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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="#">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="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">Content</span></p> | + | <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> |
- | <p align="left" class="info-24"><a href="#2">2. Summary of the experiments </a></p> | + | <p align="left" class="info-24"><a href="#2">2. Summary of the Experiments </a></p> |
| + | <p align="left" class="info-18"><a href="#2.1">2.1 C4HSL-dependent CmR expression</a></p> |
| + | <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> |
- | <p align="left" class="info-24"><a href="#4">4. Materials and methods</a></p> | + | <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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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <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> | + | <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> |
| + | </tr> |
| + | <tr> |
| + | <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> |
| </tr> | | </tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center">Fig. 3-3-1-1 Company’s Genetic Circuit</div></td> | + | <td colspan="2"><div align="center"><strong>Fig. 3-3-1-1.</strong> Genetic Circuit of Company <i>E. coli</i></div></td> |
| </tr> | | </tr> |
| + | |
| <tr> | | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
- | </tr>
| |
- | <tr>
| |
- | <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>
| |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
- | </tr>
| |
- | <tr>
| |
- | <td colspan="2"> </td>
| |
- | </tr>
| |
- | <tr>
| |
- | <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/thumb/9/9a/Tokyo_Tech_3-3-1-2.png/742px-Tokyo_Tech_3-3-1-2.png" width="300" /></a></div></td>
| |
- | <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/thumb/4/45/Tokyo_Tech_3-3-1-3.png/800px-Tokyo_Tech_3-3-1-3.png" width="300" /></a></div></td>
| |
| </tr> | | </tr> |
| | | |
- | <tr>
| |
- | <td><div align="center">Fig. 3-3-1-2. C4HSL-depemdent CmR expression Assay Flow Chart</div></td>
| |
- | <td><div align="center">Fig. 3-3-1-3. C4HSL-dependent 3OC12HSL <br />
| |
- | production Assay Flow Chart</div></td>
| |
- | </tr>
| |
| <tr> | | <tr> |
| <td colspan="2" class="entry-long"> <a name="2" id="2"></td> | | <td colspan="2" class="entry-long"> <a name="2" id="2"></td> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <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> | + | <td colspan="2"><h1>2-1. C4HSL-dependent CmR expression</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
| </tr> | | </tr> |
- | <tr>
| + | <tr> |
- | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-2-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/5/5f/Tokyo_Tech_3-3-2-1.png/800px-Tokyo_Tech_3-3-2-1.png" width="500" /></a></div></td>
| + | <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> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center">Fig.3-3-2-1. Constructed plasmids</div></td> | + | <td><div align="center"><strong>Fig. 3-3-2-1.</strong> Flow chart of C4HSL-dependent CmR expression assay</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
- | </tr> | + | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p class="info-18">We prepared four conditions as follow.</p></td> | + | <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> |
| </tr> | | </tr> |
- | <tr> | + | <tr> |
| + | <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> |
| + | </p> </td> |
| + | </tr> |
| + | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
| </tr> | | </tr> |
- | <tr>
| + | <tr> |
- | <td colspan="2" class="head">Sender: </td>
| + | <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> |
| + | </tr> |
| + | <td><div align="center"><strong>Fig. 3-3-2-2.</strong> Plasmids for the experiment of C4HSL-dependent CmR expression</div></td> |
| </tr> | | </tr> |
- | <tr>
| |
- | <td colspan="2" class="info-18"> </td>
| |
| </tr> | | </tr> |
| + | <tr> |
| + | |
| <tr> | | <tr> |
- | <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> | + | <td colspan="2"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <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> | + | <td colspan="2"><h1>2-2. C4HSL-dependent 3OC12HSL production</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <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>
| + | <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> |
| </tr> | | </tr> |
- | <tr>
| + | <tr> |
- | <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> | + | <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> |
- | </tr> | + | </tr><tr> |
- | <tr>
| + | |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <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>
| + | <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> |
| </tr> | | </tr> |
- | <tr> | + | <tr> |
- | <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>
| + | <td><div align="center"><strong>Fig. 3-3-2-3. </strong>Flow chart of C4HSL-dependent 3OC12HSL production Assay </div></td> |
| + | </tr> |
| + | |
| + | <tr><td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-2-2.png"><img src="https://static.igem.org/mediawiki/2014/2/2f/Tokyo_Tech_3-3-2-2.png" width="700" /></a></div></td> |
| </tr> | | </tr> |
- | <tr>
| + | <td><div align="center"><strong>Fig. 3-3-2-4.</strong>Plasmids for the experiment of C4HSL-dependent 3OC12HSL production</div></td> |
- | <td colspan="2"> </td>
| + | |
| </tr> | | </tr> |
- | <tr>
| + | |
- | <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"> </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"> </td> | | <td colspan="2"> </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"> </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>
| + | |
- | <td colspan="2"> </td>
| + | |
| </tr> | | </tr> |
| + | |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18">G) Culture containing Ptet-RhlR(pSB6A1) and Promoter-less-GFP(pSB3K3) cell </td> | + | <td colspan="2" class="info-18">G) The cell containing constitutive LuxR generator and Promoter-less-GFP cell…Negative control </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">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> |
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| </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> |
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| </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> |
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| </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> |
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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"><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"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"> </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"> </td> |
| + | </tr> |
| + | |
| <tr> | | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
Line 313: |
Line 338: |
| <td colspan="2"><p class="head">-Plasmids</p></td> | | <td colspan="2"><p class="head">-Plasmids</p></td> |
| </tr> | | </tr> |
- | <tr>
| + | <tr> |
- | <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Sender:</strong></td> | + | <td colspan="2"><p class="info-18">--C4HSL-dependent CmR expression</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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Line 345: |
| </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" class="info-18"><div align="left">A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI(pSB3K3)</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 329: |
Line 354: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center">Fig. 3-3-4-1.</div></td> | + | <td colspan="2"><div align="center"><strong>Fig. 3-3-4-1.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 335: |
Line 360: |
| </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">B. Ptet-GFP-Ptet-RhlR (pSB6A1), PlacIq-CmR (pSB3K3)…Positive control</td> |
- | </tr> | + | </tr |
| <tr> | | <tr> |
| <td colspan="2"> </td> | | <td colspan="2"> </td> |
Line 344: |
Line 369: |
| </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. 3-3-4-2.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 350: |
Line 375: |
| </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">C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR (pSB3K3)… Negative control</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 359: |
Line 384: |
| </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. 3-3-4-3.</strong></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18">--C4HSL-dependent 3OC12HSL production</td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 365: |
Line 396: |
| </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">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 371: |
Line 405: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-4.png"><img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Tokyo_Tech_3-3-4-4.png/800px-Tokyo_Tech_3-3-4-4.png" width="500" /></a></div></td> | + | <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. 3-3-4-4.</div></td> | + | <td colspan="2"><div align="center"><strong>Fig. 3-3-4-4.</strong></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 380: |
Line 414: |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Reporter:</strong></td> | + | <td colspan="2" class="info-18">D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3) </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-4.png"><img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Tokyo_Tech_3-3-4-4.png/800px-Tokyo_Tech_3-3-4-4.png" width="500" /></a></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><strong>Fig. 3-3-4-5.</strong></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18">Reporter</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
Line 386: |
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 395: |
Line 444: |
| </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> |
Line 401: |
Line 450: |
| </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 410: |
Line 459: |
| </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 416: |
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 425: |
Line 474: |
| </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 438: |
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 448: |
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 465: |
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 475: |
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 511: |
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 520: |
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> |