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<h1 align="center">Collaborations</h1> | <h1 align="center">Collaborations</h1> | ||
</div><!-- /page_header --> | </div><!-- /page_header --> | ||
− | + | <div id="contents" class="container"> | |
+ | <div id="contents_header" class="container_header"> | ||
+ | <h1><span>Contents</span></h1> | ||
+ | </div><!-- /contents_header --> | ||
+ | <div id="contents_contents" class="container_contents"> | ||
+ | <div id="contents_menu"> | ||
+ | <h3 class="link"><a href="#collaboration_kait">1. Collaboration with Kanagawa Institute of Technology</a></h3> | ||
+ | <h3 class="link"><a href="#workshop">2. A workshop of modeling</a></h3> | ||
+ | <h3 class="link"><a href="#asij">3. Helping a New iGEM High School Team</a></h3> | ||
+ | <h3 class="link"><a href="#collaboration_ut">4. Developing an application</a></h3> | ||
+ | <h3 class="link"><a href="#may_festival">5. May Festival</a></h3> | ||
+ | <h3 class="link"><a href="#metu">6. Writing International iGEM Protocols with iGEM 2016 team METU HS Ankara</a></h3> | ||
+ | <h3 class="link"><a href="#epfl">7. Published on iGEM news of iGEM EPFL</a></h3> | ||
+ | <h3 class="link"><a href="#meetup">8. Meetup at Boston University</a></h3> | ||
+ | </div><!-- /contents_menu --> | ||
+ | </div><!-- /contents_contents --> | ||
+ | </div><!-- /contents --> | ||
<div id="collaboration_kait" class="container"> | <div id="collaboration_kait" class="container"> | ||
<div id="collaboration_kait_header" class="container_header"> | <div id="collaboration_kait_header" class="container_header"> | ||
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<div id="kait_overview"> | <div id="kait_overview"> | ||
<div id="kait_overview_header"> | <div id="kait_overview_header"> | ||
− | <h2><span>1 | + | <h2><span>1-1. Overview</span></h2> |
</div><!-- /kait_overview_header --> | </div><!-- /kait_overview_header --> | ||
<div id="kait_overview_contents"> | <div id="kait_overview_contents"> | ||
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<div id="kait_project"> | <div id="kait_project"> | ||
<div id="kait_project_header"> | <div id="kait_project_header"> | ||
− | <h2><span>1 | + | <h2><span>1-2. Project</span></h2> |
</div><!-- /kait_project_header --> | </div><!-- /kait_project_header --> | ||
<div id="kait_project_contents"> | <div id="kait_project_contents"> | ||
− | <p class="normal_text">Team KAIT | + | <p class="normal_text">Team KAIT planned on increasing the production of Bacterial Cellulose (BC) produced by the bacteria <span style="font-style: italic">A</span>. <span style="font-style: italic">xylinum.</span> To do so, we have to take into account the cellulose synthesis pathway.</p> |
<a href="https://static.igem.org/mediawiki/2016/e/ee/T--Tokyo_Tech--Collaboration_Kait_1.png"><img src="https://static.igem.org/mediawiki/2016/e/ee/T--Tokyo_Tech--Collaboration_Kait_1.png" height="300px" /></a> | <a href="https://static.igem.org/mediawiki/2016/e/ee/T--Tokyo_Tech--Collaboration_Kait_1.png"><img src="https://static.igem.org/mediawiki/2016/e/ee/T--Tokyo_Tech--Collaboration_Kait_1.png" height="300px" /></a> | ||
<p class="caption"><span style="font-weight: bold;">Fig. 8-1-1. </span> Cellulose synthesis pathway of an <span style="font-style: italic">Acetobacter</span></p> | <p class="caption"><span style="font-weight: bold;">Fig. 8-1-1. </span> Cellulose synthesis pathway of an <span style="font-style: italic">Acetobacter</span></p> | ||
− | <p class="normal_text"> | + | <p class="normal_text">Based on the mechanisms of this pathway, iGEM 2016 team KAIT_Japan planned to increase the amount of cellulose production by diminishing the amount of G6PDH and PGI enzymes by the antisense method.</p> |
</div><!-- /kait_project_contents --> | </div><!-- /kait_project_contents --> | ||
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<div id="kait_model"> | <div id="kait_model"> | ||
<div id="kait_model_header"> | <div id="kait_model_header"> | ||
− | <h2><span>1 | + | <h2><span>1-3. Mathematical Model</span></h2> |
</div><!-- /kait_model_header --> | </div><!-- /kait_model_header --> | ||
<div id="kait_model_contents"> | <div id="kait_model_contents"> | ||
− | <p class="normal_text">Cellulose is produced basically by a series of | + | <p class="normal_text">Cellulose is produced basically by a series of enzymatic reactions, so in order to create a mathematical model for this project, we have to take into account the principal reactions taking place in this production. By doing this we obtain the <a href="javascript:void(0)" onClick="show('equation1');">following equations</a>.</p> |
<div id="equation1" class="off"> | <div id="equation1" class="off"> | ||
<p>$$ \displaystyle \frac{d[Glc]}{dt} = - \frac{V_{max_1}[Glc]}{K_{m_1} + [Glc]} $$</p> | <p>$$ \displaystyle \frac{d[Glc]}{dt} = - \frac{V_{max_1}[Glc]}{K_{m_1} + [Glc]} $$</p> | ||
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<p>$$ \frac{d[Cell]}{dt} = \frac{V_{max_{10}}[UDP-Glc]}{K_{m_{10}} + [UDP - Glc]} $$ </p> | <p>$$ \frac{d[Cell]}{dt} = \frac{V_{max_{10}}[UDP-Glc]}{K_{m_{10}} + [UDP - Glc]} $$ </p> | ||
</div><!-- /equation1 --> | </div><!-- /equation1 --> | ||
− | <p class="normal_text"> | + | <p class="normal_text">Each equation represents the concentration of each molecule. \( V_{max_n} \) and \( K_{m_n} \) represent the maximum velocity and the Michaelis constant of reaction respectively. In regards of the concentration of G6P and F6P, we had to consider the reversibility of the reaction.</p> |
<p class="normal_text">However in this case, since it was considered to only use glucose and not fructose, we can simplify the equations to the <a href="javascript:void(0);" onClick="show('equation2');">following ones</a>.</p> | <p class="normal_text">However in this case, since it was considered to only use glucose and not fructose, we can simplify the equations to the <a href="javascript:void(0);" onClick="show('equation2');">following ones</a>.</p> | ||
<div id="equation2" class="off"> | <div id="equation2" class="off"> | ||
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<div id="kait_antisense_method"> | <div id="kait_antisense_method"> | ||
<div id="kait_antisense_method_header"> | <div id="kait_antisense_method_header"> | ||
− | <h2><span>1 | + | <h2><span>1-4. Antisense Method</span></h2> |
</div><!-- /kait_antisense_method_header --> | </div><!-- /kait_antisense_method_header --> | ||
<div id="kait_antisense_method_contentes"> | <div id="kait_antisense_method_contentes"> | ||
<p class="normal_text">The antisense method consists in inhibiting the production of certain proteins by using an antisense RNA that is perfectly complementary to the target nucleotide sequence, thus preventing its transcription. </p> | <p class="normal_text">The antisense method consists in inhibiting the production of certain proteins by using an antisense RNA that is perfectly complementary to the target nucleotide sequence, thus preventing its transcription. </p> | ||
− | <p class="normal_text">In this case we are using the antisense method to prevent the production of the enzymes G6PD and PGI so by representing the binding of the antisense mRNA to the nucleotide sequence | + | <p class="normal_text">In this case we are using the antisense method to prevent the production of the enzymes G6PD and PGI so by representing the binding of the antisense mRNA to the nucleotide sequence with a Hill equation we got <a href="javascript:void(0);" onClick="show('equation3')">the following equations</a>.</p> |
<div id="equation3" class="off"> | <div id="equation3" class="off"> | ||
<p>$$ \frac{d[G6P]}{dt} = \frac{V_{max_1} [Glc]}{K_{m_1} + [Glc]} - \left(1 - \frac{\alpha_1[mRNA_1]^{n_1}}{K_1^{n_1} + [mRNA_1]^{n_1}} \right) * \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} \\ | <p>$$ \frac{d[G6P]}{dt} = \frac{V_{max_1} [Glc]}{K_{m_1} + [Glc]} - \left(1 - \frac{\alpha_1[mRNA_1]^{n_1}}{K_1^{n_1} + [mRNA_1]^{n_1}} \right) * \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} \\ | ||
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<p>$$ \frac{[PGA]}{dt} = \left(1 - \frac{\alpha_1[mRNA_1]^{n_1}}{K_1^{n_1} + [mRNA_1]^{n_1}} \right) * \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} $$</p> | <p>$$ \frac{[PGA]}{dt} = \left(1 - \frac{\alpha_1[mRNA_1]^{n_1}}{K_1^{n_1} + [mRNA_1]^{n_1}} \right) * \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} $$</p> | ||
</div><!-- /equation3 --> | </div><!-- /equation3 --> | ||
− | <p class="normal_text">Where | + | <p class="normal_text">Where \( \alpha_{n} \), \( K_{n} \) and \( n_{n} \) are constants from the Hill equation, And the concentration of the mRNAs depend on the conditions of the experiment.</p> |
</div><!-- /kait_antisense_method_contents --> | </div><!-- /kait_antisense_method_contents --> | ||
</div><!-- /kait_antisense_method --> | </div><!-- /kait_antisense_method --> | ||
<div id="kait_results"> | <div id="kait_results"> | ||
<div id="kait_results_header"> | <div id="kait_results_header"> | ||
− | <h2><span>1 | + | <h2><span>1-5. Results</span><h2> |
</div><!-- /kait_results_header --> | </div><!-- /kait_results_header --> | ||
<div id="kait_results_contents"> | <div id="kait_results_contents"> | ||
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<a href="https://static.igem.org/mediawiki/2016/a/a6/T--Tokyo_Tech--Collaboration_Kait_6.png"><img src="https://static.igem.org/mediawiki/2016/a/a6/T--Tokyo_Tech--Collaboration_Kait_6.png" /></a>(e) | <a href="https://static.igem.org/mediawiki/2016/a/a6/T--Tokyo_Tech--Collaboration_Kait_6.png"><img src="https://static.igem.org/mediawiki/2016/a/a6/T--Tokyo_Tech--Collaboration_Kait_6.png" /></a>(e) | ||
<p class="caption"><span style="font-weight: bold;">Fig. 8-1-2. </span> | <p class="caption"><span style="font-weight: bold;">Fig. 8-1-2. </span> | ||
− | (a) Concentrations without applying the antisense method, | + | (a) Concentrations without applying the antisense method, |
− | (b) Concentration while inhibiting G6PD enzyme, | + | (b) Concentration while inhibiting G6PD enzyme, |
− | (c) Concentrations inhibiting PGI enzyme, | + | (c) Concentrations inhibiting PGI enzyme, |
− | (d) Concentrations inhibiting both G6PD and PGI enzymes, | + | (d) Concentrations inhibiting both G6PD and PGI enzymes, |
(e) Concentrations strongly inhibiting both enzymes | (e) Concentrations strongly inhibiting both enzymes | ||
</p> | </p> | ||
</div><!-- /kait_results_images --> | </div><!-- /kait_results_images --> | ||
− | <p class="normal_text">We can see that | + | <p class="normal_text">We can see that the more we inhibit the enzymes G6PD and PGI, the production of BC increases; so we can assume this model is correct. However, we cannot say it is the most appropriate to our case since it has not been corroborated with the experiments. We managed, though, to create the basis for a future more precise model.</p><br> |
<div align="center"><img src="https://static.igem.org/mediawiki/2016/5/55/T--Tokyo_Tech--KAITlogo.jpg" height="200"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/5/55/T--Tokyo_Tech--KAITlogo.jpg" height="200"><br></div> | ||
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-3 </span> | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-3 </span> | ||
logo of KAIT_Japan</p></div> | logo of KAIT_Japan</p></div> | ||
+ | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:KAIT_Japan/Collaborations" align="center"> >Read iGEM KAIT_JAPAN's Collaboration page< </a> | ||
+ | </p> | ||
</div><!-- /kait_results_contents --> | </div><!-- /kait_results_contents --> | ||
</div><!-- /kait_results --> | </div><!-- /kait_results --> | ||
</div><!-- /collaboration_kait_contents --> | </div><!-- /collaboration_kait_contents --> | ||
</div><!-- /collaboration_kait --> | </div><!-- /collaboration_kait --> | ||
− | + | ||
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<div id="workshop" class="container"> | <div id="workshop" class="container"> | ||
<div id="workshop_header" class="container_header"> | <div id="workshop_header" class="container_header"> | ||
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<div id="workshop_contents" class="container_contents"> | <div id="workshop_contents" class="container_contents"> | ||
− | <p class="normal_text">On August 16th, we hosted a workshop of dry teams. The participating universities were Gifu University, Tokyo University of Agriculture and Technology, University of Tokyo and Kanazawa Institute of Technology. The iGEM | + | <p class="normal_text">On August 16th, we hosted a workshop of dry teams. The participating universities were Gifu University, Tokyo University of Agriculture and Technology, University of Tokyo and Kanazawa Institute of Technology. The iGEM team Tokyo_Tech and the iGEM team UT-Tokyo taught modeling methods to the other iGEM teams present. We exchanged our ideas, and thereby we gained new knowledge on modeling.</p> |
<div align="center"><img src="https://static.igem.org/mediawiki/2016/f/f5/T--Tokyo_Tech--Collabologos.png" height="180"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/f/f5/T--Tokyo_Tech--Collabologos.png" height="180"><br></div> | ||
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-4 </span> | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-4 </span> | ||
logo of UT-Tokyo(left), Tokyo-NoKoGen(center),iGEM Gifu(right) </p></div> | logo of UT-Tokyo(left), Tokyo-NoKoGen(center),iGEM Gifu(right) </p></div> | ||
+ | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:Gifu/Collaborations" align="center"> >Read iGEM Gifu's Collaboration page< </a> | ||
+ | </p> | ||
+ | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:UT-Tokyo/Collaborations" align="center"> >Read iGEM UT-Tokyo's Collaboration page< </a> | ||
+ | </p> | ||
+ | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="http://tokyonokogen.wixsite.com/tokyo-noko-gen" align="center"> >Read team Tokyo-NoKoGen page< </a> | ||
+ | </p> | ||
</div><!-- /workshop_contents --> | </div><!-- /workshop_contents --> | ||
</div><!-- /workshop --> | </div><!-- /workshop --> | ||
− | + | ||
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<div id="asij" class="container"> | <div id="asij" class="container"> | ||
<div id="asij_header" class="container_header"> | <div id="asij_header" class="container_header"> | ||
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</div><!-- /asij_header --> | </div><!-- /asij_header --> | ||
<div id="asij_contents" class="container_contents"> | <div id="asij_contents" class="container_contents"> | ||
− | <p class="normal_text">We visited The American School in Japan on September 14th and gave a modeling lecture. We explained our | + | <p class="normal_text">We visited The American School in Japan on September 14th and gave a modeling lecture. We explained our project's overview and taught modeling methods. We also talked about what iGEM is because the American School in Japan is a new iGEM team. The iGEM team Tokyo Tech has collaborated with many universities so far. This visit enabled us to collaborate with a high school.</p> |
<div align="center"><img src="https://static.igem.org/mediawiki/parts/e/e3/T--Tokyo_Tech--HSlogo.png" height="100"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/parts/e/e3/T--Tokyo_Tech--HSlogo.png" height="100"><br></div> | ||
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-5 </span> | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-5 </span> | ||
logo of The American School in Japan </p></div> | logo of The American School in Japan </p></div> | ||
+ | |||
+ | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:ASIJ_Tokyo/Attributions" align="center"> >Read iGEM ASIJ_Tokyo's Attribution page< </a> | ||
+ | </p> | ||
</div><!-- /asij_contents --> | </div><!-- /asij_contents --> | ||
</div><!-- /asij --> | </div><!-- /asij --> | ||
− | + | ||
+ | |||
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<div id="collaboration_ut" class="container"> | <div id="collaboration_ut" class="container"> | ||
<div id="ut_header" class="container_header"> | <div id="ut_header" class="container_header"> | ||
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<div id="ut_contents" class="container_contents"> | <div id="ut_contents" class="container_contents"> | ||
− | <h2>4 | + | <h2>4-1. Abstract</h2> |
− | <p class="normal_text">We developed an Android application based on the suggestion from iGEM 2016 team UT-Tokyo of turning <span style="font-style:italic;">E. coli</span> cultivation and genetic modification into an application so that more people know synthetic biology.</p> | + | <p class="normal_text">We developed an Android application based on the suggestion from iGEM 2016 team UT-Tokyo of turning <span style="font-style:italic;">E. coli</span> cultivation and genetic modification into an application so that more people can know about synthetic biology.</p> |
− | <h2>4 | + | <h2>4-2. Explanation of the Application</h2> |
− | <p class="normal_text">When a player taps the main screen, <span style="font-style:italic;">E. coli</span> | + | <p class="normal_text">When a player taps the main screen, <span style="font-style:italic;">E. coli</span> in a medium increases. Additionally, the more <span style="font-style: italic;">E. coli</span> increases, the more experience points a player gains, which increases the player’s level. Leveling up also gives the player access to gene ligation techniques.</p> |
<p class="normal_text">This application is distributed on Google Play. Here is the URL.</p> | <p class="normal_text">This application is distributed on Google Play. Here is the URL.</p> | ||
− | <p class="normal_text">At present, players can only increase the number of <span style="font-style: italic;">E. coli</span>. | + | <p class="normal_text">At present, players can only increase the number of <span style="font-style: italic;">E. coli</span>. However, in the future, we aim to upgrade the application so that players can do genetic modification in the application.</p> |
</div><!-- /ut_contents --> | </div><!-- /ut_contents --> | ||
</div><!-- /collaboration_ut --> | </div><!-- /collaboration_ut --> | ||
− | + | ||
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− | + | ||
− | <div id=" | + | <div id="may_festival" class="container container_bottom"> |
− | <div id=" | + | <div id="may_festival_header" class="container_header"> |
− | <h1><span>5. May | + | <h1><span>5. May Festival</span></h1> |
− | </div><!-- / | + | </div><!-- /may_festival_header --> |
− | <div id=" | + | <div id="may_festival_contents" class="container_contents"> |
− | <p class="normal_text">The Japanese iGEM teams took part in the school festival at the University of Tokyo. Our team shared ideas and gave each other | + | <p class="normal_text">The Japanese iGEM teams took part in the school festival at the University of Tokyo. Our team shared ideas and gave each other feedback. We introduced iGEM and synthetic biology to the public.</p> |
<p class="normal_text">See the Human Practice page for further information.</p> | <p class="normal_text">See the Human Practice page for further information.</p> | ||
− | + | <div align="center"><h3>Participants</h3></div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:Gifu" align="center"> >Read iGEM 2016 team Gifu page< </a> | |
− | + | </p> | |
− | + | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:KAIT_Japan" align="center"> >Read iGEM 2016 team KAIT_Japan page< </a> | |
− | + | </p> | |
− | + | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:Kyoto" align="center"> >Read iGEM 2016 team Kyoto page< </a> | |
− | </div><!-- | + | </p> |
− | </div><!-- / | + | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:UT-Tokyo" align="center"> >Read iGEM 2016 team UT-Tokyo page< </a> |
− | + | </p> | |
− | <!-- | + | <p class="caption" style="font-size: 16px; text-align: center;"><a href ="http://tokyonokogen.wixsite.com/tokyo-noko-gen" align="center"> >Read team Tokyo-NoKoGen page< </a> |
− | + | </p> | |
+ | |||
+ | </div><!-- may_festival_contents --> | ||
+ | </div><!-- /may_festival --> | ||
+ | |||
+ | <!-- May festival up to here --> | ||
+ | |||
<div id="metu" class="container"> | <div id="metu" class="container"> | ||
<div id="metu_header" class="container_header"> | <div id="metu_header" class="container_header"> | ||
− | <h1><span> | + | <h1><span>6. Writing International iGEM Protocols with iGEM 2016 team METU HS Ankara</span></h1> |
</div><!-- /metu_header --> | </div><!-- /metu_header --> | ||
<div id="metu_contents" class="container_contents"> | <div id="metu_contents" class="container_contents"> | ||
+ | <p class="normal_text"> iGEM 2016 team METU HS Ankara asked our team to write International iGEM Protocols as a collaboration this year, and we decided to translate them into Japanese.<br> | ||
+ | Since they are basic protocols, we can’t make any successful experiments without them . We are sure that their activities will be able to help other iGEM teams. We are so grateful to be able to help in such activities. | ||
+ | </p> | ||
+ | <div align="center"><img src="https://static.igem.org/mediawiki/2016/d/d1/T--Tokyo_Tech--METUphoto.jpg" height="150"> <img src="https://static.igem.org/mediawiki/2016/2/2d/T--Tokyo_Tech--METUlogo.png" height="150"></div> | ||
+ | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-6 </span> | ||
+ | team METU HS Ankara's members <span style="font-weight: bold;">Fig.8-1-7 </span> | ||
+ | logo of team METU HS Ankara </p> | ||
+ | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Team:METU_HS_Ankara/Collaborations | ||
+ | " align="center">>Read iGEM METU HS Ankara's Collaboration page< </a> | ||
+ | </p></div> | ||
+ | </div> | ||
</div><!-- /metu_contents --> | </div><!-- /metu_contents --> | ||
</div><!-- /metu --> | </div><!-- /metu --> | ||
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<div id="epfl" class="container container_bottom"> | <div id="epfl" class="container container_bottom"> | ||
<div id="epfl_header" class="container_header"> | <div id="epfl_header" class="container_header"> | ||
− | <h1><span> | + | <h1><span>7. Published on iGEM news of iGEM EPFL</span></h1> |
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<div id="epfl_contents" class="container_contents"> | <div id="epfl_contents" class="container_contents"> | ||
− | <p class="normal_text"> This year, our team was introduced on the page of iGEM EPFL, “iGEMnews”, where it | + | <p class="normal_text"> This year, our team was introduced on the page of iGEM EPFL, “iGEMnews”, where it is written about other teams or their projects.<br> |
− | We appreciate having such an opportunity because there are only a few chances for us to let people know about our team. <br><br> | + | We appreciate having such an opportunity because there are only a few chances for us to let people know about our team. </p><br><br> |
<div align="center"><img src="https://static.igem.org/mediawiki/igem.org/c/c4/T--Tokyo_Tech--EPFLlogo.png" height="200"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/igem.org/c/c4/T--Tokyo_Tech--EPFLlogo.png" height="200"><br></div> | ||
− | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1- | + | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig.8-1-8 </span> |
− | + | logo of iGEM.TODAY<br> | |
− | <a href ="http://igem.today/2016/09/24/enter-the-snow-white-world-with-the-tokyo-tech-team/">iGEM News link</a> | + | <a href ="http://igem.today/2016/09/24/enter-the-snow-white-world-with-the-tokyo-tech-team/" align="center"> >Read iGEM EPFL's iGEM News link!!< </a> |
+ | </p></div> | ||
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+ | <div id="meetup_header" class="container_header"> | ||
+ | <h1><span>8. Meetup at Boston University</span></h1> | ||
+ | </div><!-- /meetup_header --> | ||
+ | <div id="meetup_contents" class="container_contents"> | ||
+ | <p class="normal_text">On October 26th, our team is going to host a meetup in Boston University. We are looking forward to sharing ideas with other iGEM teams. Each team will have the opportunity to present their projects and exchange their ideas in detail with other iGEM teams and faculty advisors right before the Giant Jamboree. | ||
+ | </p> | ||
+ | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><a href ="https://2016.igem.org/Community/Meetups#Japanese" align="center"> >Read Community/Meetups page< </a> | ||
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Latest revision as of 23:42, 19 October 2016
![](https://static.igem.org/mediawiki/2016/f/f6/T--Tokyo_Tech--goTop.png)
Collaborations
Contents
1. Collaboration with Kanagawa Institute of Technology
1-1. Overview
Our team collaborated with iGEM 2016 team KAIT_Japan and other teams, as we were asked to help them with the modeling in an early stage. From iGEM 2016 team KAIT_Japan we were asked to help them create a mathematical model for their project.
1-2. Project
Team KAIT planned on increasing the production of Bacterial Cellulose (BC) produced by the bacteria A. xylinum. To do so, we have to take into account the cellulose synthesis pathway.
![](https://static.igem.org/mediawiki/2016/e/ee/T--Tokyo_Tech--Collaboration_Kait_1.png)
Fig. 8-1-1. Cellulose synthesis pathway of an Acetobacter
Based on the mechanisms of this pathway, iGEM 2016 team KAIT_Japan planned to increase the amount of cellulose production by diminishing the amount of G6PDH and PGI enzymes by the antisense method.
1-3. Mathematical Model
Cellulose is produced basically by a series of enzymatic reactions, so in order to create a mathematical model for this project, we have to take into account the principal reactions taking place in this production. By doing this we obtain the following equations.
$$ \displaystyle \frac{d[Glc]}{dt} = - \frac{V_{max_1}[Glc]}{K_{m_1} + [Glc]} $$
$$ \displaystyle \frac{d[Frc]}{dt} = - \frac{V_{max_5}[Frc]}{K_{m_5} + [Frc]} - \frac{V_{max_6}[Frc]}{K_{m_6} + [Frc]} $$
$$ \displaystyle \frac{d[G6P]}{dt} = - \frac{V_{max_1}[Glc]}{K_{m_1} + [Glc]} - \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} - \frac{V_{f_3} \frac{[G6P]}{K_{s_3}} - V_{s_3} \frac{[F6P]}{K_{P_3}}}{1 + \frac{[G6P]}{K_{s_3}} + \frac{[F6P]}{K_{P_3}}} - \frac{V_{max_4}[G6P]}{K_{m_4} + [G6P]} $$
$$ \displaystyle \frac{d[F6P]}{dt} = \frac{V_{max_5} [Frc]}{K_{m_5} + [Frc]} + \frac{V_{max_8} [FDP]}{K_{m_8} + [FDP]} + \frac{V_{f_3} \frac{[G6P]}{K_{s_3} - V_{s_3} \frac{[F6P]}{K_{P_3}}}}{1 + \frac{[G6P]}{K_{s_3}} + \frac{[F6P]}{K_{P_3}}} $$
$$ \displaystyle \frac{[F1P]}{dt} = \frac{V_{max_6}[Frc]}{K_{m_6} + [Frc]} - \frac{V_{max_7} [F1P]}{K_{m_7} + [F1P]} $$
$$ \displaystyle \frac{d[FDP]}{dt} = \frac{V_{max_7} [F1P]}{K_{m_7} + [F1P]} - \frac{V_{max_8} [FDP]}{K_{m_8} + [FDP]} $$
$$ \displaystyle \frac{d[PGA]}{dt} = \frac{V_{max_2} [G6P]}{K_{m_2} + [G6P]} - \frac{V_{max_{11}}[PGA]}{K_{m_{11}} + [PGA]} $$
$$ \displaystyle \frac{d[G1P]}{dt} = \frac{V_{max_4} [G6P]}{K_{m_4} + [G6P]} - \frac{V_{max_9} [G1P]}{K_{m_9} + [G1P]} $$
$$ \frac{[UDP - Glc]}{dt} = \frac{V_{max_9}[G1P]}{K_{m_9} + [G1P]} - \frac{V_{max_{10}}[UDP-Glc]}{K_{m_{10}} + [UDP-Glc]} $$
$$ \frac{d[Cell]}{dt} = \frac{V_{max_{10}}[UDP-Glc]}{K_{m_{10}} + [UDP - Glc]} $$
Each equation represents the concentration of each molecule. \( V_{max_n} \) and \( K_{m_n} \) represent the maximum velocity and the Michaelis constant of reaction respectively. In regards of the concentration of G6P and F6P, we had to consider the reversibility of the reaction.
However in this case, since it was considered to only use glucose and not fructose, we can simplify the equations to the following ones.
$$ \frac{d[Glc]}{dt} = - \frac{V_{max_1} [Glc]}{K_{m_1} + [Glc]} $$
$$ \displaystyle \frac{d[G6P]}{dt} = - \frac{V_{max_1}[Glc]}{K_{m_1} + [Glc]} - \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} - \frac{V_{f_3} \frac{[G6P]}{K_{s_3}} - V_{s_3} \frac{[F6P]}{K_{P_3}}}{1 + \frac{[G6P]}{K_{s_3}} + \frac{[F6P]}{K_{P_3}}} - \frac{V_{max_4}[G6P]}{K_{m_4} + [G6P]} $$
$$ \frac{d[F6P]}{dt} = \frac{V_{f_3} \frac{[G6P]}{K_{s_3}}}{ 1 + \frac{[G6P]}{K_{s_3}} + \frac{[F6P]}{K_{P_3}}} $$
$$ \frac{d[PGA]}{dt} = \frac{V_{max_2} [G6P]}{K_{m_2} + [G6P]} $$
$$ \frac{d[G1P]}{dt} = \frac{V_{max_4} [G6P]}{K_{m_4} + [G6P]} - \frac{V_{max_9} [G1P]}{K_{m_9} + [G1P]} $$
$$ \frac{d[UDP- Glc]}{dt} = \frac{V_{max_{9}} [G1P]}{K_{m_{9}} + [G1P]} - \frac{V_{max_{10}} [UDP-Glc]}{K_{m_{10}} + [UDP-Glc]} $$
$$ \frac{d[Cell]}{dt} = \frac{V_{max_{10}} [UDP-Glc]}{K_{m_{10}} + [UDP-Glc]} $$
1-4. Antisense Method
The antisense method consists in inhibiting the production of certain proteins by using an antisense RNA that is perfectly complementary to the target nucleotide sequence, thus preventing its transcription.
In this case we are using the antisense method to prevent the production of the enzymes G6PD and PGI so by representing the binding of the antisense mRNA to the nucleotide sequence with a Hill equation we got the following equations.
$$ \frac{d[G6P]}{dt} = \frac{V_{max_1} [Glc]}{K_{m_1} + [Glc]} - \left(1 - \frac{\alpha_1[mRNA_1]^{n_1}}{K_1^{n_1} + [mRNA_1]^{n_1}} \right) * \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} \\ - \left(1 - \frac{\alpha_2[mRNA_2]^{n_2}}{K_2^{n_2} + [mRNA_2]^{n_2}} \right) * \frac{V_{f_3} \frac{[G6P]}{K_{s_3}} - V_{s_3} \frac{[F6P]}{K_{P_3}}}{1 + \frac{[G6P]}{K_{s_3}} + \frac{[F6P]}{K_{P_3}}} - \frac{V_{max_4}[G6P]}{K_{m_4} + [G6P]} $$
$$ \frac{d[F6P]}{dt} = \left( 1 - \frac{alpha_2[mRNA_2]^{n_2}}{K_2^{n_2} + [mRNA_2]^{n_2}} \right) * \frac{V_{f_3} \frac{[G6P]}{K_{s_3}} - V_{s_3} \frac{[F6P]}{K_{P_3}}}{1 + \frac{[G6P]}{K_{s_3}} + \frac{[F6P]}{K_{P_3}}} $$
$$ \frac{[PGA]}{dt} = \left(1 - \frac{\alpha_1[mRNA_1]^{n_1}}{K_1^{n_1} + [mRNA_1]^{n_1}} \right) * \frac{V_{max_2}[G6P]}{K_{m_2} + [G6P]} $$
Where \( \alpha_{n} \), \( K_{n} \) and \( n_{n} \) are constants from the Hill equation, And the concentration of the mRNAs depend on the conditions of the experiment.
1-5. Results
Applying this mathematical model we got the following graphs.
![](https://static.igem.org/mediawiki/2016/1/10/T--Tokyo_Tech--Collaboration_Kait_2.png)
![](https://static.igem.org/mediawiki/2016/2/21/T--Tokyo_Tech--Collaboration_Kait_3.png)
![](https://static.igem.org/mediawiki/2016/0/0c/T--Tokyo_Tech--Collaboration_Kait_4.png)
![](https://static.igem.org/mediawiki/2016/f/fa/T--Tokyo_Tech--Collaboration_Kait_5.png)
![](https://static.igem.org/mediawiki/2016/a/a6/T--Tokyo_Tech--Collaboration_Kait_6.png)
Fig. 8-1-2. (a) Concentrations without applying the antisense method, (b) Concentration while inhibiting G6PD enzyme, (c) Concentrations inhibiting PGI enzyme, (d) Concentrations inhibiting both G6PD and PGI enzymes, (e) Concentrations strongly inhibiting both enzymes
We can see that the more we inhibit the enzymes G6PD and PGI, the production of BC increases; so we can assume this model is correct. However, we cannot say it is the most appropriate to our case since it has not been corroborated with the experiments. We managed, though, to create the basis for a future more precise model.
![](https://static.igem.org/mediawiki/2016/5/55/T--Tokyo_Tech--KAITlogo.jpg)
Fig.8-1-3 logo of KAIT_Japan
2. A workshop of modeling
On August 16th, we hosted a workshop of dry teams. The participating universities were Gifu University, Tokyo University of Agriculture and Technology, University of Tokyo and Kanazawa Institute of Technology. The iGEM team Tokyo_Tech and the iGEM team UT-Tokyo taught modeling methods to the other iGEM teams present. We exchanged our ideas, and thereby we gained new knowledge on modeling.
![](https://static.igem.org/mediawiki/2016/f/f5/T--Tokyo_Tech--Collabologos.png)
Fig.8-1-4 logo of UT-Tokyo(left), Tokyo-NoKoGen(center),iGEM Gifu(right)
>Read iGEM Gifu's Collaboration page<
3. Helping a New iGEM High School Team
We visited The American School in Japan on September 14th and gave a modeling lecture. We explained our project's overview and taught modeling methods. We also talked about what iGEM is because the American School in Japan is a new iGEM team. The iGEM team Tokyo Tech has collaborated with many universities so far. This visit enabled us to collaborate with a high school.
![](https://static.igem.org/mediawiki/parts/e/e3/T--Tokyo_Tech--HSlogo.png)
Fig.8-1-5 logo of The American School in Japan
4. Developing an application
4-1. Abstract
We developed an Android application based on the suggestion from iGEM 2016 team UT-Tokyo of turning E. coli cultivation and genetic modification into an application so that more people can know about synthetic biology.
4-2. Explanation of the Application
When a player taps the main screen, E. coli in a medium increases. Additionally, the more E. coli increases, the more experience points a player gains, which increases the player’s level. Leveling up also gives the player access to gene ligation techniques.
This application is distributed on Google Play. Here is the URL.
At present, players can only increase the number of E. coli. However, in the future, we aim to upgrade the application so that players can do genetic modification in the application.
5. May Festival
The Japanese iGEM teams took part in the school festival at the University of Tokyo. Our team shared ideas and gave each other feedback. We introduced iGEM and synthetic biology to the public.
See the Human Practice page for further information.
Participants
>Read iGEM 2016 team Gifu page<
>Read iGEM 2016 team KAIT_Japan page<
>Read iGEM 2016 team Kyoto page<
6. Writing International iGEM Protocols with iGEM 2016 team METU HS Ankara
iGEM 2016 team METU HS Ankara asked our team to write International iGEM Protocols as a collaboration this year, and we decided to translate them into Japanese.
Since they are basic protocols, we can’t make any successful experiments without them . We are sure that their activities will be able to help other iGEM teams. We are so grateful to be able to help in such activities.
![](https://static.igem.org/mediawiki/2016/d/d1/T--Tokyo_Tech--METUphoto.jpg)
![](https://static.igem.org/mediawiki/2016/2/2d/T--Tokyo_Tech--METUlogo.png)
Fig.8-1-6 team METU HS Ankara's members Fig.8-1-7 logo of team METU HS Ankara
7. Published on iGEM news of iGEM EPFL
This year, our team was introduced on the page of iGEM EPFL, “iGEMnews”, where it is written about other teams or their projects.
We appreciate having such an opportunity because there are only a few chances for us to let people know about our team.
![](https://static.igem.org/mediawiki/igem.org/c/c4/T--Tokyo_Tech--EPFLlogo.png)
Fig.8-1-8
logo of iGEM.TODAY
>Read iGEM EPFL's iGEM News link!!<
8. Meetup at Boston University
On October 26th, our team is going to host a meetup in Boston University. We are looking forward to sharing ideas with other iGEM teams. Each team will have the opportunity to present their projects and exchange their ideas in detail with other iGEM teams and faculty advisors right before the Giant Jamboree.