Difference between revisions of "Team:Tokyo Tech/Collaborations"

 
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<h1>Collaboration</h1>
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    <h1>Collaboration</h1>
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<h2>Helping us</h2>
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<h3>Team Nagahama</h3>
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<p>彼らは、我々に化学走性の実験について、2014年の彼らのプロジェクトを基に以下の2点のアドバイスを頂きました。</p>
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<p>1) アガーの濃度は0.3%が最も大腸菌の走性を示しやすいこと<br>
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2)大腸菌はアガーの表面に乗せるのではなく、チップをアガーの内部にさして大腸菌を挿入し実験を行うこと</p>
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<p>また、彼らは私たちに教えてくれた実験方法でwild typeでの化学走性実験を手伝ってくれました。 <font color="#780000">※長浜のプロトコルを載せるかどうか</font></p>
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        <h2 class="smalltitle">We helped Nagahama</h2>
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        <h3 class="sub5">Abstract</h3>
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[[File:Tokyo_Tech_nagahama1.png]]
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　　　　　　    <p class="text2">We helped team Nagahama by constructing a model and running simulations. By calculating the sufficient amount of culture fluid of <i>E.coli</i> which produce Geraniol to preserve food in a certain lunch box.
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<p>fig1. 大腸菌の正の走化性</p>
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The project is about making a method of preserving food not by cooling but by flavor, ‘KOZOKO: Flavorator'. </p><br>
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<h3 class="sub5">Setting the situation and Method</h3>
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　　　　　　    <p class="text2">We assumed a situation and constructed a model that we were preserving rice in a certain lunch box and laying the “Geraniol sheet” which contains concentrated Geraniol produced by <i>E.coli</i> on the bottom of the lunch box.<br>
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<li>Lについて…プレートの中央：大腸菌(JM109)、右：アスパラギン酸(10µM、40µl)</li>
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&nbsp;&nbsp;&nbsp;The size of the lunch box was 10W×10D×4H. Rice was packed and the ‘Geraniol sheet’ was laid on the bottom of the lunch box. The “Geraniol sheet” was 8W×8D×0.2H. The sheet contained concentrated Geraniol produced by <i>E.coli</i> in a culture fluid. <br>
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<li>Rについて…プレートの中央：大腸菌(JM109)、右：滅菌水(40µl)</li>
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&nbsp;&nbsp;&nbsp;As we laid the “Geraniol sheet” on the bottom of the lunch box, Geraniol contained in the sheet started to diffuse. We calculated the least concentration of Geraniol in the sheet in order to have the Geraniol concentration be above the effective bactericidal concentration even after laying the sheet for 24hours.</p><br><br>
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<li>培養時間：108時間</li>
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        <h3 class="sub5">Results</h3>
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<li>温度：30℃</li>
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            <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/0/0c/Tokyo_Tech_modeling_nagahama1.png" width="50%"/></div>
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            <h4 align="center" class="fig"><strong>Fig.&nbsp;7-5-1-1.</strong>The State of Diffusion in the xy Plain at z=0[mm]</h4>
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<p><img src="https://static.igem.org/mediawiki/2015/Tokyo-Tech-nagahama2.png"><br>
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fig2. 大腸菌の負の走化性</p>
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<li>Lについて…プレートの中央：大腸菌(JM109)、右：カドミウム(100mM、4µL)</li>
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<li>Rについて…プレートの中央：大腸菌(JM109)、右：滅菌水(40µl)</li>
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            <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/9/90/Tokyo_Tech_medeling_nagahama2.png" width="30%"/></div>
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<li>培養時間：110時間</li>
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<li>温度：30℃</li>
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            <h4 align="center" class="fig"><strong>Fig.&nbsp;7-5-1-2.</strong>The State of Diffusion in the yz Plain at x=50[mm]</h4>
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<p><font color="#ffb601">残念ながら今回は私たちの設計した遺伝子では、期間内に走性を示す結果を出すことが出来なかったため、大会にデータとして載せることが出来ませんでした。<br>
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しかし、長浜バイオ大学から頂いたアドバイスは非常に役立ちました。ありがとうございました。</p>
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<p>(※大会のデータにないということを載せるかどうか検討中)</p>
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            <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/6/6d/Tokyo_Tech_modeling_nagahama3.png" width="50%"/></div>
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            <h4 align="center" class="fig"><strong>Fig.&nbsp;7-5-1-3.</strong>The State of Diffusion in the xy Plain at z=40</h4>
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        <p class="text2">We use the culture fluid that <i>E.coli</i> were incubated for 48 hours. After the 48 hour of incubation, the culture fluid contained 183mg/L of Geraniol.</p>
 +
        <p class="text2">From our simulation, the culture fluid of <i>E.coli</i> should be concentrated 10,000 times in order to have the Geraniol concentration be above the effective bactericidal concentration even after laying the sheet for 24hours. The sufficient amount of culture fluid which we calculated in order to preserve rice in the box was 128L under our model.</p>
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<p class="text">This work was done using Matlab. For more information see <a href="https://2015.igem.org/Team:Tokyo_Tech/Collaborations_code">here</a>.</p><br>
  
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        <h2 class="smalltitle">We were helped by Nagahama</h2>
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        <h4 class="text"><p>From their past experiences in 2014, iGEM Team Nahahama gave us these 2 advices about chemotaxis experiments.<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;<strong>1.</strong> In order to increase the chemotactic activity of <i>E. coli</i>, the best concentration of agar is 0.3 %.<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;<strong>2.</strong> It is better to directly stick the chip inside the agar and then inject the <i>E .coli</i>, than to place the <i>E. coli</i> on top of the agar.
 +
        <p>Also, Team Nagahama gave us the raw data along with the protocol of the experiments for assaying the chemotactic activity of a wild type <i>E.coli</i>, following the protocol written above.</p>
 +
 
 +
<table width="940 px" border="0px">
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      <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/9/9a/Tokyo_Tech_nagahama1.png" width="450px"/></div>
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;7-5-2-1.</strong>Positive Chemotaxis of <i>E.coli</i></h4>
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<table width="940 px" border="0px">
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      <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/9/9a/Tokyo_Tech_nagahama1.png" width="450px"/></div>
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;7-5-2-2.</strong>Negative Chemotaxis of <i>E.coli</i></h4>
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        <p>Our plan at first was to integrate the chemotaxis experiment into our overall project. Unfortunately, we were unable to obtain positive results from the gene that we constructed, before the Giant Jamboree.
 +
However, the advice we received from Team Nagahama helped us a lot. We would like to say thanks to all the help we received from them.</p>
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      <h2 class="smalltitle">May Festival</h2>
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        <h4 class="text"><p>
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The Japanese iGEM teams took part in the school festival at the University of Tokyo.
 +
Our teams shared ideas and gave each other feedbacks. Together, we introduced synthetic biology to the public.<br>
 +
See the <a href="https://2015.igem.org/Team:Tokyo_Tech/Practices">“Policy & Practices”</a> page for further information.
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      <h2 class="smalltitle">Meetup with the iGEM LZU-China Team</h2>
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      <h4 class="text"><p>On the l9th of July, we held a meetup with the iGEM LZU-China team at Tokyo Institute of Technology.In this event, we each introduced our project along with the project from our previous year.
 +
We exchanged ideas about each other’s project and gave each other feedbacks.
 +
The iGEM LZU-China team also participated in our “Prisoner’s Dilemma Experiment” that we conducted. This experiment is a sociological experiment concerning the safety of genetic modification and is part of our “Policy & Practices”.
 +
See the <a href="https://2015.igem.org/Team:Tokyo_Tech/Practices">“Policy & Practices”</a> page for further information.
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</p><br>
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      <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/5/51/Tokyo_Tech_Meetup_with_the_iGEM_LZU-China_Team.jpg" width="360px"/></div>
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;7-5-4-1</strong> Meetup with the iGEM LZU-China Team</h4>
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      <h2 class="smalltitle">Meetup at Boston University</h2>
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      <h4 class="text"><p>On September 23th, our team is going to host a meetup in Boston University. We are looking forward to sharing ideas with other iGEM teams. Teams will have the opportunity to present their projects and exchange their ideas in details with other iGEM teams and faculty advisors right before the Giant Jamboree.<br>
 +
Meetup page: <a href="https://2015.igem.org/Meetups/Tokyo_Tech_Sept">Meetups/Tokyo Tech Sept</a>
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</p><br><br><br>
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Latest revision as of 03:25, 19 September 2015

Collaboration

　　

We helped Nagahama

Abstract

　　　　　　

We helped team Nagahama by constructing a model and running simulations. By calculating the sufficient amount of culture fluid of E.coli which produce Geraniol to preserve food in a certain lunch box. The project is about making a method of preserving food not by cooling but by flavor, ‘KOZOKO: Flavorator'.


Setting the situation and Method

　　　　　　

We assumed a situation and constructed a model that we were preserving rice in a certain lunch box and laying the “Geraniol sheet” which contains concentrated Geraniol produced by E.coli on the bottom of the lunch box.
   The size of the lunch box was 10W×10D×4H. Rice was packed and the ‘Geraniol sheet’ was laid on the bottom of the lunch box. The “Geraniol sheet” was 8W×8D×0.2H. The sheet contained concentrated Geraniol produced by E.coli in a culture fluid.
   As we laid the “Geraniol sheet” on the bottom of the lunch box, Geraniol contained in the sheet started to diffuse. We calculated the least concentration of Geraniol in the sheet in order to have the Geraniol concentration be above the effective bactericidal concentration even after laying the sheet for 24hours.



Results

Fig. 7-5-1-1.The State of Diffusion in the xy Plain at z=0[mm]


Fig. 7-5-1-2.The State of Diffusion in the yz Plain at x=50[mm]


Fig. 7-5-1-3.The State of Diffusion in the xy Plain at z=40


We use the culture fluid that E.coli were incubated for 48 hours. After the 48 hour of incubation, the culture fluid contained 183mg/L of Geraniol.

From our simulation, the culture fluid of E.coli should be concentrated 10,000 times in order to have the Geraniol concentration be above the effective bactericidal concentration even after laying the sheet for 24hours. The sufficient amount of culture fluid which we calculated in order to preserve rice in the box was 128L under our model.

This work was done using Matlab. For more information see here.


　
　　

We were helped by Nagahama

From their past experiences in 2014, iGEM Team Nahahama gave us these 2 advices about chemotaxis experiments.
    1. In order to increase the chemotactic activity of E. coli, the best concentration of agar is 0.3 %.
    2. It is better to directly stick the chip inside the agar and then inject the E .coli, than to place the E. coli on top of the agar.

Also, Team Nagahama gave us the raw data along with the protocol of the experiments for assaying the chemotactic activity of a wild type E.coli, following the protocol written above.

Fig. 7-5-2-1.Positive Chemotaxis of E.coli


Fig. 7-5-2-2.Negative Chemotaxis of E.coli

Our plan at first was to integrate the chemotaxis experiment into our overall project. Unfortunately, we were unable to obtain positive results from the gene that we constructed, before the Giant Jamboree. However, the advice we received from Team Nagahama helped us a lot. We would like to say thanks to all the help we received from them.

　
　　

May Festival

The Japanese iGEM teams took part in the school festival at the University of Tokyo. Our teams shared ideas and gave each other feedbacks. Together, we introduced synthetic biology to the public.
See the “Policy & Practices” page for further information.


　
　　

Meetup with the iGEM LZU-China Team

On the l9th of July, we held a meetup with the iGEM LZU-China team at Tokyo Institute of Technology.In this event, we each introduced our project along with the project from our previous year. We exchanged ideas about each other’s project and gave each other feedbacks. The iGEM LZU-China team also participated in our “Prisoner’s Dilemma Experiment” that we conducted. This experiment is a sociological experiment concerning the safety of genetic modification and is part of our “Policy & Practices”. See the “Policy & Practices” page for further information.


Fig. 7-5-4-1 Meetup with the iGEM LZU-China Team

　
　　

Meetup at Boston University

On September 23th, our team is going to host a meetup in Boston University. We are looking forward to sharing ideas with other iGEM teams. Teams will have the opportunity to present their projects and exchange their ideas in details with other iGEM teams and faculty advisors right before the Giant Jamboree.
Meetup page: Meetups/Tokyo Tech Sept