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| - | <title>Tokyo_Tech</title>
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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/Plux and Prhl reporter assay" style="width:400px; margin-left:-135px;">Plux and Prhl reporter assay</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;">Improved Prhl reporter assay</a></li>
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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>
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| - | <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>
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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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| - | </ul>
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| - | </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="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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| - | <div class="entry-long">
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| - | <td> </td>
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| - | <td><div align="center"><span class="title-small">Contents</span></div></td>
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| - | <td><p class="info-18"><a href="#" class="info-24">1. Overview</a></p></td>
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| - | <td><p class="info-18"><a href="#" class="info-24">2. Why we change Prhl</a></p></td>
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| - | <td><p class="info-18"><a href="#" class="info-24">3. Bank AHL dependent switching</a></p></td>
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| - | <td> </td>
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| - | <td><div align="center" class="title-small">Overview</div></td>
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| - | <td> </td>
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| - | <td><h2>1. Mathematical model</h2></td>
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| - | <td class="head"><strong>1.1 Introduction</strong></td>
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| - | <td><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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| - | </div></td>
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| - | <td><div align="center"><img src="figm1.png" width="333" height="222" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-1-1. </strong>circuit design</div></td>
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| - | <td> </td>
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| - | <td><div align="center"><img src="figm2.png" width="500" height="663" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-1-2.</strong> corresponding mathematical model</div></td>
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| - | <td> </td>
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| - | <td> </td>
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| - | <td><h3 class="head">・Table 4-1-1-1-1 meaning of parameters</h3></td>
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| - | <td> </td>
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| - | <td><div align="center"><img src="table4-1-1-1-1.png" width="500" height="323" /></div></td>
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| - | <td> </td>
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| - | <td><p class="info-18">Detail designs are shown below.</p></td>
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| - | <td> </td>
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| - | <td><p class="head"><strong>1.2 Cell population</strong> </p></td>
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| - | <td><div align="center"><img src="modeling4.png" width="500" height="174" /></div></td>
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| - | <td><blockquote>
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| - | <blockquote>
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| - | <div align="center"><strong>Fig. 4-1-1-2-1.</strong> equations for cell population </div>
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| - | </blockquote></td>
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| - | <td><p class="info-18">The equations above describe how cells grow in the culture. Equation (1), (2), (3) describe populations of Bank, Company, and Customer for each of them. All first terms of the equations are considered carrying capacity. Second terms of (2) and (3) describe the effect of chloramphenicol and chloramphenicol resistance gene. Note that in second terms <img width="114" height="19" src="modeling_clip_image002.png" alt="说明: Macintosh HD:Users:takuya:Documents:iGEM:projectBank:wiki_modeling:equations:equationsForBank1005chlorampheicol.jpg" /> are set to 0 once the value becomes minus.</p></td>
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| - | <td><p class="head"><strong>1.3 Signaling molecules</strong></p></td>
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| - | <td><div align="center"><img src="modeling5.png" width="500" height="104" /></div></td>
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| - | <td><blockquote>
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| - | <div align="center"><strong> Fig. 4-1-1-3-1. </strong>equations for signaling molecules </div>
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| - | <td><p class="info-18">These equations describe concentrations of C4HSL and 3OC12HSL.<br />
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| - | First and Second terms of (4) describe 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 for 3OC12HSL. First term describes the production of 3OC12HSL from LasI in Bank. Second term is for decomposition of 3OC12HSL by AiiA in Bank cell. Third term is for degradation of 3OC12HSL.</p></td>
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| - | <td><p class="head"><span class="head"><strong>1.4 Bank</strong></span></p></td>
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| - | <td><div align="center"><img src="modeling6.png" width="500" height="196" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-1-4-1.</strong> equations for Bank</div></td>
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| - | <td 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 C4HSL. </p>
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| - | <p class="info-18">In order 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><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 align="center" class="info-18"><img src="modeling7.png" width="500" height="104" /></p></td>
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| - | <td><div align="center"><strong>Fig. 4-1-1-5-1.</strong> equations for Company</div></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 align="center" class="info-18"><img src="modeling8.png" width="500" height="103" /></p></td>
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| - | <td><div align="center"><strong>Fig. 4-1-1-6-1.</strong> equations for Customer</div></td>
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| - | <td><p class="info-18">In the presence of 3OC12HSL, RhlI and CmR will be expressed.</p></td>
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| - | <td><h2>2. Story simulation details</h2></td>
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| - | <td><p class="head"><strong>2.1. Company and Customer co-culture simulation</strong></p></td>
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| - | <td class="info-18"><p class="info-18">The system which includes only Company and Customer was simulated before our experiments. From the analysis we performed, we noticed that strength levels of Prhl and Plux promoters should be equally strong as shown in Fig. 4-1-2-1-2.(Detail analysis is shown in other modeling page.)</p></td>
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| - | <td><div align="center"><img src="fig4-1-2-1-2.png" width="300" height="276" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-1-2.</strong> Company and Customer growth dependency of Prhl and Plux strength levels</div></td>
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| - | <td><p class="info-18">When the strength levels of Prhl and Plux promoters are in the red area, Company and Customer can grow well. Otherwise when strength levels are in the blue area, either Company or Customer cannot grow well. </p>
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| - | <p class="info-18">With the optimized parameter values, Company and Customer grows well as shown in Fig. 4-1-2-1-3. </p></td>
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| - | <td><div align="center"><img src="fig4-1-2-1-3.png" width="300" height="223" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-1-3.</strong> Company and Customer can grow wll with optimised parameters</div></td>
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| - | <li class="head"><strong>2.2 Introduction of Bank</strong></li>
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| - | <td><p class="info-18">Company and Customer cannot grow well with less initial amounts than previous simulation as shown in Fig. 4-1-2-2-1.</p></td>
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| - | <td><div align="center"><img src="fig4-1-2-2-1.png" width="300" height="225" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-2-1.</strong> Company and Customer cannot grow with less initial amounts</div></td>
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| - | <td><p class="info-18">But once we add the Bank to the system, they can grow well with the C4HSL produced by the Bank as shown in Fig. 4-1-2-2-2.</p></td>
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| - | <td><div align="center"><img src="fig4-1-2-2-2.png" width="300" height="223" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-2-2.</strong> Addition of Bank make the system grow well</div></td>
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| - | <td><p class="info-18">Along with the growth of the system, Bank eventually changes its state from distribution state to collection state. This is shown in Fig. 4-1-2-2-3.</p></td>
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| - | <td><div align="center"><img src="fig4-1-2-2-3.png" width="270" height="202" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-2-3.</strong> Bank changes its state from Distribution State to Collection State</div></td>
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| - | <td> </td>
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| - | <td><p class="info-18">RhlI is expressed mainly in Distribution State. And AiiA is expressed mainly in collection state. Fig. 4-1-2-2-3 shows the Bank was first in Distribution State and in the following changed to Collection State.</p></td>
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| - | <td class="head"><strong>2.3 Economic wave </strong></td>
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| - | <td><p class="info-18">With the advice from entrepreneurs, we introduced economic wave to our system. Detail is shown in Economic Wave page in the modeling.</p>
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| - | <p class="info-18">Once the economic wave is introduced to our system, Company and Customer cannot grow well because of the recession during the economic wave. This is shown in Fig. 4-1-2-3-1. </p></td>
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| - | <td><div align="center"><img src="fig4-1-2-3-1.png" width="300" height="224" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-3-1.</strong> Company and Customer cannot grow with economic wave</div></td>
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| - | <td><p class="info-18">As in the real economy, we also introduced Bank to this system. The result was different depending on the harshness of the economic wave. If the economic wave is moderate, then the Bank can help Company and Customer to grow well even in the presence of economic wave. This is shown in Fig. 4-1-2-3-2.</p></td>
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| - | <td><div align="center"><img src="fig4-1-2-3-2.png" width="300" height="224" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-3-2.</strong> Bank can help Company and Customer even in the presence of economic wave</div></td>
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| - | <td><p class="info-18">But if the economic wave is more harsh than the previous one, then Bank cannot help Company and Customer enough. The result is shown in Fig. 4-1-2-3-3.</p></td>
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| - | <td><div align="center"><img src="fig4-1-2-3-3.png" width="300" height="225" /></div></td>
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| - | <td><div align="center"><strong>Fig. 4-1-2-3-3.</strong> Bank cannot help Company and Customer enough in the presence of harsh economic wave</div></td>
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