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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> |
- | <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> | + | <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> |
| </li> | | </li> |
- | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling">Modeling</a></li> | + | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling">Modeling</a> |
| + | <ul> |
| + | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Overview" style="width:400px; margin-left:-135px;">Overview</a></li> |
| + | <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> |
| + | <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> |
| + | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Economic Wave" style="width:400px; margin-left:-135px;">Economic Wave</a></li> |
| + | </ul> |
| + | </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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| <div id="page"> | | <div id="page"> |
| <div id="content-over"> | | <div id="content-over"> |
- | <div class="post">
| + | <div class="post"> |
| <h2 class="title">Experiment</h2> | | <h2 class="title">Experiment</h2> |
| <span class="meta">3OC12HSL-dependent C4HSL production</span> | | <span class="meta">3OC12HSL-dependent C4HSL production</span> |
- | <div class="entry-long">
| + | <div class="entry-long"> |
| <p> </p> | | <p> </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> |
| + | |
| + | <p align="center"><span class="title-small">Contents</span></p> |
| + | <p align="left" class="info-24"><a href="#Introduction">1. Introduction </a></p> |
| + | <p align="left" class="info-24"><a href="#Summary">2. Summary of the Experiments</a></p> |
| + | <p align="left" class="info-18"><a href="#Summary">2-1. 3OC12HSL-dependent CmR expression</a></p> |
| + | <p align="left" class="info-18"><a href="#2.2">2-2. 3OC12HSL-dependent C4HSL production</a></p> |
| + | <p align="left" class="info-24"><a href="#Results">3. Results </a></p> |
| + | <p align="left" class="info-18"><a href="#Results">3.1. 3OC12HSL-dependent CmR expression</a></p> |
| + | <p align="left" class="info-18"><a href="#3.2">3.2. 3OC12HSL-dependent C4HSL production</a></p> |
| + | <p align="left" class="info-24"><a href="#Materials">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="#4.2">4.2. Assay Protocol </a></p> |
| + | <p align="left" class="info" style="text-indent:40px;"><a href="#4.2.1">4.2.1. 3OC12HSL-depemdent CmR expression</a></p> |
| + | <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="#Reference">5. Reference</a></p> |
| + | <div class="title" style="clear: both;"> </div> |
| <table width="900" border="0"> | | <table width="900" border="0"> |
| <tr> | | <tr> |
- | <td width="890"><div align="center" class="title-small">3OC12HSL-dependent C4HSL production module</div></td> | + | <td width="890" class="entry-long"><a name="Introduction" id="Introduction"></a></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td> </td> | | <td> </td> |
| + | </tr> |
| + | <tr> |
| + | <td><h2>1. Introduction</h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><h2>1. Summary of the experiment </h2></td> | + | <td><p class="info-18">We designed a signal-dependent signal production in our system by using signaling molecules and antibiotics resistance gene. In our bank story, we used signaling molecule 3OC12HSL as product.</p></td> |
| + | </tr> |
| + | <tr> |
| + | <td><p class="info-18">For construction of the 3OC12HSL-dependent chloramphenicol resistance gene product(CmR) and C4HSL production module, we constructed a new part Plux-CmR-RhlI (<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>). Plux-CmR-RhlI cell is an engineered <i>E. coli</i> that contains 3OC12HSL-dependent RhlI generator and a constitutive LuxR generator. As a constitutive LuxR generator, we used Ptet-LuxR. In our bank story, this part imitates the function of Customer. (Fig. 3-4-1-1) We confirmed the 3OC12HSL-dependent growth by measuring the optical density, and 3OC12HSL-dependent C4HSL production by using reporter cell.</p></td> |
| </tr> | | </tr> |
| + | |
| <tr> | | <tr> |
- | <td><p class="info-18">Construction of the 3OC12HSL-dependent C4HSL production and chloramphenicol resistance expression module</p> </td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <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> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-1-1.png"><img src="https://static.igem.org/mediawiki/2014/a/a6/Tokyo_Tech_3-4-1-1.png" width="513" height="228" /></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">For construction of the 3OC12HSL-dependent chloramphenicol resistance (CmR) and C4HSL production module, we constructed a new part Plux-CmR-rhlI (BBa_K1529265). Plux-CmR-RhlI cell is an engineered E.coli that contains a 3OC12HSL-dependent rhlI generator and a constitutive luxR generator. We constructed a new Biobrick part Plux-CmR-rhlI by combining Plux-CmR (BBa_K39562) and rhlI (BBa_). As a constitutive luxR generator, we used Pret-luxR (BBa_S0319). In our bank story, this part is customer.</p> </td> | + | <td><div align="center"><strong>Fig. 3-4-1-1. </strong>Genetic Circuit of Customer</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="head">1-1 3OC12HSL-dependent C4HSL production </p></td> | + | <td> </td> |
| </tr> | | </tr> |
| + | |
| <tr> | | <tr> |
- | <td><p class="info-18">First, we performed a reporter assay by using rhl reporter cell to characterize the function of 3OC12HSL-dependent C4HSL production. As the negative control of C4HSL production, we prepared C4HSL non-producer cell. C4HSL non-producer cell contains PlacIq-CmR instead of Plux-CmR-rhlI. The cell of negative control does not produce C4HSL even in the presence of 3C12HSL.</p></td> | + | <td> </td> |
| + | </tr> |
| + | <tr> |
| + | <td class="entry-long"><a name="Summary" id="Summary"></a></td> |
| + | </tr> |
| + | <tr> |
| + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">Sender</p></td> | + | <td><h2>2. Summary of the experiments</h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td> | + | <td><h1>2-1. 3OC12HSL-dependent CmR expression</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-1-2.png"><img src="https://static.igem.org/mediawiki/2014/1/16/Tokyo_Tech_3-4-1-2.png" width="500" /></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td> | + | <td><div align="center"> <strong>Fig. 3-4-2-1.</strong> 3OC12HSL-dependent CmR expression assay flow chart </div></td> |
| + | </tr><tr> |
| + | <td><p class="info-18">We confirmed the function of 3OC12HSL-dependent CmR expression by measuring the optical density of the cell cultures containing chloramphenicol.(Fig. 3-4-2-1) </p> |
| + | <p class="info-18"> In this experiment, we prepared two plasmids A and B (See Fig. 3-4-2-2).Right after the 3OC12HSL induction, we added chloramphenicol into the medium including Customer cell. We measured the optical density for about eight hours to estimate the concentration of the cell. </p> |
| + | </td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-2-1.png"><img src="https://static.igem.org/mediawiki/2014/6/65/Tokyo_Tech_3-4-2-1.png" width="500" height="184" /></a></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"><strong>Fig. 3-4-2-2.</strong> Plasmids for the experiment of 3OC12HSL-dependent CmR expression</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">Repoter</p></td> | + | <td><a name="2.2" id="2.2"></a></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| + | <td><h1>2-2. 3OC12HSL-dependent C4HSL production</h1></td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-1-3.png"><img src="https://static.igem.org/mediawiki/2014/b/b7/Tokyo_Tech_3-4-1-3.png" width="500" /></a></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"><strong>Fig. 3-4-2-3.</strong> 3OC12HSL-dependent C4HSL production assay flow chart</div></td> |
| + | </tr> |
| + | <tr> |
| <td> </td> | | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td> | + | <td><p class="info-18">We performed a reporter assay by using reporter cell C, D and E to characterize the function of 3OC12HSL-dependent C4HSL production. Plux-CmR-RhlI cell containing constitutive LuxR generator expresses RhlI and produces C4HSL (RhlI) in the presence of 3OC12HSL. Since C4HSL is excreted to the culture, the supernatant of the sender cell contains C4HSL when this part works as expected.</td> |
| + | </tr> |
| + | <tr> |
| + | <td><p class="info-18"> The reporter cell was incubated in the supernatant of the culture of the sender cell. When there are C4HSL in the supernatant, the reporter cell expresses GFP.(Fig. 3-4-2-3) We checked the fluorescence intensity of the reporter cell to confirm the production of C4HSL. The fluorescence intensity of the reporter cell was measured by flow cytometer.</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td> | + | <td class="info-18"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-2-2.png"><img src="https://static.igem.org/mediawiki/2014/8/8b/Tokyo_Tech_3-4-2-2.png" width="700"/></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><img src="http://sg.openrice.com/images/v4/previewimg/sr1-icon-noResult.png" alt="" width="600" /></div></td> | + | <td><div align="center"><strong>Fig. 3-4-2-4.</strong> Plasmids for the experiment of 3OC12HSL-dependent C4HSL production</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">We prepared four culture conditions as follow.</p></td> | + | <td><p class="info-18">We prepared the following conditions for the induction of the reporter cells. (PlacIq-CmR cell was used as the negative control of RhlI. See Fig.3-4-2-4)</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> A) Culture containing Plux-CmR-RhlI cell with 3OC12HSL induction</td> | + | <td class="info-18"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> B) Culture containing Plux-CmR-RhlI cell without 3OC12HSL induction</td> | + | <td class="info-18">(1) Culture containing sender A (Plux-CmR-RhlI) with 3OC12HSL induction</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> C) Culture containing Plux-CmR cell with 3OC12HSL induction</td> | + | <td class="info-18">(2) Culture containing sender A (Plux-CmR-RhlI) without induction |
| + | </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> D) Culture containing Plux-CmR cell without 3OC12HSL induction</td> | + | <td class="info-18">(3) Culture containing sender B (PlacIq-CmR) with 3OC12HSL induction </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 class="info-18">(4) Culture containing sender B (PlacIq-CmR) without induction </td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">(5)5 microM of synthetic C4HSL in LB medium </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| + | <td class="info-18">(6) DMSO in LB medium </td> |
| + | </tr> |
| + | <tr> |
| <td> </td> | | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">In the reporter assay, we used a Rhl reporter strain that contains Ptet-rhlR 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><p class="info-18">Reporter cells</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td> </td> | + | <td class="info-18"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">C. The cell containing constitutive RhlR generator and Prhl(RL)-GFP</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="head">1-2 3OC12HSL-dependent growth</p></td> | + | <td class="info-18">D. The cell containing constitutive RhlR generator and PlacUV5-GFP…Positive control</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">The cell which contains Plux-CmR-rhlI can grow in the medium even containing chloramphenicol .( Chloramphenicol is one of the antibiotics. ) | + | <td class="info-18">E. The cell containing constitutive RhlR generator and Promoter-less-GFP…Negative control</td> |
- | </p> </td>
| + | |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">After induction, we added chloramphenicol into the medium and measured optical density hourly after induction. </p></td> | + | <td> </td> |
| </tr> | | </tr> |
| + | <tr> |
| + | <td class="entry-long"><a name="Results" id="Results"></a></td> |
| + | </tr> |
| <tr> | | <tr> |
| <td> </td> | | <td> </td> |
| + | </tr> |
| + | <tr> |
| + | <td><h2>3. Results</h2></td> |
| + | </tr> |
| + | <tr> |
| + | <td> <a name="3.1" id="3.1"></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><h2>2. Results</h2></td> | + | <td><h1>3-1. 3OC12HSL-dependent CmR expression assay</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="head">2-1 3OC12HSL-dependent C4HSL production</p></td> | + | <td><p class="info-18">We tested two types of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)</p> |
| + | <p class="info-18">Fig. 3-4-3-1 and Fig. 3-4-3-2 show the condition in the absence and the presence of chloramphenicol, respectively.</p> |
| + | <p class="info-18">Fig. 3-4-3-1 shows that every cell can grow in the absence of chloramphenicol.</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">We measured GFP expression in the reporter cell by flow cytometer</p></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-3-1.png"><img src="https://static.igem.org/mediawiki/2014/f/f1/Tokyo_Tech_3-4-3-1.png" width="700" /></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="head">2-2 3OC12HSL-dependent growt</p> </td> | + | <td><div align="center"><strong>Fig. 3-4-3-1.</strong> 3OC12HSL-dependent customer growth in no chloramphenicol</div></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><div align="center"></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-1-1.png"><img src="https://static.igem.org/mediawiki/2014/6/62/Tokyo_Tech_3-1-1.png" alt="" width="450" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-3-2.png"><img src="https://static.igem.org/mediawiki/2014/5/5d/Tokyo_Tech_3-4-3-2.png" width="700" /></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center">Fig. 3-2-1 </div></td> | + | <td><div align="center"><strong>Fig. 3-4-3-2.</strong> 3OC12HSL-dependent Customer growth in 100 microg / mL chloramphenicol</div></td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td><p class="info-18">On the other hand, in the presence of chloramphenicol, the cell containing Plux-CmR-RhlI can grow only when it was induced by 3OC12HSL. Without the induction of 3OC12HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Plux-CmR-RhlI expressed CmR when induced by 3OC12HSL as expected.</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-1-2.png"><img src="https://static.igem.org/mediawiki/2014/b/be/Tokyo_Tech_3-1-2.png" alt="" width="450" /></a></div></td> | + | <td><a name="3.2" id="3.2"></a> <a name="3.2" id="3.2"></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center">Fig. 3-2-2 </div></td> | + | <td><h1>3-2. 3OC12HSL-dependent C4HSL production assay</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">As Fig 3-2-1 shows, the cell containing Plux-CmR-RhlI can grow with induction of 3OC12SL, but can’t without induction. Plux-CmR-RhlI cell grows more slowly than the positive control. The amount of CmR is lower than the positive control, Compared Fig 3-2-1 to Fig 3-2-2, With Cm, the cell grow more slowly than without Cm. geExpression of CmR in Plux-CmR-RhlI depende on induction by adding 2OC12HSL. </p> </td> | + | <td><p class="info-18">Fig. 3-4-3-3 shows the fluorescence intensities generated by reporter cells. When the reporter cell C (Plux-CmR-RhlI) was incubated in the condition (1) (the culture of the induced Customer 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 95-fold higher fluorescence intensity.</p> |
| + | <p class="info-18">This result indicates that Customer cell produced C4HSL in response to 3OC12HSL induction by the function of Plux-CmR-RhlI.</p> |
| + | <p class="info-18">From this experiment, we confirmed that a new part Plux-CmR-RhlI synthesized C4HSL (RhlI) as expected.</p></td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-3-3.png"><img src="https://static.igem.org/mediawiki/2014/d/d6/Tokyo_Tech_3-4-3-3.png" width="500" height="320" /></a></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td><div align="center"><strong>Fig. 3-4-3-3.</strong> Customer excretes C4HSL when C12HSL exists</div></td> |
| + | </tr> |
| + | <tr> |
| + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 212: |
Line 308: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><h2>3. Materials and methods</h2></td> | + | <td class="entry-long"> <a name="Materials" id="Materials"></a></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 218: |
Line 314: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="head">3-1 Construction</p></td> | + | <td><h2>4. Materials and methods</h2></td> |
| + | </tr> |
| + | <tr> |
| + | <td> <a name="4.1" id="4.1"></td> |
| + | </tr> |
| + | <tr> |
| + | <td><h1>4-1 Construction</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 224: |
Line 326: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">All the samples were JM2.300 strain</p></td> | + | <td><p class="info-18">All the samples were JM2.300 strain.</p> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td><p class="head">-Plasmids</p></td> | | <td><p class="head">-Plasmids</p></td> |
| + | </tr> |
| + | <tr> |
| + | <td style="text-indent:0px;"><h3>3OC12HSL-dependent CmR expression</h3></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 233: |
Line 338: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="head">3-2 Protocol </p></td> | + | <td class="info-18"><div align="left">A.Ptet-LuxR-Plac-RFP(pSB6A1), Plux-CmR-RhlI(pSB3K3) </div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18" style="text-indent:0px;">3-2-1. 3OC12HSL-dependent C4HSL production assay by using reporter assay</p></td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18"><strong>Prepare the supernatant of the sender cell</strong></p></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-1.png"><img src="https://static.igem.org/mediawiki/2014/5/5f/Tokyo_Tech_3-4-4-1.png" width="500" /></a></div></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><div align="center"> <strong>Fig. 3-4-4-1. </strong></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 37°C <br /> | + | <td><div align="center"></div></td> |
- | until the observed OD590 reaches 0.5.</td>
| + | |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">3. Centrifuge 1mL of the sample at 5000g, RT for 1 minute.</td> | + | <td class="info-18">B. Ptet-GFP-Ptet-RhlR (pSB6A1), PlacIq-CmR (pSB3K3)...Positive control</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">4. Suspend the pellet in <u>1 mL of LB containing Ampicillin(50μg/mL)and Kanamycin (30μg/mL)</u></td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">5. Add 30µL of suspension in the following medium.</td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-2.png"><img src="https://static.igem.org/mediawiki/2014/7/74/Tokyo_Tech_3-4-4-2.png" width="500" /></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Add 3µL of 5µM C12HSL to 3mL LB containing Amp and Kan</td> | + | <td><div align="center"><strong>Fig. 3-4-4-2.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Add 3µL DMSO to 3 µM of LB containing Amp and Kan</td> | + | <td> </td> |
| </tr> | | </tr> |
- |
| |
| <tr> | | <tr> |
- | <td class="info-18">6. Grow the samples of sender cell at 37°C for 4 hours.</td> | + | <td><h3>3OC12HSL-dependent C4HSL production</h3></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> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">8. Centrifuge sample at 9000g, 4°C for 1minute.Filter sterilize supernatant.</td> | + | <td class="info-18" style="text-indent:0px;"><strong>Sender:</strong></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">9. Use the supernatant in reporter assay</td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> </td> | + | <td class="info-18">A. Ptet-LuxR-Plac-RFP(pSB6A1), Plux-CmR-RhlI(pSB3K3)</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18"><strong>Reporter Assay</strong></p></td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">1. Grow the colony of Reporter cell(D~F) in LB containing antibiotic O/N at 37°C.</td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-3.png"><img src="https://static.igem.org/mediawiki/2014/8/88/Tokyo_Tech_3-4-4-3.png" width="500" /></a></div></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 37C until you reach an 0.5 OD590.(fresh culture)</td> | + | <td><div align="center"><strong>Fig. 3-4-4-3.</strong></div></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> </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 class="info-18">B. Ptet-LuxR-Plac-RFP(pSB6A1), Plux-CmR(pSB3K3)...Negative control</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">5. Add 30µL of suspension in the following medium.</td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Filtrate of A①+3mL of LB containing Amp and Kan</td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-4.png"><img src="https://static.igem.org/mediawiki/2014/8/8b/Tokyo_Tech_3-4-4-4.png" width="500" /></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Filtrate of A②+3mL of LB containing Amp and Kan</td> | + | <td><div align="center"><strong>Fig. 3-4-4-4.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Filtrate of B①+3mL of LB containing Amp and Kan</td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Filtrate of B②+3mL of LB containing Amp and Kan</td> | + | <td class="info-18" style="text-indent:0px;"><strong>Reporter:</strong></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Filtrate of C①+3mL of LB containing Amp and Kan</td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Filtrate of C②+3mL of LB containing Amp and Kan</td> | + | <td class="info-18"><p align="left" class="info-18">C. Ptet-RhlR(pSB6A1), Plux-GFP(pSB3K3)</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> C4HSL+3mL of LB containing Amp and Kan</td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> DMSO + 3mL of LB containing Amp and Kan</td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-5.png"><img src="https://static.igem.org/mediawiki/2014/b/b7/Tokyo_Tech_3-4-4-5.png" width="500" /></a></div></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><div align="center"><strong>Fig. 3-4-4-5.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">7. Start preparing the flow cytometer 1 h before the end of incubation.</td> | + | <td> </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 class="info-18">D. Ptet-RhlR(pSB6A1), PlacUV5-GFP(pSB3K3)...Positive control</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">9. Remove the supernatant by using P1000 pipette.</td> | + | <td> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">10. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend.</td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-6.png"><img src="https://static.igem.org/mediawiki/2014/a/a8/Tokyo_Tech_3-4-4-6.png" width="500" /></a></div></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><div align="center"><strong>Fig. 3-4-4-6.</strong></div></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> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> </td> | + | <td class="info-18">E. Ptet-RhlR(pSB6A1), Promoter-less-GFP(pSB3K3)...Negative control</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="head"><p>3-2-2. 3OC12HSL-depemdent CmR expression</p></td> | + | <td> </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><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-7.png"><img src="https://static.igem.org/mediawiki/2014/b/b3/Tokyo_Tech_3-4-4-7.png" width="500" /></a></div></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><div align="center"><strong>Fig. 3-4-4-7.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">3. Centrifuge 1mL of the sample at 5000g, RT for 1 minute.</td> | + | <td> </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><a name="4.2" id="4.2"></a></td> |
| + | </tr> |
| + | <tr> |
| + | <td><h1>4-2. Assay Protocol </h1><a name="4.2.1" id="4.2.1"></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">5. Add 30µL of suspension in the following medium.</td> | + | <td><p class="info-18" style="text-indent:0px;"><strong>4-2-1. 3OC12HSL-depemdent CmR expression</strong></p></td> |
| </tr> | | </tr> |
| + | |
| <tr> | | <tr> |
- | <td class="info-18"> Add 3µL of 5µM C12HSL to 3mL LB containing Amp,Kan(concentration is described upper) and Cm(100 microg /mL)</td> | + | <td class="info-18">1.Prepare the overnight culture of cell A and B at 37°C.</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> Add 3µ DMSO to 3mL of LB containing Amp and Kan</td> | + | <td class="info-18">2.Make a 1:100 dilution in 3 mL of fresh LB containing antibiotics and grow the cell at 37°C until the observed OD590 reaches 0.5 (→fresh culture) </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">6. Grow the samples of sender cell at 37°C for 4 hours.</td> | + | <td class="info-18">3. Add 30 microL of suspension in the following medium.</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" style="text-indent:50px;">1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 500 microM)</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> </td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">2) 3 mL of LB containing Amp and Kan + 30 microL DMSO</td> |
| </tr> | | </tr> |
| + | |
| <tr> | | <tr> |
- | <td><h2>4. Reference</h2></td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100microg / mL) + 30 microL C4HSL (final concentration is 500 microM)</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">4) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100microg / mL) + 30 microL DMSO</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">4. Grow the samples of sender cells at 37°C for more than 10 hours. Measure optical density every hour. (If optical density is over 1.0, dilute the cell medium.)</td> |
| + | </tr> |
| + | <tr> |
| + | <td> <a name="4.2.2" id="4.2.2"></td> |
| + | </tr> |
| + | <tr> |
| + | <td><p class="info-18" style="text-indent:0px;"><strong>4-2-2. 3OC12HSL-dependent C4HSL production</strong></p></td> |
| + | </tr> |
| + | |
| + | <tr> |
| + | <td class="info-18">Prepare the supernatant of the sender cell</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">1. Grow the colony of sender cell in LB containing antibiotic O/N at 37°C.</td> |
| + | </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 37°C until the observed OD590 reaches 0.5.</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">3. Add 30 microL of the culture containing the cells in the following medium.</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">a) Add 30 microL of 500 microM 3OC12HSL to 3 mL LB containing Amp and Kan</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">b) Add 30 microL DMSO to 3 mL LB containing Amp and Kan</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">4 .Grow the samples of sender cell at 37°C for 8 hours.</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">5. Centrifuge sample at 9000x g, 4°C for 1minute. Filter sterilize supernatant. (Pore size is 0.22 microm. ) Use this supernatant in reporter assay.</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td class="info-18"> </td> | | <td class="info-18"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18" style="text-indent:0px;"><strong>Reporter Assay</strong></td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">1. Grow the colony of Reporter cell (described upper) in LB containing antibiotic (Amp and Kan) over night at 37°C.</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB+ antibiotics and grow the cells at 37°C until you reach an 0.5 in OD590 (fresh culture).</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">3. Add 30 microL of the culture containing reporter cell in the following medium.</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">1) 2.7 mL filtrate of Aa +300 microL LB</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">2) 2.7 mL filtrate of Ab +300 microL LB</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">3) 2.7 mL filtrate of Ba +300 microL LB</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">4) 2.7 mL filtrate of Bb +300 microL LB</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">5) 3 mL LB + 500 microM C4HSL 30 microM (final concentration is 5 microM)</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18" style="text-indent:50px;">6) 3 mL LB + DMSO 30 microL</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">4. Grow the samples of Reporter cell in incubator at 37°C for 4 hours.</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">5. Start preparing the flow cytometer 1 h before the end of incubation.</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">6. After incubation, take the sample, and centrifuge at 9000x g, 1 min, 4°C.</td> |
| + | </tr> |
| + | <tr> |
| + | <td class="info-18">7. Remove the supernatant by using P1000 pipette.</td> |
| + | </tr> |
| + | <tr> |
| + | <td 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> |
| + | <td class="info-18">9. Dispense all of each suspension into a disposable tube through a cell strainer.</td> |
| + | </tr> |
| + | <tr> |
| + | <td 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> |
| + | <td> </td> |
| + | </tr> |
| + | <tr> |
| + | <td> </td> |
| + | </tr> |
| + | <tr> |
| + | <td class="entry-long"><a name="Reference" id="Reference"></a></td> |
| + | </tr> |
| + | <tr> |
| + | <td> </td> |
| + | </tr> |
| + | <tr> |
| + | <td><h2>5. Reference</h2></td> |
| + | </tr> |
| + | <tr> |
| + | <td 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> |
| <p> </p> | | <p> </p> |
- | </div>
| + | </div> |
- | </div>
| + | </div> |
| </div> | | </div> |
| <!-- end #content --> | | <!-- end #content --> |