Difference between revisions of "Team:TokyoTech/Medal"

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    <label for="vmcb-a"><a href="https://2017.igem.org/Team:TokyoTech">Home</a></label>
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    <label for="vmcb-b"><a href="https://2017.igem.org/Team:TokyoTech/Medal">Achievements</a></label>
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      <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Description" class="w3-bar-item w3-button w3-hover-white">Description</a></li>
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          <label for="vmcb-d2"><a style="text-align: center;">Bacteria to <br>Human Cells ▼</a></label>
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              <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Improvement" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">TraI Improvement <br>Assay</a></li>
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              <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraR_Reporter_Assay" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white" >TraR Reporter <br>Assay</a></li>
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              <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Transcriptome_Analysis" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Transcriptome <br>Analysis</a></li>
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              <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Chimeric_Transcription_Factor" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Chimeric <br> Transcription <br> Factor Assay</a></li>
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    <label for="vmcb-e"><a href="https://2017.igem.org/Team:TokyoTech/Model">Modelling</a></label>
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     <li><a href="#overview" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">1</a></li>
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     <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Overview</a></li>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP/Silver" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Silver</a></li>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP/Gold_Integrated" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Gold (Integrated)</a></li>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Demonstrate" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Demonstrate</a></li>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Collaborations" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Collaborations</a></li>
 
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    <label for="vmcb-g"><a>About us</a></label>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Team" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Team</a></li>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Attributions" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Attributions</a></li>
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    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Sponsors" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Sponsors</a></li>
 
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<div class="w3-container" id="contact" style="margin-top:30px"><!-- ページタイトル -->
 
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<h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px" align="center">Achievements</h1>
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     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Results</b></h1><!-- 小見出し -->
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     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Medal Criteria</b></h1><!-- 小見出し -->
 
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            <!-- Bronze -->
 
 
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               <th rowspan="4">Bronze</th>
 
               <th rowspan="4">Bronze</th>
 
               <td class="prize_element_td">Register and attend</td>
 
               <td class="prize_element_td">Register and attend</td>
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               <td><p class="normal_text">We registered for iGEM, had a great summer, and attended the Giant Jamboree.</p></td>
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               <td><p style="font-size: 16px">We registered for iGEM, had a great summer, and attended the Giant Jamboree.</p></td>
 
             </tr>
 
             </tr>
 
             <tr>
 
             <tr>
 
               <td class="prize_element_td">Deliverables</td>
 
               <td class="prize_element_td">Deliverables</td>
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               <td><p class="normal_text">We met all deliverables on the Requirements page.</p></td>
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               <td><p style="font-size: 16px">We met all deliverables on the Requirements page.</p></td>
 
             </tr>
 
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             <tr>
 
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               <td class="prize_element_td">Attribution</td>
 
               <td class="prize_element_td">Attribution</td>
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               <td><p class="normal_text">We created a page on our team wiki with clear <a href="https://2016.igem.org/Team:Tokyo_Tech/Attributions">attribution</a> of each aspect of our project.</p></td>
+
               <td><p style="font-size: 16px">We created an <a href="https://2017.igem.org/Team:TokyoTech/Attributions">"Attributions"</a> page on our team wiki with clear attribution of each aspect in our project. (Click <a href="https://2017.igem.org/Team:TokyoTech/Attributions">here</a>)</p></td>
 
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               <td class="prize_element_td">Part</td>>
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               <td class="prize_element_td">Characterization / Contribution</td>
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               <td><p class="normal_text">We documented 5 new BioBrick Parts (<a href="http://parts.igem.org/Part:BBa_K1949100">BBa_K1949100</a>, <a href="http://parts.igem.org/Part:BBa_K1949101">BBa_K1949101</a>, <a href="http://parts.igem.org/Part:BBa_K1949102">BBa_K1949102</a>, <a href="http://parts.igem.org/Part:BBa_K1949000">BBa_K1949000</a>, <a href="http://parts.igem.org/Part:BBa_K1949001">BBa_K1949001</a>) central to our project and submitted them to the iGEM Registry . <br />
+
               <td><p style="font-size: 16px">We participated in the <a href="https://2017.igem.org/Team:TokyoTech/InterLab">Interlab Measurement Study</a>. (Click <a href="https://2017.igem.org/Team:TokyoTech/InterLab">here</a> to read more.)
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                <a href="https://2016.igem.org/Team:Tokyo_Tech/Parts">Read more</a></p></td>
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              </td>
 
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             <!-- /Bronze -->
 
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               <th rowspan="3">Silver</th>
 
               <th rowspan="3">Silver</th>
 
               <td class="prize_element_td">Validated Part</td>
 
               <td class="prize_element_td">Validated Part</td>
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               <td><p class="normal_text">We experimentally validated and documented 4 new BioBrick Parts/Devices (<a href="http://parts.igem.org/Part:BBa_K1949050">BBa_K1949050</a>, <a href="http://parts.igem.org/Part:BBa_K1949052">BBa_K1949052</a>, <a href="http://parts.igem.org/Part:BBa_K1949030">BBa_K1949030</a>, <a href="http://parts.igem.org/Part:BBa_K1949032">BBa_K1949032</a>) of our own design and construction that work as expected.<br />
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               <td><p style="font-size: 16px">We experimentally validated and documented new BioBrick Parts/Devices (<a href="http://parts.igem.org/Part:BBa_K2505000">BBa_K2505000</a>, <a href="http://parts.igem.org/Part:BBa_K2505001">BBa_K2505001</a>, <a href="http://parts.igem.org/Part:BBa_K2505005">BBa_K2505005</a> of our own design and construction that work as expected.<br /></p></td>
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                <a href="https://2016.igem.org/Team:Tokyo_Tech/Parts">Read more</a></p></td>
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             </tr>
 
             </tr>
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             <tr>
 
             <tr>
 
               <td class="prize_element_td">Collaboration</td>
 
               <td class="prize_element_td">Collaboration</td>
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               <td><p class="normal_text">We helped team <a href="https://2016.igem.org/Team:Tokyo_Tech/Collaborations#collaboration_kait">KAIT_Japan</a> model their system and <a href="https://2016.igem.org/Team:Tokyo_Tech/Collaborations#asij">taught a new high school team ASIJ</a> about modeling.<br />
+
               <td><p style="font-size: 16px">We helped <a href="https://2017.igem.org/Team:Tokyo_Tech/Collaborations#ionis">Team IONIS-Paris</a> with offering a BioBrick part, mentored Team ASIJ Tokyo</a> about the modeling and qualitative analysis and held a practice session with KAIT Japan at Boston University.<br />
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                <a href="https://2016.igem.org/Team:Tokyo_Tech/Collaborations">Read more</a></p></td>
+
              (Click <a href="https://2017.igem.org/Team:TokyoTech/Collaborations">here</a> to read more.)</p></td>
 
             </tr>
 
             </tr>
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             <tr>
 
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               <td class="prize_element_td">Human Practices</td>
 
               <td class="prize_element_td">Human Practices</td>
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               <td><p class="normal_text">We considered our project from three aspects: <a href="https://2016.igem.org/Team:Tokyo_Tech/Human_Practices#education">education</a>, <a href="https://2016.igem.org/Team:Tokyo_Tech/Human_Practices#ethics"> ethics</a>, and <a href="https://2016.igem.org/Team:Tokyo_Tech/Human_Practices#economy">economy</a>. To achieve this, we have done various outreach activities: School-visits, creating videos and a card game, hosting a symposium of bioethics, developing our original ethics code, and creating devices of protein production control. We also designed some genetic circuits which recreate other versions of Sow White. Through these activities, we could communicate with the public and improve our project from their feedback.<br />
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               <td><p style="font-size: 16px">We organized a symposium for middle school and high school students, held a workshop at high school to raise the awareness of young generation, attended summer school to learn about the relation between synthetic biology and social epidemiology.<br />
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                <a href="#human_practice">Read more</a>
+
              (Click <a href="https://2017.igem.org/Team:TokyoTech/HP">here</a> to read more.)
 
               </p></td>
 
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             <!-- Gold -->
 
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               <th rowspan="3">Gold</th>
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               <th rowspan="4">Gold</th>
 
               <td class="prize_element_td">Integrated Human Practices</td>
 
               <td class="prize_element_td">Integrated Human Practices</td>
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               <td><p class="normal_text">We held many activities in respect to our three aspects: education, ethics and economy. For example, we gave lessons to the students at 6 different high schools (269 students in total) and held a symposium. In addition, we applied the advice and ideas we got from the students and experts into our project. As a result, our Wet lab and Dry lab integrated to make <a href="https://2016.igem.org/Team:Tokyo_Tech/Model#abstract">"ACADwarfs,"</a> as well as figure out the concept of<a href="https://2016.igem.org/Team:Tokyo_Tech/Toxin_Assay/mazEF_System_Assay#Queen"> "TA system ～the Queen's Caprice～."</a>  <br />
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               <td><p style="font-size: 16px">By integrating with our Human Practices and the results from our wet lab experiments and modeling, iGEM2017 Team TokyoTech 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.<br />
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                 <a href="https://2016.igem.org/Team:Tokyo_Tech/HP/Gold">Read more</a></p></td>
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                 (Click <a href="https://2017.igem.org/Team:TokyoTech/HP/Gold_Integrated"> here</a> to read more.)</p></td>
 
             </tr>
 
             </tr>
 +
 
             <tr>
 
             <tr>
 
               <td class="prize_element_td">Improvement / Characterization</td>
 
               <td class="prize_element_td">Improvement / Characterization</td>
−
               <td><p class="normal_text">We correctly improved a BioBrick Parts (<a href="http://parts.igem.org/Part:BBa_R0071">BBa_R0071</a>) and characterized 6 BioBrick Parts/Device (<a href="http://parts.igem.org/Part:BBa_C0071">BBa_C0071</a>, <a href="http://parts.igem.org/Part:BBa_C0171">BBa_C0171</a>, <a href="http://parts.igem.org/Part:BBa_K1529300">BBa_K1529300</a>, <a href="http://parts.igem.org/Part:BBa_K1529310">Bba_K1529310</a>, <a href="http://parts.igem.org/Part:BBa_K1096002">BBa_K1096002</a>, <a href="http://parts.igem.org/Part:BBa_K1096001">BBa_K1096001</a>)<br />
+
               <td><p style="font-size: 16px">We correctly improved a BioBrick Part (<a href="http://parts.igem.org/Part:BBa_K553001">BBa_K553001</a>) <br />
−
                <a href="https://2016.igem.org/Team:Tokyo_Tech/Description">Read more</a></p></td>
+
              (Click <a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Improvement">here</a> to read more.)</p></td>
 
             </tr>
 
             </tr>
 +
 
             <tr>
 
             <tr>
−
               <td class="prize_element_td">Proof of concept</td>
+
               <td class="prize_element_td">Model your project</td>
−
               <td><p class="normal_text">We demonstrated 4 <a href="#proof">functional proof of concept</a> of our project: <a href="https://2016.igem.org/Team:Tokyo_Tech/Proof#Pcold">New cold inducible promoter</a>, <a href="https://2016.igem.org/Team:Tokyo_Tech/Proof#Rhl">Rhl system assay</a>, <a href="https://2016.igem.org/Team:Tokyo_Tech/Proof#TA">TA system</a>, <a href="https://2016.igem.org/Team:Tokyo_Tech/Proof#AmiE">Degradation of C12 by AmiE</a>. <br />
+
               <td><p style="font-size: 16px">We simulated the whole co-culture system and it turned out the improvement of <span style="font-style: italic;">traI</span> is necessary. We improved the gene using point mutation and after reflecting a new parameter in the simulation, we observed that the population of <span style="font-style: italic;">E. coli</span> is controlled.<br />
−
                <a href="#proof">Read more</a>
+
                (Click <a href="https://2017.igem.org/Team:TokyoTech/Model">here</a> to read more.)</p></td>
−
              </p></td>
+
 
             </tr>
 
             </tr>
 +
 +
            <tr>
 +
              <td class="prize_element_td">Demonstrate</td>
 +
              <td><p style="font-size: 16px">We conducted assay to measure the toxicity of bacterial signaling molecules and validated that our project have to work under realistic conditions.<br />
 +
                (Click <a href="https://2017.igem.org/Team:TokyoTech/Demonstrate">here</a>  to read more.)</p></td>
 +
            </tr>
 +
 
             <!-- /Gold -->
 
             <!-- /Gold -->
 
           </tbody>
 
           </tbody>
 
         </table>
 
         </table>
−
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−
 
+
−
 
+
−
    <div class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px;text-align: center">
+
−
    <figure>
+
−
    <img src="https://static.igem.org/mediawiki/2017/c/c6/T--TokyoTech--modeling_result_1021.png" style="max-width:50%">
+
−
    <figcaption style="font-family: Poppins;font-size: 16px">Fig. Result of modeling (After improvement of TraI)</figcaption>
+
−
    </figure>
+
−
    </div>
+
−
  </div>
+
  
 
<hr>
 
<hr>
  
 
<div class="w3-container" id="results" style="margin-top:20px">
 
<div class="w3-container" id="results" style="margin-top:20px">
−
     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Discussion</b></h1>
+
     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Best Information Processing</b></h1><!-- 小見出し -->
 
     <hr style="width:50px;border:5px solid red" class="w3-round">
 
     <hr style="width:50px;border:5px solid red" class="w3-round">
−
    <p style="font-family: Poppins;font-size: 16px">考察
 
−
    </p>
 
  
−
</div>
+
    <p style="font-size: 16px; text-indent: 1em">In iGEM history, many teams including Tokyo_Tech tried information processing between bacteria. This year we tried to establish an artificial cross-kingdom communication between human cell and bacteria then enable their co-culture. We call this new artificial human-bacteria co-culture living system “Coli sapiens.” Many factors like growth rate of human cells and bacterial cells are quite different and it is difficult to consider the all parameters to the model. In complex systems, only essential parameters were selected and an abstract model was designed.</p>
 +
    <p style="font-size: 16px; text-indent: 1em">To evaluate this model, drylab comprehensively simulated the property of the system using data from the experiments. As a result, our simulation contributed to the suggestion of part improvement to wetlab. This part improvement increased the feasibility of the model and it indicated that concentration of <span style="font-style: italic">E. coli</span> could be controlled by human cells and the condition for co-culture. Thus, we succeeded in engineering a new living system of co-existence between human cells and <span style="font-style: italic">E. coli</span>. This could be a progress for iGEM.</p>
 +
 
 +
  </div>
  
 
<hr>
 
<hr>
  
 
<div class="w3-container" id="results" style="margin-top:20px">
 
<div class="w3-container" id="results" style="margin-top:20px">
−
     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Reference</b></h1>
+
     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Proof of Concept</b></h1><!-- 小見出し -->
 
     <hr style="width:50px;border:5px solid red" class="w3-round">
 
     <hr style="width:50px;border:5px solid red" class="w3-round">
−
     <p style="font-family: Poppins;font-size: 16px">参考文献
+
     <p style="font-size: 16px; text-indent: 1em">If we can establish a co-culture system, we can find a way to achieve population balance to sustain the co-existence and apply for the medical field like a cancer treatment. In addition, since human and bacteria have originally co-existed, the establishment of a co-culture system will contribute to the development of organism closer to life.</p>
−
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<p id="pageTop" style="text-align:right"><a href="#wrap"><img src="https://static.igem.org/mediawiki/2017/0/0d/T--TokyoTech--page_top_2.png" style="width:200px"></a></p>
 +
</div>
  
−
<div class="w3-light-grey w3-container w3-padding-32" style="margin-top:75px;padding-right:58px"><p class="w3-right">Hajime Fujita:  <a href="96haji.me" title="W3.CSS" target="_blank" class="w3-hover-opacity">All Rights Reserved</a></p></div>
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Latest revision as of 22:48, 1 November 2017

<!DOCTYPE html> Coli Sapiens

iGEM Tokyo Tech

Achievements

Medal Criteria

Bronze Register and attend

We registered for iGEM, had a great summer, and attended the Giant Jamboree.
Deliverables

We met all deliverables on the Requirements page.
Attribution

We created an "Attributions" page on our team wiki with clear attribution of each aspect in our project. (Click here)
Characterization / Contribution

We participated in the Interlab Measurement Study. (Click here to read more.)

Silver Validated Part

We experimentally validated and documented new BioBrick Parts/Devices (BBa_K2505000, BBa_K2505001, BBa_K2505005 of our own design and construction that work as expected.
Collaboration

We helped Team IONIS-Paris with offering a BioBrick part, mentored Team ASIJ Tokyo about the modeling and qualitative analysis and held a practice session with KAIT Japan at Boston University.
(Click here to read more.)
Human Practices

We organized a symposium for middle school and high school students, held a workshop at high school to raise the awareness of young generation, attended summer school to learn about the relation between synthetic biology and social epidemiology.
(Click here to read more.)

Gold Integrated Human Practices

By integrating with our Human Practices and the results from our wet lab experiments and modeling, iGEM2017 Team TokyoTech 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.
(Click here to read more.)
Improvement / Characterization

We correctly improved a BioBrick Part (BBa_K553001)
(Click here to read more.)
Model your project

We simulated the whole co-culture system and it turned out the improvement of traI is necessary. We improved the gene using point mutation and after reflecting a new parameter in the simulation, we observed that the population of E. coli is controlled.
(Click here to read more.)
Demonstrate

We conducted assay to measure the toxicity of bacterial signaling molecules and validated that our project have to work under realistic conditions.
(Click here to read more.)

Best Information Processing

In iGEM history, many teams including Tokyo_Tech tried information processing between bacteria. This year we tried to establish an artificial cross-kingdom communication between human cell and bacteria then enable their co-culture. We call this new artificial human-bacteria co-culture living system “Coli sapiens.” Many factors like growth rate of human cells and bacterial cells are quite different and it is difficult to consider the all parameters to the model. In complex systems, only essential parameters were selected and an abstract model was designed.

To evaluate this model, drylab comprehensively simulated the property of the system using data from the experiments. As a result, our simulation contributed to the suggestion of part improvement to wetlab. This part improvement increased the feasibility of the model and it indicated that concentration of E. coli could be controlled by human cells and the condition for co-culture. Thus, we succeeded in engineering a new living system of co-existence between human cells and E. coli. This could be a progress for iGEM.

Proof of Concept

If we can establish a co-culture system, we can find a way to achieve population balance to sustain the co-existence and apply for the medical field like a cancer treatment. In addition, since human and bacteria have originally co-existed, the establishment of a co-culture system will contribute to the development of organism closer to life.

Hajime Fujita with W3.CSS: All Rights Reserved