><p class="info-18">To  confirm function of Company cell, we performed two kinds of assays. One is C4HSL-Dependent  CmR Expression Assay. In this experiment we prepared four plasmid sets (A, B, C, D) shown  in below. (Fig. 3-3-2-1.) Concurrently with C4HSL  induction, we added chloramphenicol into the medium containing Company cell and  measured optical density for about 8 h to estimate  the concentration of the cell. The other is C4HSL-Dependent 3OC12HSL Production  Assay. In this experiment we prepared three more plasmid sets (E, F, G) shown  in below. (Fig. 3-3-2-1.) First, we  added C4HSL to the culture of sender cell, and induced the expression of LasI. Then,  the supernatants of the culture were used as the  inducer in the reporter assay. We measured the  expression of GFP in reporter cells by flow cytometer.</p>                   </td>
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                   <td colspan="2"><h1>2-1. C4HSL-dependent CmR expression</h1></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 colspan="2"><div align="center">Fig.3-3-2-1. Constructed plasmids</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 colspan="2"><p class="info-18">We prepared four conditions as  follow.</p></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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      <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 colspan="2" class="info-18">A-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Prhl(RL)-CmR-LasI(pSB3K3) cell with C4HSL induction</td>
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                   <td colspan="2" class="info-18">A-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Prhl(RL)-CmR-LasI(pSB3K3) cell with DMSO (no induction)</td>
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                   <td colspan="2"><h1>2-2. C4HSL-dependent 3OC12HSL production</h1></td>
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                  <td colspan="2" class="info-18">B-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and PlacIq-CmR(pSB3K3) cell with C4HSL induction (C4HSL-Dependent CmR Expression  Assay Positive control)</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" class="info-18">B-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and PlacIq-CmR (pSB3K3) cell with DMSO (no induction) (C4HSL-Dependent CmR Expression  Assay Positive control)</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 colspan="2" class="info-18">C-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Promoter-less-CmR(pSB3K3) cell with C4HSL induction (C4HSL-Dependent CmR Expression  Assay Negative control)</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 colspan="2" class="info-18">C-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Promoter-less-CmR (pSB3K3) cell with DMSO (no induction) (C4HSL-Dependent CmR Expression  Assay Negative control)</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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<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" class="info-18">D-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Plux-CmR(pSB3K3) cell with C4HSL induction (C4HSL-Dependent 3OC12HSL Production  Assay Negative control)</td>
+
                   <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>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">D-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1) and Plux-CmR(pSB3K3) cell with DMSO (no induction) (C4HSL-Dependent 3OC12HSL Production  Assay Negative control)</td>
+
                   <td colspan="2"><p class="info-18">(1) Culture containing Prhl(RL)-CmR-lasI cell with C4HSL induction</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">(2) Culture containing Prhl(RL)-CmR-lasI cell without induction</p></td>
 +
                </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">(3) Culture containing Plux-CmR cell with C4HSL induction</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="head">Reporter:</td>
+
                   <td colspan="2"><p class="info-18">(4) Culture containing Plux-CmR cell without induction</p></td>
                 </tr>
                 </tr>
-
                 <tr>
+
                  <tr>
 +
                  <td colspan="2"><p class="info-18">(5) 5 microM of synthetic C4HSL in LB medium </p></td>
 +
                 </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">(6) DMSO in LB medium</p></td>
 +
                </tr>
 +
                  <tr>
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">E) Culture containing Ptet-RhlR(pSB6A1) and Prhl(RL)-GFP(pSB3K3)  cell </td>
+
                   <td colspan="2"><p class="info-18">Reporter</p></td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2" class="info-18">E) The cell containing constitutive LasR generator and Plas-GFP cell</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">F) Culture containing Ptet-RhlR(pSB6A1) and PlacIq-GFP(pSB3K3)  cell </td>
+
                   <td colspan="2" class="info-18">F) The cell containing constitutive LuxR generator and PlacIq-GFP cell…Positive control</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                  <td colspan="2">&nbsp;</td>
+
                   <td colspan="2" class="info-18">G) The cell containing constitutive LuxR generator and Promoter-less-GFP cell…Negative control </td>
-
                </tr>
+
-
                <tr>
+
-
                   <td colspan="2" class="info-18">G) Culture containing Ptet-RhlR(pSB6A1) and Promoter-less-GFP(pSB3K3)  cell </td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h1>3-1. C4HSL-Dependent CmR Expression Assay</h1></td>
+
                   <td colspan="2"><h1>3-1. C4HSL-dependent CmR expression assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">After  induction, optical densities were measured to estimate the concentration of the  cell. We prepared two types of culture conditions which is different in concentration of chloramphenicol. (Without chloramphenicol and 100 microg/ml) </p></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>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <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>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-3-1. C4HSL-Dependent Company Growth in no Cm</div></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-3-1.</strong> C4HSL-Dependent Company growth with no Cm addition</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 245: Line 269:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></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 colspan="2"><div align="center">Fig. 3-3-3-2. C4HSL-Dependent Company Growth in 100  microg/mL Cm</div></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>
Line 254: Line 278:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">Fig.3-3-3-1.  shows every cell can grow in the absence of chloramphenicol. Conversely, Fig.3-3-3-2.  shows some cells cannot grow in presence of chloramphenicol. With induction of  C4HSL, the cell containing Prhl(RL)-CmR-LuxI can grow in the presence of  chloramphenicol. (The growth curve of the cell is same as the growth curve of  positive control.) However, without induction of C4HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. (The growth curve of  the cell is same as the growth curve of negative control.) As a result, only  with induction of C4HSL, Prhl(RL)-CmR-LuxI (<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>) cell can  express CmR and grow well.</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>
Line 260: Line 284:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h1>3-2. C4HSL-Dependent 3OC12HSL Production Assay</h1></td>
+
                   <td colspan="2"><h1>3-2. C4HSL-dependent 3OC12HSL Production Assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">Four hours after addition of the supernatants from  the culture of sender cells, we measured the expression of GFP in the reporter cells by flow cytometer.</p></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>
Line 269: Line 293:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></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 colspan="2"><div align="center">Fig.  3-3-3-3. C4HSL-Dependent 3OC12HSL Production Assay result</div></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</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 colspan="2"><p class="info-18">As Fig. 3-3-3-3. shows, when the supernatant of condition ??? was  used, the fluorescence intensity of the reporter cell increased. Comparing the  results of condition ??? and ???, reporter cell in the supernatant of induced  Company cell culture had the ???-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.</p></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 colspan="2"><p class="info-18">From these experiments, we confirmed that a new part  Prhl(RL)-CmR-LasI (<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>)  synthesized CmR and 3OC12HSL in the presence of C4HSL.</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>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
               
                 <tr>
                 <tr>
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
Line 309: Line 337:
                 <tr>
                 <tr>
                   <td colspan="2"><p class="head">-Plasmids</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>
 +
                  <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Sender:</strong></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>
Line 317: Line 351:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><div align="left">A. Ptet-GFP-Ptet-RhlR (psB6A1),  Prhl(RL)-CmR-lasI(pSB3K3)</div></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>
 +
                  <td colspan="2"><div align="center"><strong>Fig. 3-3-4-1.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 323: Line 360:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></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 colspan="2"><div align="center">Fig. 3-3-4-1.</div></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>
                 <tr>
                 <tr>
Line 332: Line 375:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">B. Ptet-GFP-Ptet-RhlR (psB6A1), PlacIq-CmR (pSB3K3) (C4HSL-Dependent  CmR Expression Assay Positive control)</td>
+
                   <td colspan="2" class="info-18">C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR (pSB3K3)… Negative control</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 338: Line 381:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <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>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-4-2.</div></td>
+
                   <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>
                 <tr>
                 <tr>
Line 347: Line 396:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR  (pSB3K3) (C4HSL-Dependent  CmR Expression Assay Negative control)</td>
+
                   <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>
                 <tr>
                 <tr>
Line 353: Line 405:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></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 colspan="2"><div align="center">Fig. 3-3-4-3.</div></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-4-4.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)  (C4HSL-Dependent 3OC12HSL Production Assay Negative control)</td>
+
                   <td colspan="2" class="info-18">D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)  </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <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>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-4-4.</div></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-4-5.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
-
                <tr>
+
                <tr>
-
                   <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Reporter:</strong></td>
+
                   <td colspan="2" class="info-18">Reporter</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 383: Line 435:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">E. Ptet-luxR (pSB6A1), Plux-GFP (pSB3K3) </td>
+
                   <td colspan="2" class="info-18">E. Ptrc-LasR (pSB6A1), Plas-GFP (pSB3K3) </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 389: Line 441:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <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>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-4-5.</div></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-4-6.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">F. Ptet-LuxR (pSB6A1), PlacIq-GFP (pSB3K3) (Positive  control)</td>
+
                   <td colspan="2" class="info-18">F. Ptet-LuxR (pSB6A1), PlacIq-GFP (pSB3K3)...Positive  control</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 404: Line 456:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <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>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-4-6.</div></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-4-7.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 413: Line 465:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">G. Ptet-LuxR (pSB6A1), Promoter-less-GFP (pSB3K3) (Negative  control)</td>
+
                   <td colspan="2" class="info-18">G. Ptet-LuxR (pSB6A1), Promoter-less-GFP (pSB3K3)...Negative  control</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 419: Line 471:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <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>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-4-7.</div></td>
+
                   <td colspan="2"><div align="center"><strong>Fig. 3-3-4-8.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 428: Line 480:
                 </tr>                 
                 </tr>                 
                 <tr>
                 <tr>
-
                   <td colspan="2"><h1>4-2. Assay Protocol </h1><<a name="4.2.1" id="4.2.1">/td>
+
                   <td colspan="2"><h1>4-2. Assay Protocol </h1><a name="4.2.1" id="4.2.1"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 435: Line 487:
                  
                  
                 <tr>
                 <tr>
-
                   <td colspan="2" 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">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 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 />
                   <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. If the OD becomes over 0.5, dilute to 0.5 with LB  medium.</td>
+
          until the observed OD590 reaches 0.5.(→fresh culture) </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 445: Line 497:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          1) 3 mL  of LB containing Amp and Kan + 3 microL C4HSL (5 microM)</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 colspan="2" class="info-18">          2) 3 mL  of LB containing Amp and Kan + 3 microL DMSO</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 colspan="2" class="info-18">          3) 3 mL  of LB containing Amp, Kan and Cm (final concentration is 100 microg/mL) <br />
                   <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 (500 microM)</td>
+
                                                       + 30  microL C4HSL (final concentration is 500 microM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          4) 3 mL  of LB containing Amp, Kan and Cm (final concentration is 100 microg/mL) + 30  microL DMSO</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>
Line 462: Line 514:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">5. Measure optical density every hour. (If optical  density is over 1.0, dilute the cell medium to 1/10.)</td>
+
                   <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>
                 <tr>
                 <tr>
Line 472: Line 524:
                  
                  
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">1. Prepare  the supernatant of the sender cell</td>
+
                   <td colspan="2" class="info-18"> Prepare  the supernatant of the sender cell</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">2. Grow the colony of sender cell in LB containing antibiotic O/N at 37°C.</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 colspan="2" class="info-18">3. 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.If the OD becomes over 0.5, dilute to o.5 with LB 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 until the observed OD590  reaches 0.5.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">4. Add 30 microL 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 colspan="2" class="info-18">          1) Add 30 microL of 500 microM C4HSL to 3 mL 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 colspan="2" class="info-18">          2) Add 30 microL DMSO to 3 mL of LB containing Amp+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 colspan="2" class="info-18">5 .Grow the samples of sender cell at 37°C for 4 hours.</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 colspan="2" class="info-18">6. Measure optical density  every hour. (If optical density is over 1.0, dilute the cell medium to 1/10.)</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 colspan="2" class="info-18">7. Centrifuge sample at 9000x g, 4°C for 1minute.Filter sterilize supernatant.</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 colspan="2" class="info-18">8. Use  the supernatant in reporter assay.</td>
+
                   <td colspan="2" class="info-18">7. Use  the supernatant in reporter assay.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 508: Line 560:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">1. Grow the colony  of  Reporter cell (D~F) in LB containing antibiotic(Amp and Kan) over night at 37°C.</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 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>
+
                   <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>
Line 517: Line 569:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          1) Filtrate  of A①+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          1) 2.7 mL filtrate of Aa +300 microL LB </td>
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">          2) Filtrate  of A②+3mL of  LB containing Amp and Kan</td>
+
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">          3) Filtrate  of B①+3mL of LB containing Amp and Kan</td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          4) Filtrate  of B②+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          2) 2.7 mL filtrate of Ab +300 microL LB</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          5) Filtrate  of C①+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          3) 2.7 mL filtrate of Da +300 microL LB </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          6) Filtrate  of C②+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          4) 2.7 mL filtrate of Db +300 microL LB</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          7) C4HSL+3mL of LB containing Amp and Kan</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 colspan="2" class="info-18">          8) DMSO +  3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          6) 3 mL LB + DMSO 3 microL </td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">4. Grow  the samples of Reporter cell in incubator at 37°C for 4 hours.</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 colspan="2" class="info-18">5. Start preparing the flow cytometer 1 h before the end of incubation.</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 colspan="2" class="info-18">6. After incubation, take the sample, and centrifuge at 9000x g, 1 min, 4°C.</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 colspan="2" class="info-18">7. Remove the supernatant by using P1000 pipette.</td>
+
                   <td colspan="2" class="info-18">7. Remove the supernatant by using P1000 pipette.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <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>
+
                   <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>

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