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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 class="post"> | | <div class="post"> |
| <h2 class="title">Experiment</h2> | | <h2 class="title">Experiment</h2> |
- | <span class="meta">Symbiosis Confirmation ~Co-culture Assay~</span> | + | <span class="meta">Mutualism Confirmation ~Co-culture Assay~</span> |
| <div class="entry-long"> | | <div class="entry-long"> |
| <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> |
| | | |
| <div align="center"><p class="title-small">Contents</p></div> | | <div align="center"><p class="title-small">Contents</p></div> |
- | <p class="info-24"><a href="#1">1. Summary of the experiment</a></p>
| + | <p class="info-24"><a href="#1">1. Introduction</a></p> |
- | <p class="info-24"><a href="#2">2. Results</a></p> | + | <p class="info-24"><a href="#2">2. Summary of the Experiment</a></p> |
- | <p class="info-24"><a href="#3">3. Materials and methods</a></p> | + | <p class="info-24"><a href="#3">3. Results</a></p> |
- | <p class="info-18"><a href="#3.1">3-1. Construction</a></p> | + | <p class="info-24"><a href="#4">4. Discussion</a></p> |
- | <p class="info-18"><a href="#3.2">3-2 Assay Protocol</a></p> | + | <p class="info-24"><a href="#5">5. Materials and Methods</a></p> |
- | <p class="info-24"><a href="#4">4. Reference</a></p> | + | <p class="info-18"><a href="#5.1">5-1. Construction</a></p> |
| + | <p class="info-18"><a href="#5.2">5-2 Assay Protocol</a></p> |
| + | <p class="info-24"><a href="#6">6. Reference</a></p> |
| <p> </p> | | <p> </p> |
| <div class="entry-long"> </div> | | <div class="entry-long"> </div> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center" class="title-small">Symbiosis Confirmation ~Co-culture Assay~</div></td> | + | <td colspan="2"><div align="center" class="title-small">Mutualism Confirmation ~Co-culture Assay~</div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| | | |
| <tr> | | <tr> |
- | <td colspan="2"><h2>1. Summary of the experiment </h2></td> | + | <td colspan="2"><h2>1.Introduction </h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p class="info-18">To accomplish the symbiosis of the Company cells and Customer cells, we mixe and co-cultured the two cells.</p> | + | <td colspan="2"><p class="info-18">From the results so far, Company cell containing Prhl(RL)-CmR-LasI(<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>) expresses CmR and LasI in the presence of C4HSL. This enables Company to survive and to produce 3OC12HSL. (This result is showed <a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production">here</a>.) On the other hand, Customer cell containing Plux-CmR-RhlI(<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>) expresses CmR and RhlI in the presence of 3OC12HSL. This enables Customer to survive and to produce C4HSL. (This result is showed <a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production">here</a>.) These functions will make the mutualism of Company and Customer possible.</p></td> |
- | <p class="info-18">Company’s characteristics are C4HSL-Dependent Survival and 3OC12HSL Production (<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>), and Company’s characteristics are the opposite from Customer’s.(<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>) </p>
| + | |
- | <p class="info-18">(If you want to know about these cells in more detail, see <a href="https://2014.igem.org/Team:Tokyo_Tech/Project">the project page</a>. Each cells’ functions are confirmed.) </p>
| + | |
- | <p class="info-18">From these characteristics, the symbiosis between the two cells can be established. This experiment was focused on confirmation of the symbiosis and its condition. We constructed the Company cells containing GFP and Customer cells containing RFP. By checking the fluorescence intensity of GFP with flow cytometer, the symbiosis and its condition was detected. </p> </td>
| + | |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18"><div align="center"><img src="https://static.igem.org/mediawiki/2014/c/cf/Tokyo_Tech_Fig3-1-1.png" width="751" height="234" align="middle" /></div></td> | + | <td colspan="2" class="info-18"><div align="center"> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center"> Fig. 3-5-1-1. The genetic circuit of Company and Customer</div></td> | + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-1-1.png"><img src="https://static.igem.org/mediawiki/2014/e/ef/Tokyo_Tech_3-5-1-1.png" width="600" align="middle" /></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center"></div></td> | + | <td colspan="2"><div align="center"> <strong>Fig. 3-5-1-1.</strong> The genetic circuit of Company and Customer</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h2>2. Results</h2></td> | + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="entry-long"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p align="center" class="head"><img src="https://static.igem.org/mediawiki/2014/0/0b/Tokyo_Tech_Fig3-3-2.png" width="627" height="226" /></p></td> | + | <td colspan="2"><h2>2.Summary of the Experiment</h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p align="center">Fig. 3-5-2-1. The growth of the two cells when co-cultured</p></td> | + | <td colspan="2"><p class="info-18">To characterize the mutualism of Company cell and Customer cell, we cultivated both of them in different ratio and measured the growth. We constructed the Company cell containing GFP and the Customer cell containing RFP. After cultivating both of them for six hours in the same medium, we detected the mutualism by checking the fluorescence intensity of GFP with flow cytometer. We measured the optical density every hour during the culturing. </p></td> |
| + | </tr> |
| + | <tr></p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-2-1.png"><img src="https://static.igem.org/mediawiki/2014/3/39/Tokyo_Tech_3-5-2-1.png" width="750" align="middle" /></div></td></tr> |
| + | <tr><td colspan="2"><div align="center"><strong>Fig. 3-5-2-1. </strong>The flow chart of co-culture assay</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h2>3. Materials and methods</h2></td> | + | <td colspan="2" class="entry-long"> </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h1>3-1 Construction</h1></td> | + | <td colspan="2"><h2>3. Results</h2></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-3-1.png"><img src="https://static.igem.org/mediawiki/2014/b/b8/Tokyo_Tech_3-5-3-1.png" width="500" align="middle" /></div></td></tr> |
| + | <tr> |
| + | <td colspan="2"><p align="center"><strong>Fig. 3-5-3-1. </strong>The growth of the two cells when co-cultured</p> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Fig.3-5-3-1 shows the optical densities of Company and Customer after they were co-cultured for 6 hours. These values were evaluated below: </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">The optical density of Company cell = the optical density after co-culturing for 6 h x the ratio of the cells with the fluorescence of GFP. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">The optical density of Customer cell = the optical density after co-culturing for 6 h x the ratio of the cells without fluorescence of GFP. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">As a result, the co-cultured samples were able to grow better than the samples single cultured . It means that only Customer cell can grow little by little in the medium with 100 microg/mL Chloramphenicol because of the leak of Plux promoter (Company cell can’t grow since it contains Prhl promoter which has less leak.) However, in the co-culture experiment, Customer produced C4HSL by the leakage and it induced CmR and LasI expression of Company. LasI produced 3OC12HSL, and it induced CmR and RhlI expression of Customer. This positive feedback might cause the mutualism of Company and Customer. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><h2>4. Discussion</h2></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Before conducting this experiment, we checked whether the mutualism could be achieved by mathematical modeling (Go to <a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling/Growth_Conditions_For_Company_And_Customer">modeling page</a>.) This modeling results showed that the mutualism between the Company and Customer is significantly affected by the initial cell concentration. Therefore, we conducted this assay with the following conditions as preliminary experiment. The experimental results are shown below. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-5-4-1.png"><img src="https://static.igem.org/mediawiki/2014/1/14/Tokyo_Tech_3-5-4-1.png" width="500" align="middle" /></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><strong>Fig. 3-5-4-1.</strong> The preliminary experiment results</div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Fig. 3-5-4-1 shows that the mutualism cannot be achieved when the initial population density is too low. Also, when the initial population density is too high, the mutualism cannot be characterized because of reaching a saturation of population before the measurement. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Additionally, it was found that Customer could survive in the presence of chloramphenicol even when its initial population density was low(Go to the <a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production">3OC12HSL-dependent growth experiment page</a>). </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Based on these results, we estimated that the proper condition in our experiment is adding 300 microL of Company cell and 100 microL of Customer cell to 2.6 mL of LB medium.(See Materials and methods for the detailed procedures). </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">So we characterized the mutualism between Company and Customer with the following conditions. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Detailed result of Co-culture assay.png"><img src="https://static.igem.org/mediawiki/2014/8/81/Detailed_result_of_Co-culture_assay.png" width="500"/></a></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p align="center"><strong>Fig. 3-5-4-2. </strong>Detailed result of Co-culture assay </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Optical Density.png"><img src="https://static.igem.org/mediawiki/2014/4/4c/Optical_Density.png" width="500"/></a></div></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p align="center"><strong>Fig. 3-5-4-3.</strong> Optical Density </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Fig. 3-5-4-2 revealed that when the amount of Company is 300 microL, the mutualism can be achieved in the range of 60 to 200 microL of Customer. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">Fig. 3-5-4-3 shows the time-dependent change of optical density. The growth of the cells in mutualism was faster than that of in single culture. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><p class="info-18">From these results described above, our Company and Customer constructed a mutualistic relationship. </p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><h2>5. Materials and methods</h2></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><h1>5-1 Construction</h1></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18">B. Ptet-RFP-Ptet-LuxR (pSB6A1), Plux-CmR-RhlI (pSB3K3) ...Customer</td> | + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Fig.3-5-5-1.png"><img src="https://static.igem.org/mediawiki/2014/6/62/Fig.3-5-5-1.png" width="300"/></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18">C. Ptet-GFP-Ptet-RhlR (pSB6A1), PlacIq-CmR (pSB3K3) ...Negative control (Company without 3OC12HSL production)</td> | + | <td colspan="2"><p align="center"><strong>Fig. 3-5-5-1.</strong></p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18">D. Ptet-RFP-Ptet-LuxR (pSB6A1), PlacIq-CmR (pSB3K3) ...Negative control (Customer without C4HSL production)</td> | + | <td colspan="2" class="info-18">B. Ptet-LuxR-Plac-RFP (pSB6A1), Plux-CmR-RhlI (pSB3K3) ...Customer</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h1>3-2 Assay Protocol</h1></td> | + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Fig.3-5-5-2.png"><img src="https://static.igem.org/mediawiki/2014/5/56/Fig.3-5-5-2.png" width="300"/></a></div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18">1. Prepare 2 overnight cultures for each samples A~D in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12 h.</td> | + | <td colspan="2"><p align="center"><strong>Fig. 3-5-5-2.</strong></p></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><h1>5-2 Assay Protocol</h1></td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2" class="info-18">1. Prepare overnight cultures for each samples A and B in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12 h.</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18">4. Add the culture to 3 mL of LB medium as below.</td> | + | <td colspan="2" class="info-18">4. Add the culture to LB medium as below.</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| <tr> | | <tr> |
| <td class="info-18"> </td> | | <td class="info-18"> </td> |
- | <td class="info-18">• A 30 microL + B30 microL</td> | + | <td class="info-18">• A 300 microL + B 130 microL+ LB medium 2.57 mL</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td class="info-18"> </td> | | <td class="info-18"> </td> |
- | <td class="info-18">• A 30 microL + D 30 microL</td> | + | <td class="info-18">• A 300 microL + LB medium 2.7 mL</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td class="info-18"> </td> | | <td class="info-18"> </td> |
- | <td class="info-18">• B 30 microL + D 30 microL</td> | + | <td class="info-18">• B 130 microL + LB medium 2.87 mL</td> |
| </tr> | | </tr> |
| | | |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h2>4. Reference</h2></td> | + | <td colspan="2" class="entry-long"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"> </td> |
| + | </tr> |
| + | <tr> |
| + | <td colspan="2"><h2>6. Reference</h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |