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- | <meta name="keywords" content="iGEM,2014,Tokyo_Tech,Bank E.coli" /> | + | <meta name="keywords" content="iGEM,2014,Tokyo_Tech,Bank <i>E.coli</i>" /> |
| <meta name="description" content="iGEM2014 Wiki pages" /> | | <meta name="description" content="iGEM2014 Wiki pages" /> |
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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 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="#Introduction">1. Introduction</a></p> | | <p class="info-24"><a href="#Introduction">1. Introduction</a></p> |
- | <p class="info-24"><a href="#Summary">2. Summary of the experiment</a></p> | + | <p class="info-24"><a href="#Summary">2. Summary of the Experiment</a></p> |
| <p class="info-24"><a href="#Results">3. Results</a></p> | | <p class="info-24"><a href="#Results">3. Results</a></p> |
- | <p class="info-24"><a href="#Materials">4. Materials and methods</a></p> | + | <p class="info-24"><a href="#Materials">4. Materials and Methods</a></p> |
| <p class="info-18"><a href="#Materials">4-1. Construction</a></p> | | <p class="info-18"><a href="#Materials">4-1. Construction</a></p> |
- | <p class="info-18"><a href="#Assay">4-2 Assay Protocol</a></p> | + | <p class="info-18"><a href="#Assay">4-2. Assay Protocol</a></p> |
| <p class="info-24"><a href="#Reference">5. Reference</a></p> | | <p class="info-24"><a href="#Reference">5. Reference</a></p> |
| <table width="900" border="0"> | | <table width="900" border="0"> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p class="info-18">In the modeling (Fig. 3-1-1-1.), the better interdependence between Company and Customer requires that the expression of LasI, under the control of Prhl promoter (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>), is the same level as the expression of RhlI, under the control of Plux promoter (<a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>). Thus, we firstly tested the expression level of Prhl promoter and Plux promoter by the reporter assay (Fig. 3-1-1-2.).</p></td> | + | <td colspan="2"><p class="info-18">In the modeling (Fig. 3-1-1-1), the better mutualism between Company and Customer requires that the expression of LasI under the control of Prhl promoter (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>) is the same level as the expression of RhlI under the control of Plux promoter (<a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>). Thus, we firstly tested the expression level of Prhl promoter and Plux promoter through the reporter assay (Fig. 3-1-1-2). </p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
| <td width="397"><div align="center"> | | <td width="397"><div align="center"> |
| <p><a href="https://2014.igem.org/File:Tokyo_Tech_Intensity.png"><img src="https://static.igem.org/mediawiki/2014/3/39/Tokyo_Tech_Intensity.png" width="276" height="268" /></a></p> | | <p><a href="https://2014.igem.org/File:Tokyo_Tech_Intensity.png"><img src="https://static.igem.org/mediawiki/2014/3/39/Tokyo_Tech_Intensity.png" width="276" height="268" /></a></p> |
- | <strong>Fig. 3-1-1-1.</strong> The phase diagram of Plux and Prhl intensity </div></td> | + | <strong>Fig. 3-1-1-1.</strong> The phase diagram of the intensity of Plux and Prhl promoter </div></td> |
| <td width="488"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_Plux_and.png"><img src="https://static.igem.org/mediawiki/2014/c/cf/Tokyo_Tech_Plux_and.png" width="500" height="190" align="middle" /></a></div> | | <td width="488"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_Plux_and.png"><img src="https://static.igem.org/mediawiki/2014/c/cf/Tokyo_Tech_Plux_and.png" width="500" height="190" align="middle" /></a></div> |
- | <div align="center"><strong>Fig. 3-1-1-2.</strong> Plux and Prhl Reporter Assay flow chart</div></td> | + | <div align="center"><strong>Fig. 3-1-1-2.</strong> Plux and Prhl reporter assay flow chart</div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h2>2. Summary of the experiment </h2></td> | + | <td colspan="2"><h2>2. Summary of the Experiment </h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2" class="info-18"><p class="info-18">Our purpose is to confirm actually expression levels of Prhl promoter (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>) and Plux promoter (<a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>). We prepared three plasmids sets shown in below. (Fig. 3-1-2-1.) We measured fluorescence intensity by GFP expression when we added signaling molecules.</p> | + | <td colspan="2" class="info-18"><p class="info-18">Our purpose is to confirm the expression level of Prhl promoter (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>) and Plux promoter (<a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>). We prepared two plasmids sets shown in below (Fig. 3-1-2-1). We measured the fluorescence intensity by GFP expression when we added signaling molecules.</p> |
- | <p class="info-18">We prepared four conditions as follow.</p> | + | <p class="info-18">We prepared four conditions shown in below.</p> |
| <blockquote> | | <blockquote> |
| <p class="info-18"> A-1: Culture containing Ptet-LuxR and Plux-GFP cell with 3OC12HSL<br /> | | <p class="info-18"> A-1: Culture containing Ptet-LuxR and Plux-GFP cell with 3OC12HSL<br /> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center"><strong>Fig. 3-1-2-1. </strong>Reporter plasmids </div> | + | <td colspan="2"><div align="center"><strong>Fig. 3-1-2-1. </strong>Reporter Plasmids </div> |
| <div> | | <div> |
| <div> </div> | | <div> </div> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p class="info-18">The measured activity of pre-existing Biobrick Prhl promoter (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>) was too weak to satisfy the requirement from our modeling results. (Fig. 3-1-3-1 lane 2) In other words, the expression of RhlI under the control of Plux promoter (<a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>) is higher than the expression of LasI under the control of Prhl promoter. | + | <td colspan="2"><p class="info-18">Fig. 3-1-3-1 shows our experimental data of Plux promoter and Prhl promoter. Compared with the modeling results, the expression level of the native BioBrick Prhl promoter (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>) was too weak to satisfy our requirement (Fig. 3-1-3-1 lane 2). In other words, the expression of RhlI under the control of Plux promoter (<a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>) was higher than the expression of LasI under the control of Prhl promoter. |
| </p> | | </p> |
| <div> | | <div> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><h2>4. Materials and methods</h2></td> | + | <td colspan="2"><h2>4. Materials and Methods</h2></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p class="info-24">-Plasmids</p></td> | + | <td colspan="2"><div class="info-18"><p class="info-24">-Plasmids</p> </div></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_Fig3-1-4-1.png"><img src="https://static.igem.org/mediawiki/2014/d/d6/Tokyo_Tech_Fig3-1-4-1.png" width="400" height="122" /></a></div> | + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_Fig3-1-4-1.png"><img src="https://static.igem.org/mediawiki/2014/d/d6/Tokyo_Tech_Fig3-1-4-1.png" width="500"/></a></div> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_Fig3-1-4-2.png"><img src="https://static.igem.org/mediawiki/2014/3/37/Tokyo_Tech_Fig3-1-4-2.png" width="400" height="123" /> </a></div> | + | <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_Fig3-1-4-2.png"><img src="https://static.igem.org/mediawiki/2014/3/37/Tokyo_Tech_Fig3-1-4-2.png" width="500" /> </a></div> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"> </td> | + | <td colspan="2"> <div align="center"><strong>Fig. 3-1-4-2. |
| + | </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| <tr> | | <tr> |
| <td colspan="2"><ol> | | <td colspan="2"><ol> |
- | <li class="info-18">1.Prepare 2 overnight cultures of every sample A~D in 3 mL LB medium, containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) at 37°C for 12 h. </li> | + | <li class="info-18">1. Prepare 2 overnight cultures for each sample in 3 mL LB medium, containing ampicillin (50 microg / |
| + | mL) and kanamycin (30 microg / mL) at 37°C for 12 h. </br> </li> |
| <li class="info-18"> | | <li class="info-18"> |
- | <p class="info-18">2. Dilute the overnight cultures to 1 / 100 in fresh LB medium (3 mL) containing ampicillin (50 microg / mL) and kanamycin (30 microg / mL) (fresh culture). Make glycerol stocks from the remainders.</p> | + | <p class="info-18">2. Dilute the overnight cultures to 1 / 100 in fresh LB medium (3 mL) containing ampicillin (50 microg / |
| + | mL) and kanamycin (30 microg / mL) (fresh culture). </p> |
| </li> | | </li> |
| <li class="info-18"> | | <li class="info-18"> |
- | <p class="info-18">3. Incubate the fresh cultures in 37°C until the observed OD590 reaches 0.3 (Actual value 0.42).</p> | + | <p class="info-18">3. Incubate the fresh cultures at 37°C until the OD590 reaches 0.3.</p> |
| </li> | | </li> |
- | <li class="info-18">4. Add 30 microL of 500 microM C4HSL, 500 nM 3OC12HSL or DMSO as listed below: </li> | + | <li class="info-18">4. Add 30 microL of 500 microM C4HSL, 500 nM 3OC12HSL or DMSO as listed below: </li> |
| </ol> | | </ol> |
| <blockquote> | | <blockquote> |
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| </li> | | </li> |
| <li class="info-18"> | | <li class="info-18"> |
- | <p class="info-18">7. Take 200 microL of the sample, and centrifuge at 9000 Xg, 1 min, 4°C.</p> | + | <p class="info-18">7. Take 200 microL of the sample, and centrifuge at 9000x g, 1 min, 4°C.</p> |
| </li> | | </li> |
| <li class="info-18"> | | <li class="info-18"> |
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| </ol> | | </ol> |
| <p class="info-18"> | | <p class="info-18"> |
- | 11. Measure fluorescence intensity with a flow cytometer (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company). </p> | + | 11. Measure the fluorescence intensity with a flow cytometer (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company). </p> |
| </tr> | | </tr> |
| <tr> | | <tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td colspan="2"><p class="info-18">1. Kendall M. Gray <em>et al. </em>(1994) Interchangeability and specificity of components from the quorum-sensing regulatory systems of Vibrio fischeri and Pseudomonas aeruginosa. Journal of Bacteriology 176(10): 3076–3080</p> | + | <td colspan="2"><p class="info-18">1. 1. Kendall M. Gray et al. (1994) Interchangeability and specificity of components from the quorum-sensing regulatory systems of <i>Vibrio fischeri</i> and <i>Pseudomonas aeruginosa</i>. Journal of Bacteriology 176(10): 3076–3080 |
| + | |
| + | </p> |
| </tr> | | </tr> |
| <tr> | | <tr> |