Difference between revisions of "Team:Tokyo Tech"

 
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      <h1>Home</h1>
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<p class="text">By integrating with our Policy & Practices and the results from our wet lab experiments and modeling, iGEM2015 Team Tokyo_Tech have executed our project with improved design in accordance with comments from general public, and have strengthened the public engagement of a two-way dialogue between our team and the public through this summer.  (See <a href=https://2015.igem.org/Team:Tokyo_Tech/Practices>here</a> to know how we integrated our project)</p>
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<p align="center"><img src="https://static.igem.org/mediawiki/2015/a/aa/Tokyo_Tech_home_integrated_project1.png" width="800px"></p>
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<h2 id="1" class="smalltitle">What is Prisoner’s Dilemma?</h2>
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<p><br></p>
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<p class="text">The Prisoner’s Dilemma game, a typical example analyzed in game theory, involves two prisoners who were given an option selection opportunity either to cooperate or to defect according to the payoff matrix (Fig.1-1-1) in order to pursue for the best profit. (Go to <a href="https://2015.igem.org/Team:Tokyo_Tech/Project#1">Project 1.</a> page) In our project, we decided to replicate an <i>E. coli</i>’s version of Prisoner’s Dilemma payoff matrix (Fig.1-1-2), which punishment means growth inhibition of <i>E. coli.</i>  (Go to <a href="https://2015.igem.org/Team:Tokyo_Tech/Project#2">Project 2.</a> page)</p>
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<table width="940px"><tbody><tr><td align="center" width="50%"><img src="https://static.igem.org/mediawiki/2015/3/30/Tokyo_Tech_111.png" width="85%"></td><td width="50%" align="center"><img src="https://static.igem.org/mediawiki/2015/8/85/Tokyo_Tech_112.png" width="100%"></td></tr>
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<tr><td width="50%" align="center"><h4 class="fig"><strong>Fig.1-1-1. </strong>The payoff matrix in Prisoner's Dilemma (punishment = imprisoned years)</h4></td><td width="50%" align="center"><h4 class="fig"><strong>Fig.1-1-2. </strong>Our replicated payoff matrix for growth inhibition effect on prisoner <i>coli</i></h4></td></tr></tbody></table>
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<h2 id="1" class="smalltitle">Project Overview</h2>
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<p class="text">Like the prisoners in the Dilemma game, we genetically engineered two <i>E. coli</i> acting as Prisoner A and Prisoner B, which are able to cooperate or to defect in our <i>E. coli</i>’s version of Prisoner Dilemma.  The combinations of their option (cooperation or defection) affect their profit which equals to their growth.  To cooperate, they produce AHL while to defect, they do not produce AHL.  The act of producing AHL imposes a metabolic burden on a prisoner <i>coli</i>.  Furthermore, chloramphenicol antibiotic is used to inhibit prisoner <i>coli</i>’s growth in culture.  However, AHL produced by the cooperation induces of the opponent prisoner, so that the expression of chloramphenicol resistant gene circumvents the growth inhibition effect.<br>
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(Go to <a href="https://2015.igem.org/Team:Tokyo_Tech/Project#3">Project 3.</a> page)</p>
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<table width="940px"><tbody><tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/3/38/Tokyo_Tech_113.png" width="60%"></td></tr><tr><td align="center"><h4 class="fig"><strong>Fig.1-1-3. </storng>The genetic circuits of prisoner <i>coli</i> with the options of cooperation or defection</h4></td></tr></tbody></table>
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<table width="940px"><tbody><tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/e/e9/Tokyo_Tech_114.png" width="60%"></td></tr><tr><td align="center"><h4 class="fig"><strong>Fig.1-1-4. </storng>Growth inhibition experienced by prisoner <i>coli</i> as a result of combination of option</h4></td></tr></tbody></table>
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<p class="text">Suggestion from modeling allowed us to successfully construct an improved part for precise implementation of our payoff matrix, when initial designed circuits showed leaky expression of CmR at the first stage of our experiment.  This is one of engineering principle in our iGEM activity.<br>
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Project/Modeling">here</a> for more modeling results)
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<table width="940px"><tbody<tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/e/ec/Tokyo_Tech_115.png" width="80%"></td></tr><tr><td align="center"><h4 class="fig"><strong>Fig.1-1-5. </strong>Suggestions from modeling allow us improving a previously existing part</h4></td></tr></tbody></table>
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<p class="text">Using the improved plasmids we constructed to decrease effect of leaky expression, our <i>E. coli</i> version of payoff matrix is successfully replicated through wet lab experiments (Fig.1-1-6).  In our payoff matrix, with the combination of four options between two prisoner <i>coli</i>, we succeeded to replicate four types of growth inhibition: none, low, middle, and high.<br>
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Experiment/Replicating_the_Payoff_Matrix">here</a> for more details on our wet lab experiments)</p>
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<table width="940px"><tbody><tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/9/97/Tokyo_Tech_116.png" width="60%"></td></tr><tr><td align="center"><h4 class="fig"><strong>Fig.1-1-6. </strong>The results from our wet lab replicated the payoff matrix</h4></td></tr></tbody></table>
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<p class="text">In order to enable prisoner <i>coli</i> to select its option randomly between cooperation and defection, we showed bidirectional inversion of Fim switch by FimB recombinase (BBa_K1632010).  In our knowledge, this is the first case in iGEM to show random inversion of a promoter.<br>
<h2> Welcome to iGEM 2015! </h2>
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Project#41">here</a> to know more on how prisoner <i>coli</i> decides) <br>
<p>Your team has been approved and you are ready to start the iGEM season! </p>
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Experiment/FimB_dependent_fim_switch_state_assay">here</a> to know more detail of FimB experiment results)</p>
<h4>Project description</h4>
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<p>Please refer <a href="https://2015.igem.org/Team:Tokyo_Tech/Description">here</a>!</p>
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<table width="940px"><tbody><tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/b/b4/Tokyo_Tech_117.png" width="60%"></td></tr><tr><td align="center"><h4 class="fig"><strong>Fig.1-1-7.</strong> (A) FimB allows Decision making <i>coli</i> to select option at random, inverting a promoter in a <i>fim</i> switch<br>
<h4>Meet up</h4>
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(B) The intensity of fluorescence in cells mrasured using flow cytometer<br>
<p>Tokyo Tech 2015 is going to host a meetup on 23rd of September in Boston University.Please refer <a href="https://2015.igem.org/Meetups/Tokyo_Tech_Sept">here</a>!
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(C) Colony formation using plasmid mixture extrarcted cell expressing FimB</h4></td></tr></tbody></table>
<h4>Before you start: </h4>
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<p class="text">Our game design allows <i>E. coli</i> to realize one of four strategies including tit-for-tat strategy (Fig.1-1-8), the most successful strategy for Prisoner’s Dilemma. For implementation of this strategy, we confirmed unidirectional inversion of a <i>fim</i> switch by the FimE recombinase.<br>
<p> Please read the following pages:</p>
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Parts">here</a> to know on how we designed our parts)<br>
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Experiment/FimE_dependent_fim_switch_state_assay">here</a> to know more detail of FimE experiment results)</p>
<li> <a href="https://2015.igem.org/Requirements">Requirements page </a> </li>
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<li> <a href="https://2015.igem.org/Wiki_How-To">Wiki Requirements page</a></li>
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<table width="940px"><tbody><tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/6/6c/Tokyo_Tech_118.png" width="60%"></td></tr><tr><td align="center" width="50%"><h4 class="fig"><strong>Fig.1-1-8.</strong> Prisoner A with tit-for-tat strategy in our iterated game</h4></td></tr></tbody></table>
</ul>
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<p class="text">For integration of concerns we have met through interactions with general public, about gene modification issues into our project, we designed and executed an expanded Prisoner’s Dilemma game played by the high school and undergraduate studentsWe found not only biased decision resulting from unconscious impression associated with the term “GMO”, but importance of reflecting on our iGEMer’s own conception of risks and cost & benefit by establishing a two-way dialogue.<br>
 
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(See <a href="https://2015.igem.org/Team:Tokyo_Tech/Practices">here</a> for more details)</p>
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<h4> Styling your wiki </h4>
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<table width="940px"><tbody><tr><td align="center"><img src="https://static.igem.org/mediawiki/2015/a/a7/Tokyo_Tech_119.png" width="60%"></td></tr><tr><td align="center"><h4 class="fig"><strong>Fig.1-1-9.</strong> Overall results of our expanded dilemma game among students</h4></td></tr></tbody></table>
<p>You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.</p>
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<p>While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.</p>  
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<h4> Editing your wiki </h4>
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>  
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<p> <a href="https://2015.igem.org/wiki/index.php?title=Team:Tokyo_Tech&action=edit"> Click here to edit this page! </a></p>
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<p>See tips on how to edit your wiki on the <a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation</a> page.</p>  
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<h4>Templates </h4>
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<p> This year we have created templates for teams to use freely. More information on how to use and edit the templates can be found on the
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      <img src="https://static.igem.org/mediawiki/2015/2/26/Tokyo_Tech_sponsors.png" width="800px">
<a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation </a> page.</p>  
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<h4>Tips</h4>
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    <img src="https://static.igem.org/mediawiki/2015/9/97/Tokyo_Tech_textarea_bottom.png">
<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and how you plan to do this.</li>
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away.  </li>
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2015.igem.org/Calendar_of_Events">iGEM 2015 calendar</a> </li>
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<li>Have lots of fun! </li>
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<h4>Inspiration</h4>
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
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</ul>
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<h4> Uploading pictures and files </h4>
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<p> You can upload your pictures and files to the iGEM 2015 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
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When you upload, set the "Destination Filename" to <code>Team:YourOfficialTeamName/NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)</p>
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<a href="https://2015.igem.org/Special:Upload">CLICK HERE TO UPLOAD FILES</a>
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Latest revision as of 03:55, 19 September 2015

Home

  


By integrating with our Policy & Practices and the results from our wet lab experiments and modeling, iGEM2015 Team Tokyo_Tech have executed our project with improved design in accordance with comments from general public, and have strengthened the public engagement of a two-way dialogue between our team and the public through this summer. (See here to know how we integrated our project)



What is Prisoner’s Dilemma?


The Prisoner’s Dilemma game, a typical example analyzed in game theory, involves two prisoners who were given an option selection opportunity either to cooperate or to defect according to the payoff matrix (Fig.1-1-1) in order to pursue for the best profit. (Go to Project 1. page) In our project, we decided to replicate an E. coli’s version of Prisoner’s Dilemma payoff matrix (Fig.1-1-2), which punishment means growth inhibition of E. coli. (Go to Project 2. page)


Fig.1-1-1. The payoff matrix in Prisoner's Dilemma (punishment = imprisoned years)

Fig.1-1-2. Our replicated payoff matrix for growth inhibition effect on prisoner coli



Project Overview


Like the prisoners in the Dilemma game, we genetically engineered two E. coli acting as Prisoner A and Prisoner B, which are able to cooperate or to defect in our E. coli’s version of Prisoner Dilemma. The combinations of their option (cooperation or defection) affect their profit which equals to their growth. To cooperate, they produce AHL while to defect, they do not produce AHL. The act of producing AHL imposes a metabolic burden on a prisoner coli. Furthermore, chloramphenicol antibiotic is used to inhibit prisoner coli’s growth in culture. However, AHL produced by the cooperation induces of the opponent prisoner, so that the expression of chloramphenicol resistant gene circumvents the growth inhibition effect.
(Go to Project 3. page)


Fig.1-1-3. The genetic circuits of prisoner coli with the options of cooperation or defection


Fig.1-1-4. Growth inhibition experienced by prisoner coli as a result of combination of option

Suggestion from modeling allowed us to successfully construct an improved part for precise implementation of our payoff matrix, when initial designed circuits showed leaky expression of CmR at the first stage of our experiment. This is one of engineering principle in our iGEM activity.
(See here for more modeling results)

Fig.1-1-5. Suggestions from modeling allow us improving a previously existing part


Using the improved plasmids we constructed to decrease effect of leaky expression, our E. coli version of payoff matrix is successfully replicated through wet lab experiments (Fig.1-1-6). In our payoff matrix, with the combination of four options between two prisoner coli, we succeeded to replicate four types of growth inhibition: none, low, middle, and high.
(See here for more details on our wet lab experiments)


Fig.1-1-6. The results from our wet lab replicated the payoff matrix


In order to enable prisoner coli to select its option randomly between cooperation and defection, we showed bidirectional inversion of Fim switch by FimB recombinase (BBa_K1632010). In our knowledge, this is the first case in iGEM to show random inversion of a promoter.
(See here to know more on how prisoner coli decides)
(See here to know more detail of FimB experiment results)


Fig.1-1-7. (A) FimB allows Decision making coli to select option at random, inverting a promoter in a fim switch
(B) The intensity of fluorescence in cells mrasured using flow cytometer
(C) Colony formation using plasmid mixture extrarcted cell expressing FimB

Our game design allows E. coli to realize one of four strategies including tit-for-tat strategy (Fig.1-1-8), the most successful strategy for Prisoner’s Dilemma. For implementation of this strategy, we confirmed unidirectional inversion of a fim switch by the FimE recombinase.
(See here to know on how we designed our parts)
(See here to know more detail of FimE experiment results)


Fig.1-1-8. Prisoner A with tit-for-tat strategy in our iterated game


For integration of concerns we have met through interactions with general public, about gene modification issues into our project, we designed and executed an expanded Prisoner’s Dilemma game played by the high school and undergraduate students. We found not only biased decision resulting from unconscious impression associated with the term “GMO”, but importance of reflecting on our iGEMer’s own conception of risks and cost & benefit by establishing a two-way dialogue.
(See here for more details)


Fig.1-1-9. Overall results of our expanded dilemma game among students