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| - | <title>Tokyo_Tech</title>
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| - | <link rel="stylesheet" href="https://2014.igem.org/Team:Tokyo_Tech/style2.css?action=raw&ctype=text/css" type="text/css" media="screen"/>
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| - | <img src="https://static.igem.org/mediawiki/2014/thumb/b/b7/Tokyo_Tech_Logo.png/613px-Tokyo_Tech_Logo.png" height="150" /></h1></div>
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| - | <div align="right"><img src="https://static.igem.org/mediawiki/2014/b/b4/Tokyo_Tech_Logo2.png" height="150" /></div>
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| - | <!-- end #header -->
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| - | <div id="menu">
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| - | <ul>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech">Home</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Project">Project</a></li>
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| - | <li><a href="#">Experiment</a>
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| - | <ul>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3oxoC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3oxoC12HSL production</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3oxoC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3oxoC12HSL-dependent C4HSL production</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Symbiosis confirmation by co-culture </a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Prhl_reporter_assay" style="width:400px; margin-left:-135px;">Prhl reporter assay </a></li>
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| - | <li class="current_page_item"><a href="https://2014.igem.org/Team:Tokyo_Tech/Modeling">Modeling</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">Parts</a></li>
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| - | <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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| - | <li><a href="#">More</a>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/About_Us" style="width:240px; margin-left:-53px;">About Us</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Safety" style="width:240px; margin-left:-53px;">Safety</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Attribution_and_Contribution" style="width:240px; margin-left:-53px;">Attribution and Contribution</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Collaboration" style="width:240px; margin-left:-53px;">Collaboration</a></li>
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| - | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Sponsors" style="width:240px; margin-left:-53px;">Sponsors</a></li>
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| - | <li><a href="https://igem.org/Team.cgi?id=1529" style="width:240px; margin-left:-53px;">Official Team Page</a></li>
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| - | <h2 class="title">Modeling</h2>
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| - | <span class="meta">What we found here is so amazing</span>
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| - | <td colspan="2"><div align="center"><span class="title-small">Content</span></div></td>
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| - | <td colspan="2"><p class="info-18"><a href="#" class="info-24">1. IntroductiOverview</a></p></td>
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| - | <td colspan="2"><p class="info-18"><a href="#" class="info-24">2. Why we change Prhl</a></p></td>
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| - | <td colspan="2"><p class="info-18"><a href="#" class="info-24">3. Bank AHL dependent switching</a></p></td>
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| - | <td colspan="2"><div align="center" class="title-small">Overview</div></td>
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| - | <td colspan="2"><h2>1. Introduction</h2></td>
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| - | <td colspan="2" class="head"><strong>1.1 Mathematical model</strong></td>
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| - | <td colspan="2"><div align="left" class="info-18">
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| - | <p class="info-18">Since our genetic circuit is complex, it is very difficult to predict the system’s behavior intuitively. Thus we constructed mathematical model to predict the behavior.</p>
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| - | <td height="287"><h2 align="center"><img src="figm1.png" width="333" height="222" /></h2></td>
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| - | <td rowspan="3"><div align="center"><img src="figm2.png" width="365" height="484" /></div></td>
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| - | <td height="27"><div align="center">Fig. 1 circuit design</div></td>
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| - | <td height="24"> </td>
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| - | <td><div align="center"> Fig. 1 corresponding mathematical model</div></td>
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| - | <td colspan="2"><p class="info-18">Detail designs are shown below.</p></td>
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| - | <td colspan="2"><p class="head"><strong>1.2 Cell population</strong> </p></td>
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| - | <td colspan="2"><img src="modeling4.png" width="435" height="151" /></td>
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| - | <td colspan="2"><p class="info-18">These equations above describe how cells grow in the culture. Equation (1),(2),(3) describe populations of Bank, Company, and Customer each. All first terms of the equations are meant for carrying capacity. Second terms of (2) and (3) describe the effect of chloramphenicol and chloramphenicol resistance gene. Note that these second terms are set to 0 once the value becomes minus in order to avoid the effect of chloramphenicol promote the growth of cells.</p></td>
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| - | <td colspan="2"><p class="head"><strong>1.3 Signaling molecules
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| - | <td colspan="2"><img src="modeling5.png" width="433" height="90" /></td>
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| - | <td colspan="2"><p class="info-18">These equations describe concentrations of C4HSL and 3OC12HSL.</p>
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| - | <p class="info-18">First and Second term of (4) describes production of C4HSL from RhlI in Bank and Company cells. Third term is meant for decomposition of C4HSL by AiiA in Bank cell. Fourth term is for degradation of C4HSL.</p>
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| - | <p class="info-18">Same goes on 3OC12HSL. First term describes the production of 3OC12HSL from LasI in Bank. Second term is for decomposition of C12HSL by AiiA in Bank cell. Third term is for degradation of 3OC12HSL.</p></td>
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| - | <td colspan="2"><p class="head"><span class="head"><strong>1.4 Bank</strong></span></p></td>
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| - | <td colspan="2"><img src="modeling6.png" width="374" height="146" /></td>
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| - | <td colspan="2" class="info-18"><p class="info-18">Bank has two states changing during the cultivation. (6) and (7) describe Distribution state. LacI represses the translation of TetR as described in first term of (8). RhlI will distribute C4HSL which represents money. On the other hand, (8) and (9) describe Collection state. TetR represses LacI. AiiA decomposes C4.</p>
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| - | <p class="info-18">To achieve the state switching depend on the concentration of C4HSL, TetR and AiiA are regulated not only by LacI but also by C4HSL. This makes the system be able to switch depends on the concentration of C4HSL. </p></td>
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| - | <td colspan="2"><p class="head"><strong>1.5 Company</strong></p></td>
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| - | </tr></table><table width="900" border="0">
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| - | <td width="890"><p class="info-18"><img src="modeling7.png" width="390" height="81" /></p></td>
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| - | <td><p class="info-18">In the presence of C4HSL, LasI and CmR will be expressed.</p></td>
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| - | <td><p class="head"><strong>1.6 Customer
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| - | </strong></p></td>
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| - | <td><p class="info-18"><img src="modeling8.png" width="438" height="90" /></p></td>
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| - | <td><p class="info-18">In the presence of C12, RhlI and CmR will be expressed.</p></td>
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| - | <td><h2>2. Story simulation details</h2></td>
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