Difference between revisions of "Team:Tokyo Tech/Human Practices"

 
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<h1 align="center">Human Practice</h1>
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<h1 align="center">Human Practices</h1>
 
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<h3 class="link"><a href="#introduction">1. Introduction</a></h3>
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<h3 class="link"><a href="#introduction">1. Overview</a></h3>
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<h3 class="link"><a href="#overview">2. Overview</a></h3>  
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<h3 class="link"><a href="#overview">2. 3E</a></h3>  
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<h3 class="link"><a href="#3E">3. 3E</a></h3>
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<h3 class="link"><a href="#3E">3. Policy and Practices</a></h3>
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<h3 class="link"><a href="#Policy_and_Practices">4. Policy and Practices</a></h3>
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<h3 class="link"><a href="#Policy_and_Practices">4. Snow White versions</a></h3>
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<h3 class="link"><a href="#Snow_White_Versions">5. Snow White Versions</a></h3>
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<h1><span>Introduction</span></h1>
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<h1><span>1. Overview</span></h1>
 
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<p class="normal_text">iGEM 2016 Tokyo_Tech Team has had outstanding projects every year especially in terms of experiments and modeling. This year, in order to develop further, we had hold outreach activities positively from the beginning of our project. We also had dialogues with the public and stakeholders to apply their advice to our project. Moreover, we had built this project considering the contribution to society.
+
<p class="normal_text">At the beginning of our iGEM activities, we felt that people seem to be unfamiliar with synthetic biology and its social contribution. In order to solve these issues, we chose to show our concepts through Snow White, one of the most famous stories around the world. Besides, we held many outreach activities,  dialogued with experts, and created a model called "3E": education, ethics, and economy. We also designed some ideas based to our research (Toxin-Antitoxin system etc.) for society. <br>
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  Currently, synthetic biology is unfamiliar to the public, and in most cases, they cannot comprehend it easily. However, using the Snow White story that everyone knows, our project is interesting and accessible. We did human practice activities to raise public interest in synthetic biology and to inspire the public to learn it with a familiar story, Snow White.
+
We contributed to raising public awareness of synthetic biology and improving our project through science communication.</p>
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What is more, our research about Toxin-Antitoxin system (TA system) and Quorum Sensing (QS) created "ACA Dwarfs" and "TA system &#126;Queen's Caprice&#126;." Additionally, we are doing the experiments of <span style="font-style: italic">E. coli</span> mutants that secrete proteins extracellularly. It makes a giant step towards technological developments in economy in the future.
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</ul>
 
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<h1><span>Overview</span></h1>
 
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<p class="normal_text">Through communicating with the public, it was shown that people tend to have an erroneous idea about genetic modification and <span style="font-style: italic">E. coli</span>, and they have almost no idea about synthetic biology. Additionally, there is some evidence that they cannot understand the contribution to society primarily. In order to solve these problems, we created a model called 3E model to find out the contribution of this project from three aspects: education, ethics, and economy. We are aiming to make our iGEM activity have an utmost contribution to society.
 
−
Additionally, we summarized in chronological order how the outreach activities, the classes we gave and the dialogues with experts had made changes in our project, and what we thought and did with their advice.
 
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Moreover, there have been a lot of versions of Grimm's  Snow White. Although we were not able to use experiments to represent all the different versions of the story, we were able to design a genetic circuit.
 
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<h1><span>3E</span></h1>
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<h1><span>2. 3E</span></h1>
 
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<p class="normal_text">We take our project into consideration from three aspects: education, ethics, and economy. From these three aspects, we can approach in various ways, thereby we can grasp our project multilaterally. So far, we had worked on many activities to inform the public distinctly of <span style="font-style: italic">E. coli</span>, genetic modification, and synthetic biology. Once we faced some issues, we had many discussions and tried solving the problems. Secondly, we had thought about ethics as a key point in our project and made ethics code of iGEM 2016 Tokyo_Tech Team. Furthermore, we coordinated activities to achieve the protein production control using TA systems. Although it is difficult to use commercially at present, it is a great achievement that we created the idea and technology regarded as a steppingstone. This page shows all of our human practice activities.
+
<p class="normal_text">We approach the social meaning of our project from three aspects: Education, Ethics, and Economy. Education plays an important role to raise scientific literacy as one of the most fundamental activities in daily life. Ethics is indispensable when you are engaged in synthetic biology. Economic profit is produced by technological application of synthetic biology. To approach the social meaning (of our project) from these aspects, we worked on many activities. This page shows all of our human practice activities.</p>
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</p>
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<div id="education_overview" class="3e_contents">
 
<div id="education_overview" class="3e_contents">
 
<h3 class="3e_contents_header">Overview</h3>
 
<h3 class="3e_contents_header">Overview</h3>
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<p class="normal_text">After exchanging opinions with the public in school festivals(including May festival, Suzukake festival and Homecoming day), we found that the knowledge about genetic modification, <span style="font-style:italic;">E. coli</span> and synthetic biology is less well known.</p>
+
<p class="normal_text">After exchanging opinions with the public in school festivals (including May festival, Suzukake festival and Homecoming day), we found that the majority of people do not know much about synthetic biology. We thought that attributes to the lack of opportunity to stimulate their curiosity. Therefore, using a familiar fairy tale, Snow White, as a main theme, we designed our project. We also gave classes and made YouTube videos to raise the awareness. After the classes we gave, students improved their awareness of genetic modification and <span style="font-style: italic;">E. coli</span>. Furthermore we created a special card game for the public in order to let them study science independently and delightfully. It can be used as a new type of educational tool and requires the basic knowledge about Toxin&#8208;Antitoxin system(TA system) and Quorum Sensing(QS).</p>
−
<p class="normal_text">Therefore, we gave classes and made YouTube videos of genetic modification, <span style="font-style: italic;">E. coli</span>, and synthetic biology to have the public, especially the youth, know them.</p>
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−
<p class="normal_text">In order to let the general public, especially the youth, know more about the knowledge about <span style="normal_text">E. coli</span> and synthetic biology, we gave related classes to high school students as well as making teaching videos which can be viewed on YouTube.</p>
+
−
<p class="normal_text">Using the familiar story of Snow White as a base to our project, many people got interested on it because of the story, but thanks to that they also got interested in synthetic biology.</p>
+
−
<p class="normal_text">As a result, more and more people got interested in synthetic biology and <span style="font-style:italic;">E. coli</span> because of the plot of Snow White we used which is familiar to the most.</p>
+
−
<p class="normal_text">Moreover, after the classes we gave, students improved their awareness of genetic modification and <span style="font-style: italic;">E. coli</span>.</p>
+
−
<p class="normal_text">&nbsp;</p>
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<p class="normal_text">We worked on the development of an educational tool for the high school students in order to let the youth study science independently and delightfully. It is a card game about TA system and QS. It attracted more of their attention than only talking about the knowledge.</p>
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</div><!-- /education_overview -->
 
</div><!-- /education_overview -->
 
 
 
<div id="education_school_visit" class="3e_contents">
 
<div id="education_school_visit" class="3e_contents">
 
<h3 class="3e_contents_header">School-visits</h3>
 
<h3 class="3e_contents_header">School-visits</h3>
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<p class="normal_text">During the May Festival, the Suzukake Festival and the Home-Coming Day, when we talked to the general public, we found out that the <span style="font-style: italic;">E. coli</span> is being rather misunderstood. So in order to solve this misunderstanding, and to provide more people with a more accurate information about <span style="font-style: italic">E. coli</span>, gene reconfiguration, and synthetic biology in general we decided to conduct some School-visits. As a result, we managed to give classes in 6 Schools and to 269 middle and high school students in total. Furthermore, this activity turned out to be a good opportunity to learn how our project impacted in the general public. We can also say that the fact that the ideas we obtained here managed to positively influence our project is a result out of itself.</p>
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<p class="normal_text">In order to enhance the understanding of youths, we decided to conduct some School-visits. As a result, we gave lectures to 269 middle and high school students from 6 schools. Furthermore, these activities were good opportunities to learn how our project can impact the general public.</p>
−
<p class="normal_text">The details are organized for each school, so if anyone were to do this kind of lectures in the future, fell free to use this as reference.</p>
+
<p class="normal_text">The detail of each school visit is organized on our wiki, so you can use it as a reference if you come to get involved in this kind of activity.</p>
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<div id="school_visit_images">
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<p class="normal_text">If your mouse is over photos you can see the explanation. You can see the details when you click the photo,
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<!-- Ochanomizu -->
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<a href="https://static.igem.org/mediawiki/2016/6/63/T--Tokyo_Tech--HumanPractice_Ochanomizu.pdf" class="school_visit_image"><img src="https://static.igem.org/mediawiki/2016/8/8f/T--Tokyo_Tech--Otchanomizu.jpg" /></a>
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<p class="normal_text">There is not only one story for Snow<br />White, but there exist several ones.</p>
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<h4>We designed a circuit in order<br />to recreate the story using our<br />own parts!</h4>
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<p class="normal_text">Does no other character apart from Snow White, the Prince and the Queen appear?</p>
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<h4>We decided to include the Mirror in the Story!</h4>
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<a href="https://static.igem.org/mediawiki/2016/3/38/T--Tokyo_Tech--HumanPractice_ToritsuNishi.pdf" class="school_visit_image"><img src="https://static.igem.org/mediawiki/2016/d/d7/T--Tokyo_Tech--Toritsu_West_Lecture.jpg" /></a>
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<p class="normal_text">It is interesting to recreate the story of Snow White, but is there a way to apply Tokyo_Tech’s project into medicine or agriculture?</p>
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<h4>Could we use the TA system for any contribution to society?</h4>
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<p class="normal_text">“I was surprised to see how you can use <span style="font-style:italic;">E. coli</span> to make this kind of playful experiments!”
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It changed my impression that <span style="font-style:italic;">E. coli</span> equals food poison, and now I fell some kind of respect for it.
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<div id="gakugei_left"><p class="normal_text">We usually hear the term gene recombination, but never how it’s done. It sounds hard!</p></div>
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<div id="gakugei_right"><p class="normal_text">I was surprised that it wasn’t as hard as I thought. It looks like it could be used in several fields. I’d like to try it too.</p></div>
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<p class="normal_text">We included the opinion of the students in our card game and improved it!</p>
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<p class="normal_text">What kind of lecture should we perform in order to let students understand better the gene recombination technics.</p>
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<h4>Let’s ask the Science Comunicator</h4>
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<p class="normal_text">As a result of incorporating what we learn after talking to the science communicator in our lectures... we obtained even better results!</p>
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<div id="education_video" class="3e_contents">
 
<div id="education_video" class="3e_contents">
 
<h3 class="3e_contents_header">Video</h3>
 
<h3 class="3e_contents_header">Video</h3>
−
<p class="normal_text">"It is difficult." "I don't get it" "What are you doing?"</p>
+
<p class="normal_text">"It is difficult." "I don't get it." "What are you doing?"</p>
−
<p class="normal_text">These are words that the public told us about our activities, which means that the public did not understand our activity well.Therefore, we made intelligible videos to improve this situation. Moreover, the third episode is dubbed into Japanese, English, Chinese and Spanish so that more people will be able to understand. </p>
+
<p class="normal_text">These are words that the public told us about our activities, which means that the public did not understand our activity well. Therefore, we made intelligible videos to improve this situation.</p>
 
<p class="normal_text">The first episode: What is <span style="font-style: italic;">E. coli</span>?<br />
 
<p class="normal_text">The first episode: What is <span style="font-style: italic;">E. coli</span>?<br />
 
<a href="https://youtu.be/VJre_GtDRo4" target="_blank">https://youtu.be/VJre_GtDRo4</a></p>
 
<a href="https://youtu.be/VJre_GtDRo4" target="_blank">https://youtu.be/VJre_GtDRo4</a></p>
 
<p class="normal_text">The second episode: How to modify genes? What can we do by modifying the genes of <span style="font-style:italic;">E. coli</span>?<br />
 
<p class="normal_text">The second episode: How to modify genes? What can we do by modifying the genes of <span style="font-style:italic;">E. coli</span>?<br />
 
<a href="https://youtu.be/nJtvFeMDbac" target="_blank">https://youtu.be/nJtvFeMDbac</a></p>
 
<a href="https://youtu.be/nJtvFeMDbac" target="_blank">https://youtu.be/nJtvFeMDbac</a></p>
−
<p class="normal_text">The second episode: How to modify genes? What can we do by modifying the genes of <span style="font-style:italic;">E. coli</span>?<br />
+
<p class="normal_text">The third episode: "Snow White"<br />
−
<a href=" " target="_blank"> </a></p>
+
<a href="https://youtu.be/BCej9LzkYlc " target="_blank"> https://youtu.be/BCej9LzkYlc</a></p>
 
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</div><!-- /education_video -->
 
 
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<h3 class="3e_contents_header">Card Game</h3>
 
<h3 class="3e_contents_header">Card Game</h3>
 
<p class="normal_text">The public will not understand our project unless they experience it.</p>
 
<p class="normal_text">The public will not understand our project unless they experience it.</p>
−
<p class="normal_text">So we made a card game containing two functions so that the public can understand the basis of our project, TA system and Quorum Sensing.</p>
+
<p class="normal_text">So we made a card game containing two functions so that the public can understand the basis of our project, TA system and QS. Click here to download the kit with the rulebook that we developed through trial and error so everyone can play easily. If you get interested in this card game, you can print it out and play it yourself.</p>
−
<p class="normal_text">In order to let the public understand TA system and Quorum Sensing, which is the basis of our project, we made the card game contains 2 functions.</p>
+
<p class="normal_text"><a href="https://static.igem.org/mediawiki/2016/2/22/T%E3%83%BC%E3%83%BCTokyo%EF%BC%BFTech%E3%83%BC%E3%83%BCcardgame_rule.pdf">Card Game Rule</a></p>
−
<p class="normal_text">Click here to download the kit with the rulebook that we developed through trial and error so everyone can play easily. If you get interested in this card game, you can print it out and play it yourself.</p>
+
                                        <p class="normal_text"><a href="https://static.igem.org/mediawiki/2016/0/0c/T%E3%83%BC%E3%83%BCTokyo%EF%BC%BFTech%E3%83%BC%E3%83%BCcardgame_parts.pdf">Card Game Parts</a></p>
 
</div><!-- /education_card_game -->
 
</div><!-- /education_card_game -->
 
 
 
<div id="education_expert" class="3e_contents">
 
<div id="education_expert" class="3e_contents">
−
<h3 class="3e_contents_header">Expert [Ogawa Tatsuya]</h3>
+
<h3 class="3e_contents_header"><a href="https://2016.igem.org/Team:Tokyo_Tech/Human_Practices/National_museum">Expert [Ogawa Tatsuya]</a></h3>
 
<p class="normal_text">We noticed that the ways of manifesting and expressing our project are important when we explain our project to the public.</p>
 
<p class="normal_text">We noticed that the ways of manifesting and expressing our project are important when we explain our project to the public.</p>
−
<p class="normal_text">He gave us the advice that we should insert a punch line in our project to summarize our project to the audience's satisfaction. We should not only talk about the results but also convince the audience through our explanation.Hence, we should construct the whole concept, thinking what listeners will think after explanation about our project. </p>
+
<p class="normal_text">He gave us the advice that we should insert a punch line in our project to summarize our project to the audience's satisfaction. We should not only talk about the results but also convince the audience through our explanation. Hence, we should construct the whole concept, thinking what listeners will think after explanation about our project. </p>
−
<p class="normal_text">Hence, we should try to think about what we want to impress the listeners most after they listened to our project's explanation. Based on the advice, we rethink the flow of our project and arrange the flow of our project accordingly.</p>
+
 
</div><!-- /education_expert -->
 
</div><!-- /education_expert -->
 
 
 
<div id="education_summary" class="3e_contents">
 
<div id="education_summary" class="3e_contents">
 
<h3 class="3e_contents_header">Summary</h3>
 
<h3 class="3e_contents_header">Summary</h3>
−
<p class="normal_text">We raised the public's attention of genetic modification, <span style="font-style:italic;">E. coli</span> and synthetic biology through our activities.  
+
<p class="normal_text">We raised the public's attention of genetic modification, <span style="font-style:italic;">E. coli</span> and synthetic biology through our activities. Since we found our activities are influential to many people, we want to continue these to inform the utility of synthetic biology to the public even after iGEM. </p>
−
<p class="normal_text">Since we found our activities are influential to many people, we want to continue these to inform the utility of synthetic biology to the public even after iGEM. </p>
+
 
</div><!-- /education_summary -->
 
</div><!-- /education_summary -->
 
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<div id="ethics" class="container_contents container_contents_3e">
 
<div id="ethics" class="container_contents container_contents_3e">
 
<h2 class="container_contents_header"><img src="https://static.igem.org/mediawiki/2016/9/95/T--Tokyo_Tech--Ethics_String.png" /></h2>
 
<h2 class="container_contents_header"><img src="https://static.igem.org/mediawiki/2016/9/95/T--Tokyo_Tech--Ethics_String.png" /></h2>
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                                <div id="ethics_ovevrview" class="3e_contents">
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                                        <h3 class="3e_contents_header">Overview</h3>
 +
                                        <p class="normal_text"> There always exists ethic problem about research of life science. Especially synthetic biology, there are a lot of problems in this field. The judge about the boundary between the research allowed and the research restricted is extremely difficult. However, as researchers of life science, iGEM 2016 team Tokyo_Tech must take into account the problems arising deeply. In this case, we organized a symposium where we can discuss with the experts and exchange opinions with them. Moreover, we start to think about our ethic code of synthetic biology, basing on the things we learned from this symposium.</p>
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<p style="text-align: center;" class="normal_text">[<a href="javascript:void(0);" onClick="show('ethics_hide'); return false;" class="showHidden">Read More</a>]</p>
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                                </div><!-- /ethics_overview -->
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                                <div id="ethics_symposium" class="3e_contents">
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                                <h3 class="3e_contents_header">Symposium</h3>
 +
                                        <p class="normal_text">We discussed with 6 researchers who is working on synthetic biology in this symposium. Then we learned that which one should be deal with between ethics of technology and ethics of science is decided by the thing that between developing technology and scientific research, which field your study is most likely to belong to. We have interests in this thing , so when we think about ethic code, we make it based on this.</p>
 +
                                        <p class="normal_text">Firstly, the reason why the ethic of technology and the one of science are different is because the goals of studies are different. The goal of debeloping technology is mainly application in the society, as a result, it is necessary to include appropriateness of method, usability, security and management of risk. On the other hand, researcher do the scientific studies due to the spirit of inquiry, therefore, it is necessary to include appropriateness and completely mutual criticism among researchers. We aim to make our project be applied to developing technology which is usable to society, therefore, we think about our ethic code referencing the ethic of technology. However, thinking about the ethic directly is difficult, so at the first step, we want to think about ethic related to what kind of problems in our project.</p>
 +
                                </div><!-- /ethics_symposium -->
 +
                           
 +
                                <div id="ethics_iGEM_Tokyo_Tech2016’s ethic problem" class="3e_contents">
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                                <h3 class="3e_contents_header">iGEM_Tokyo_Tech2016's ethic problem</h3>
 +
                                        <p class="normal_text">As what we said in Future work, we are thinking that whether TA system can be applied to DDS and to decreasing risk of mutidrug-resistant bacteria appearing . In the temporary society, according to the law, taking out the designate genetically modified organism is restricted. Additionally, research institutes are focus on the construction whether it can leak genetically modified organism or not. However, the solution to the leak of genetically modified organism are being developed. And the utility of <span style="font-style: italic;">E. coli</span> which will extinct even without being dealed with to become weak under the dry condition. </p>
 +
                                        <p class="normal_text">We thought about the danger of synthetic biology to our human being so far, on the other hand, we also need to take account into the creature used in experiments. We are using <span style="font-style: italic;">E. coli</span> in our project this time.when we actually did the experiment, <span style="font-style: italic;">E. coli</span> is systematically different with human being, so we hard to have a sense of guilty even though we make them work to meet our own needs. However, how about the other creatures? Their lives are likely to be decided by species when we didn’t even realize it.</p>
 +
                                        <p class="normal_text">In addition, in order to decrease the amount of creatures used in experiments as possible as we can, using modeling is important．In the past, modeling is used to decide the most suitable amount of reagent and time. We apply it to enhance consciousness that we try our best to decrease the amount of creature utilized.</p>
 +
                                </div><!-- /ethics_iGEM_Tokyo_Tech2016’s ethic problem -->
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                                <div id="ethics_our synthetic biology research’s code of ethics" class="3e_contents">
 +
                                <h3 class="3e_contents_header">Our ethic code of synthetic biology</h3>
 +
                                      <p class="normal_text">It is becoming possible currently that Through machine learning about construction elements of creature, we regard construction elements as spare parts , design some creature functions and create artificial intelligence. Although through this people will get profit, the other creatures will be faced with new dangers. In order to prevent creatures from dangers, people who work on synthetic biology should follow the things shown below.
 +
</p>
 +
<ul>
 +
                                      <li><p class="normal_text">We should respect every life and be grateful to every life utilized in experiment.</p></li>
 +
                                        <li><p class="normal_text">We should concern about the influences on life environment of utilized sample and testee.</p></li>
 +
                                        <li><p class="normal_text">We should be aware of our position as a researcher and never utilize any specimens escaping from the law in gene modification experiments and etc; and we should never perform any fraud of experimental results, unauthorized reproduction or any other kind of plagiarism that would put in doubt one’s dignity.</p></li>
 +
                                        <li><p class="normal_text">We should always respect the others' position, and try our best to make up for deficiency mutually like in the Asilomar Conferences. Specially, since cooperation between wet and dry teams is important, we need to share information daily and never fail to communicate in order to improve the understanding of each other.</p></li>
 +
                                        <li><p class="normal_text">Compared to the analytic approach, the synthetic approach has to take in consideration more topics including technology and ethic. So it is not something easily achievable. Take in account that not everything is going to go as expected.</p></li>
 +
                                        <li><p class="normal_text">Through reducing the amount of creature utilized, we need to concern about environment, give a whole impression and do simulation to clarify the goals.</p></li>
 +
                                        <li><p class="normal_text">When "designing" biomolecules or biological systems, we should take into account the use of artistic activities to make our project easier to understand to the general public.</p></li>
 +
</ul>
 +
                                </div><!-- /ethics_Our synthetic biology research’s code of ethics -->
 +
 +
                                <div id="ethics_final remarks" class="3e_contents">
 +
                                <h3 class="3e_contents_header">Final remarks</h3>
 +
                                        <p class="normal_text">Because there is no clear boundary, it is hard to find clear answer of ethic problems such as genetically modification. For example, the boundary of living and non living creature depends on species. Moreover, there are always different opinions because of culture and religon. All the things above are the reason making ethic problems become complicated. </p>
 +
                                        <p class="normal_text">On the other hand, as reality, ordinary people tend to think towards questions that it is scientist who should take into account theses problems, and have nothing to do with the problems. In order to change the way they are thinking, it is important to have the opportunities that we can get information from scientists in symposium and lectures given to high school students. We need to let ordinary people know that ethic problems do have relation with them, which is also merit for scientists. when we were giving the lecture to high school students, we know something new through the conversation among ordinary people, which is different when we talk with scientists. Everyone can feel the ethic problems closing to their daily life through thinking about what kind of questions will happen and discussing with each other. Moreover, by popularizing this, there is a goal that all the actions taken are right after thinking about life ethic.</p>
 +
                                </div><!-- /ethics_Final remarks-->
 +
 +
                                <div id="ethics_referance" class="3e_contents">
 +
                                <h3 class="3e_contents_header">Reference
 +
                                      <p class="normal_text">1. Nudeshina, Jiro Ph.D. To what extent should research on life be free? -dialogue with scientists (in Japanese) Iwanami Shoten Publisheres, Tokyo, 2010</p>
 +
                                      <p class="normal_text">2.Makoto Masuda. [Internet].Japan: Gouseiseibutsugaku－sonokanouseitokadai－ [cited July 18th, 2011]. Available from http://www.tbr.co.jp/pdf/sensor/sen_a216.pdf</p>
 +
                                      <p class="normal_text">3. TA Note 07 [Internet]. Japan: Seimeikinounokozotekikenkyunogenzyotosya　kaitekikadai：nihonniokerugouseiseibutsugakutoha？(Present state and social problems on structural research of life function: What is ‘Synthetic Biology’ in Japan?)　[cited October 7th, 2016] Available from http://i2ta.org/news/i2ta/ta-note-07.html</p>
 +
                                      <p class="normal_text">4. The Institution of Professional Engineers, Japan [Internet]. Japan: Gizyutushi- rinrikoryo [cited October 7th, 2016]
 +
Available from www.engineer.or.jp/c_topics/000/000025.html</p>
 +
                                      <p class="normal_text">5. Japanese Association of Certified Social Workers [Internet]. Japan: Rinrikoryotokoudoukihan [cited October 7th, 2016] Available from:
 +
http://www.jacsw.or.jp/01_csw/05_rinrikoryo/
 +
                                      <p class="normal_text">6. Japanese Nursing Association [Internet]. Japan: Kangosyanorinrikoryo
 +
[cited October 7th, 2016] Available from: http://www.nurse.or.jp/nursing/practice/rinri/rinri.html</p>
 +
                                      <p class="normal_text">7.  John R Pringle, James R Broach,Elizabeth W Jones. The Molecular and Cellular Biology of the Yeast Saccharomyces. Vol. 3. Cell Cycle and Cell Biology. US: Cold Spring Harbor Laboratory Press; 1997.</p>
 +
                                </div><!-- /ethics_reference-->
 +
 +
</div><!-- /ethics_hide -->
 
</div><!-- /ethics -->
 
</div><!-- /ethics -->
 
 
Line 365: Line 791:
 
<h3 class="3e_contents_header">Overview</h3>
 
<h3 class="3e_contents_header">Overview</h3>
 
<p class="normal_text">In order to use our project in society, we decided to approach it from a big perspective, economy. Our project includes a basic research, so, we thought that we should work on our project in terms of economy, instead of more specific fields such as environment and medicine, to make our project flexible to the upcoming technology. Among many elements of our project, in this page we focus on TA system.</p>
 
<p class="normal_text">In order to use our project in society, we decided to approach it from a big perspective, economy. Our project includes a basic research, so, we thought that we should work on our project in terms of economy, instead of more specific fields such as environment and medicine, to make our project flexible to the upcoming technology. Among many elements of our project, in this page we focus on TA system.</p>
−
<p class="normal_text">We had a dialogue with experts to think our project from an economic perspective. This dialogue was the big turning point of our project.</p>
+
<p class="normal_text">We had a dialogue with experts to think our project from an economic perspective. This dialogue was the biggest turning point of our project.</p>
 
</div><!-- /economy_overview -->
 
</div><!-- /economy_overview -->
 
 
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<p class="normal_text">
 
<p class="normal_text">
 
Prof. Nakasaki is a professor on the department of international development engineering at Tokyo Tech. He is researching about bio-refinery, prevention of plant disease by functional compost and DNA sensor of compost maturity. One of his research aims to produce chemical materials efficiently such as L-lactone and ethanol that is biodegradable plastic materials.</p>
 
Prof. Nakasaki is a professor on the department of international development engineering at Tokyo Tech. He is researching about bio-refinery, prevention of plant disease by functional compost and DNA sensor of compost maturity. One of his research aims to produce chemical materials efficiently such as L-lactone and ethanol that is biodegradable plastic materials.</p>
−
<p class="normal_text">He is doing the research for industrial use of genetic recombination technology, so we thought that he is eligible for dialogues from the economic perspective. Therefore, we set up a meeting.</p>
 
 
<p class="normal_text">&nbsp;</p>
 
<p class="normal_text">&nbsp;</p>
 
<p class="normal_text">He showed interest in the fact that TA system inhibits the cell growth of <i>E. coli</i> and can even "resuscitate" it. And also in the protein expression that comes with this mechanism. During the dialogue, we were given with the positive option that continuously repeating the control of protein production can lead to a technology which reduces the risk of the appearance of multiple-drug-resistant bacteria. Therefore, from the view point of economy, we set a goal to control protein production.</p>
 
<p class="normal_text">He showed interest in the fact that TA system inhibits the cell growth of <i>E. coli</i> and can even "resuscitate" it. And also in the protein expression that comes with this mechanism. During the dialogue, we were given with the positive option that continuously repeating the control of protein production can lead to a technology which reduces the risk of the appearance of multiple-drug-resistant bacteria. Therefore, from the view point of economy, we set a goal to control protein production.</p>
 
<p class="normal_text"><span style="font-weight: bold;">After this dialogue,</span> we have done two things to implement the protein production control.</p>
 
<p class="normal_text"><span style="font-weight: bold;">After this dialogue,</span> we have done two things to implement the protein production control.</p>
 
<ol type="i">
 
<ol type="i">
−
<li><p class="normal_text">ACA Rise and Fall Code"<br />
+
<li><p class="normal_text"><a href="https://2016.igem.org/Team:Tokyo_Tech/Model#abstract">ACA Rise and Fall Code</a><br />
 
<img src="https://static.igem.org/mediawiki/2016/8/8b/T--Tokyo_Tech--ACA_Dwarfs.jpg" width="150px" class="align_left" />
 
<img src="https://static.igem.org/mediawiki/2016/8/8b/T--Tokyo_Tech--ACA_Dwarfs.jpg" width="150px" class="align_left" />
 
The development of a software which adjusts the number of ACA (Adenine-Cytosine-Adenine) sequence in the DNA.</p>
 
The development of a software which adjusts the number of ACA (Adenine-Cytosine-Adenine) sequence in the DNA.</p>
−
<p class="clear">&nbsp;</p></li>
+
<p class="tokyo_tech_clear">&nbsp;</p></li>
−
<li><p class="normal_text">The experiments of creating <i>E. coli</i> mutants which secrete protein extracellularly</p>
+
<li><p class="normal_text">
−
                                                     <p class="normal_text"> "TA system ~Queen's Caprice~"
+
<a href="https://2016.igem.org/Team:Tokyo_Tech/The experiments of creating E. coli mutants which secrete protein extracellularly">The experiments of creating <i>E. coli</i> mutants which secrete protein extracellularly</a></p>
 +
                                                     <p class="normal_text"> <a href="https://2016.igem.org/Team:Tokyo_Tech/Toxin_Assay/mazEF_System_Assay#Queen">"TA system ~Queen's Caprice~"</a>
 
</p>
 
</p>
 
<p class="normal_text">These resulted in big success to obtain protein production control.</p></li>
 
<p class="normal_text">These resulted in big success to obtain protein production control.</p></li>
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<div id="future_work" class="container">
 
<div id="future_work" class="container">
 
<div id="future_work_header" class="container_header">
 
<div id="future_work_header" class="container_header">
−
<h1><span>Future Work</span></h1>
+
<h1><span style="border-bottom: solid 2px;">Future Work</span></h1>
 
</div><!-- /future_work_header -->
 
</div><!-- /future_work_header -->
 
<div id="future_work_contents" class="container_contents">
 
<div id="future_work_contents" class="container_contents">
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<p class="normal_text">We consider the possibility of the protein production system is controlled by Maz system and signal transfer mechanism. To improve the performance of controlling the production by Maz system, we developed a tool for increasing or decreasing the number of ACA sequence, which is the specific site cleaved by MazF homo dimmer. Maz system.</p>
 
<p class="normal_text">We consider the possibility of the protein production system is controlled by Maz system and signal transfer mechanism. To improve the performance of controlling the production by Maz system, we developed a tool for increasing or decreasing the number of ACA sequence, which is the specific site cleaved by MazF homo dimmer. Maz system.</p>
 
<ol type="i">
 
<ol type="i">
−
<li><p class="normal_text">controlling the protein production </p></li>
+
<li><p class="normal_text">Controlling the protein production </p></li>
−
<li><p class="normal_text">selectivity of the target mRNA</p></li>
+
<li><p class="normal_text">Selectivity of the target mRNA</p></li>
−
<li><p class="normal_text">system of communicating with outside </p></li>
+
<li><p class="normal_text">System of communicating with outside </p></li>
 
</ol>
 
</ol>
−
<p class="normal_text">Combining i. and ii., it is expected that the target protein is obtained effectively and with favorite rate. Furthermore, adding iii., we could design an automatic and advanced information-processing system. In other words, we could design an oscillatory cell-to-cell communication in which one cell containing man system, receives an extrinsic signal (Maz system is controlled by the type of the signal), then the cell produces the substance which affects other cells.</p>
+
<p class="normal_text">Combining i. and ii., it is expected that the target protein is obtained effectively and with favorite rate. Furthermore, adding iii., we could design an automatic and advanced information-processing system. In other words, we could design an oscillatory cell-cell communication in which one cell containing man system, receives an extrinsic signal (Maz system is controlled by the type of the signal), then the cell produces the substance which affects other cells.</p>
 
<p class="normal_text">To increase the selectivity of repressing the protein production by Maz system, we develop a tool of increasing or decreasing the number of ACA sequence named "ACA Dwarfs." This application makes our future work much more realistic than other iGEM teams (see <a href="https://2016.igem.org/Team:Tokyo_Tech/Model">Model page</a>).</p>
 
<p class="normal_text">To increase the selectivity of repressing the protein production by Maz system, we develop a tool of increasing or decreasing the number of ACA sequence named "ACA Dwarfs." This application makes our future work much more realistic than other iGEM teams (see <a href="https://2016.igem.org/Team:Tokyo_Tech/Model">Model page</a>).</p>
 
<p class="normal_text">Furthermore, a lot of vital phenomena are oscillatory. So we could apply this oscillatory system to DDS (Drug Delivery System) or to decrease the risk of the appearance of the multi-drug-resistant strains. </p>
 
<p class="normal_text">Furthermore, a lot of vital phenomena are oscillatory. So we could apply this oscillatory system to DDS (Drug Delivery System) or to decrease the risk of the appearance of the multi-drug-resistant strains. </p>
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<p class="normal_text">Introducing maz system to human cells and orchestrating the human original signal transduction system and Maz system, we design the mechanism that the cell secrets drug depended on the internal condition. For example, when a maz system introduced cell receives the blood glucose level increase, the cell synthesizes the insulin.</p>
 
<p class="normal_text">Introducing maz system to human cells and orchestrating the human original signal transduction system and Maz system, we design the mechanism that the cell secrets drug depended on the internal condition. For example, when a maz system introduced cell receives the blood glucose level increase, the cell synthesizes the insulin.</p>
 
</li>
 
</li>
−
                                       <li><p class="normal_text">Our Quorum Sensing and TA systems might be applicable to control the Intestinal Flora</p>
+
                                       <li><p class="normal_text">Our TA systems and QS might be applicable to control the Intestinal Flora</p>
 
                                               <h3 align="header">1.Introduction</h3>
 
                                               <h3 align="header">1.Introduction</h3>
−
                                               <p class="normal_text">These days, Intestinal Flora draws a lot of attention because it will greatly affect our health. If the balance of intestinal flora is lost, it will lead into an illness or might even change your personality. It is assumed that intestinal flora consists of communication systems among various bacteria. However, no such communication systems have been found. So, it will contribute to the society to clarify the mechanism of intestinal flora and to find a way of controlling it.
+
                                               <p class="normal_text">These days, Intestinal Flora draws a lot of attention because it will greatly affect our health. If the balance of intestinal flora is lost, it will lead into an illness or might even change your personality. It is assumed that intestinal flora consists of communication systems among various bacteria. However, no such communication systems have been found. So, it will contribute to the society to clarify the mechanism of intestinal flora and to find a way of controlling it.</p>
−
Our project focused on the cell-cell communication through Toxin-Antitoxin system (TA system) and Quorum Sensing (QS), and proved the initial step to explain and control the system of the intestinal symbiosis.</p>
+
<p class="normal_text">Our project focused on the cell-cell communication through TA system and QS, and proved the initial step to explain and control the system of the intestinal symbiosis.</p>
 +
 
 +
<p class="normal_text" style="text-align:center;"><a href="javascript:void(0);" onClick="show('modeling_detail');" class="showHidden"><img src="https://static.igem.org/mediawiki/2016/5/54/T--Tokyo_Tech--readmore.png"></a></p>
 +
 
 +
<div id="modeling_detail" class="off">
 
         <h3 align="header">2. The results of our project</h3>                                     
 
         <h3 align="header">2. The results of our project</h3>                                     
 
  <h4 align="header">2-1. TA System Assay</h4>
 
  <h4 align="header">2-1. TA System Assay</h4>
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<h4 align="header">2-2. AHL and AmiE Assay</h4>
 
<h4 align="header">2-2. AHL and AmiE Assay</h4>
−
  <p class="normal_text">We indicated that QS of <i>Pseudomonas aeruginosa genes</i>and <i>V. fischeri</i>, and <i>amiE</i>, which selectively degrades AHLs, could work in <i> E. coli</i>. Sometimes, these genes are toxic to <i>E. coli</i>, but this was solved by, for example, tagging <i>ssrA</i> or experimenting at low temperatures (see AHL Reporter assay page and AmiE assay page). </p></br>
+
  <p class="normal_text">We indicated that QS of <i>Pseudomonas aeruginosa genes</i>and <i>V. fischeri</i>, and <i>amiE</i>, which selectively degrades AHLs, could work in <i> E. coli</i>. Sometimes, these genes are toxic to <i>E. coli</i>, but this was solved by, for example, tagging <i>ssrA</i> or experimenting at low temperatures (see AHL reporter assay page and AmiE assay page). </p></br>
  
 
<h4 align="header">2-3. Temperature-dependent Promoters</h4>
 
<h4 align="header">2-3. Temperature-dependent Promoters</h4>
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<p class="normal_text"> We simulated our final genetic circuits containing the genes of TA system, QS and temperature-dependent promoters. The simulation showed that the circuits could perform favorably by improving some parts (see Model page and Rhl system assay page). </p>
 
<p class="normal_text"> We simulated our final genetic circuits containing the genes of TA system, QS and temperature-dependent promoters. The simulation showed that the circuits could perform favorably by improving some parts (see Model page and Rhl system assay page). </p>
 
                                                     <h3 align="header">3. Discussion</h3>
 
                                                     <h3 align="header">3. Discussion</h3>
−
  <p class="normal_text">In conclusion, we proved that the genes of other bacterial QS and temperature-dependent promoters worked in <i>E. coli</i> and that <i>E. coli</i> original TA system gene under expression-inducing promoters regulated the growth in WET experiments. From these results, the simulation showed that <i>E. coli</i> containing TA system gene and QS gene under various expression-inducing promoters communicated with each other. </br>
+
  <p class="normal_text">In conclusion, we proved that the genes of other bacterial QS and temperature-dependent promoters worked in <i>E. coli</i> and that <i>E. coli</i> original TA system gene under inducible promoters regulated the growth in WET experiments. From these results, the simulation showed that <i>E. coli</i> containing TA system gene and QS gene under various inducible promoters communicated with each other. </br>
−
  Besides, by simulating that the genetic circuits worked properly with the three types of expression-inducing promoters, we suggest that intestinal bacterial growth is controlled by nutritional condition, temperature and intestinal bacterial density. The three types of promoters were the sugar-dependent promoters (PBAD, Plac), the temperature-dependent promoters (Pcold, Pheat) and the AHL-dependent promoters (Prhl, Plux and Plas).
+
  Besides, by simulating that the genetic circuits worked properly with the three types of inducible promoters, we suggest that intestinal bacterial growth is controlled by nutritional condition, temperature and intestinal bacterial density. The three types of promoters were the sugar-dependent promoters (PBAD, Plac), the temperature-dependent promoters (Pcold, Pheat) and the AHL-dependent promoters (Prhl, Plux and Plas).
 
  Our project therefore helps to understand the symbiosis of intestinal flora. Furthermore, we are quite sure that we could engineer the <i>E. coli</i> or other bacteria which have function of regulating the symbiosis.</p>
 
  Our project therefore helps to understand the symbiosis of intestinal flora. Furthermore, we are quite sure that we could engineer the <i>E. coli</i> or other bacteria which have function of regulating the symbiosis.</p>
 +
 +
</div>
 
                                                           </li>
 
                                                           </li>
  
Line 451: Line 883:
 
<div id="Policy_and_Practices" class="container">
 
<div id="Policy_and_Practices" class="container">
 
    <div id="policy_and_practice_header" class="container_header">
 
    <div id="policy_and_practice_header" class="container_header">
−
<h1><span>Policy & Practices</span></h1>
+
<h1><span>3. Policy & Practices</span></h1>
 
    </div><!-- /policy_and_practice_header -->
 
    </div><!-- /policy_and_practice_header -->
 
    <div class="container_contents">
 
    <div class="container_contents">
−
<p class="normal_text">In promoting our project, we had dialogues with the public and experts. Based on the opinions from them, we developed our project. This led to success in creation of a well-rounded project with the connection between the public and experts, keeping from our narrow view.</p>
+
<p class="normal_text">During promotion of our project, we had dialogues with the public and experts. Based on the opinions from them, we developed our project. Keeping from our narrow view, this led to success in creation of a well-rounded project with connection between the public and experts.</p>
−
<p class="normal_text">This page explains the changes that some events had made to our project in chronological order.</p>
+
<p class="normal_text">This page explains changes that some events had made to our project in chronological order.</p>
 
<img src="https://static.igem.org/mediawiki/2016/8/8d/T--Tokyo_Tech--Integrated_Slide_Figure.jpg" alt="Integrated_Silde_Figure" width="800px" usemap="#practice_map" />
 
<img src="https://static.igem.org/mediawiki/2016/8/8d/T--Tokyo_Tech--Integrated_Slide_Figure.jpg" alt="Integrated_Silde_Figure" width="800px" usemap="#practice_map" />
 
<map name="practice_map">
 
<map name="practice_map">
Line 470: Line 902:
 
 
 
<div id="general_public">
 
<div id="general_public">
−
    <p class="normal_text">In the school festivals, we did poster presentation. Through the diverse dialogues with the general public about our preliminary idea of several projects, we found out that the public preferred the Snow White project.</p>
+
    <p class="normal_text">In the school festivals, we did poster presentation. Through diverse dialogues with the general public about our preliminary idea of several projects, we found out that the public preferred the Snow White project, one of the preliminary projects. As we figured out even though contents of Snow White project are difficult to understand, the public still showed great interest in it because it brought a sense of familiarity to the most. And this obviously leads to the public's deeper understanding of Snow White project than the others. Thus, we selected Snow White as our project.</p>
−
    <p class="normal_text">Even though the contents of Snow White project are difficult to understand for the public, they still showed great interest in it because it brought a sense of familiarity to them. And this obviously lead to the public's deeper understanding of Snow White project than the others. Thus we determined our project as Snow White.</p>
+
 
</div><!-- /general_public -->
 
</div><!-- /general_public -->
 
 
 
<div id="school_visits">
 
<div id="school_visits">
−
    <p class="normal_text">Then in the classes we gave to the high school students, we were asked that why there are only three characters in the story. Accordingly, we found suitable characters and environmental factors to add into the story. </p>
+
    <p class="normal_text">Then, in the classes we gave to high school students, we were asked the reason why there are only three characters in the story. Accordingly, we found suitable characters and environmental factors to add into the story.</p>
 
</div><!-- /school_visits -->
 
</div><!-- /school_visits -->
 
 
 
<div id="dialog">
 
<div id="dialog">
−
    <p class="normal_text">Another question from the students was that representing the story was interesting, but how our project can contribute to the society. This actually inspired us a lot for we started to focus on the consideration of the prospect of our project.</p>
+
    <p class="normal_text">Another question from the students is that representing the story is interesting, but how our project can contribute to the society. Because this comment actually inspired us a lot, we started to focus on the consideration of the prospect of our project. After having dialogue with experts, we obtained a comment that TA system has a potential to be linked to development of effective technology. However, at present, there exits problems when using a TA system to control the protein production. We cannot selectively produce only desired protein because other proteins would be also produced at the same time. Then, our dry lab used JAVA to develop software named "ACADwarfs" adjusting number of ACA base sequence as a solution to the problem.
−
</div><!-- /dialog -->
+
</p>
−
+
−
<p class="normal_text"><span style="font-weight: bold;">After having dialogue with expert,</span> we obtained the comment that TA system has the potential to be linked to the development of effective technology.</p>
+
−
<p class="normal_text">However, at present there exit problems when using a TA system to control the protein production.
+
−
We cannot selectively produce only desired protein, because other proteins also would be produced at the same time.</p>
+
−
<p class="normal_text"><span style="font-weight: bold;">Then</span> our dry lab used Java to reseach into the development of ACA base sequence's number adjustable software which we call it "ACA Dwarfs" as a solution to the problem.</p>
+
 
    </div>
 
    </div>
 
     
 
     
Line 492: Line 918:
 
    <div class="container_contents">
 
    <div class="container_contents">
 
<p class="normal_text">&nbsp;</p>
 
<p class="normal_text">&nbsp;</p>
−
<p class="normal_text">In this way, we integrated Human Practices to out project. However, we have done much more activities for Human Practices and show them in detail below.</p>
+
<p class="normal_text">In this way, we integrated Human Practices to out project. However, we have done much more activities for Human Practices and show them in detail, below.</p>
 
<p class="normal_text">&nbsp;</p>
 
<p class="normal_text">&nbsp;</p>
 
 
Line 516: Line 942:
 
    <div class="practice_left integrated_human integrated_human_contents">
 
    <div class="practice_left integrated_human integrated_human_contents">
 
<a class="integrated_human_header" href="https://2016.igem.org/Team:Tokyo_Tech/Collaborations#may_festival">Public Engagement / Dialogue<br />May Festival</a>
 
<a class="integrated_human_header" href="https://2016.igem.org/Team:Tokyo_Tech/Collaborations#may_festival">Public Engagement / Dialogue<br />May Festival</a>
−
<p class="normal_text">At the school festival of University of Tokyo, the public (parents and friends of students at University of Tokyo, and people who hung around the festival) advised on our project in a poster session.  </p>
+
<p class="normal_text">At the university festival of University of Tokyo, the public (parents and friends of students at University of Tokyo, and the other visitors of the festival) advised on our project in a poster session.  </p>
 
<p class="normal_text">Among the projects, the ones with approachable themes were quite popular.</p>
 
<p class="normal_text">Among the projects, the ones with approachable themes were quite popular.</p>
 
    </div>
 
    </div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="54px" /></div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="54px" /></div>
 
    <div class="practice_right practices practices_contents">
 
    <div class="practice_right practices practices_contents">
−
<p class="integrated_human_header">Settle on "Snow White" from prospective projects</p>
+
<p class="integrated_human_header">Select "Snow White" from prospective projects</p>
−
<p class="normal_text">Snow White is the story everyone knows, and people can understand the story pretty much. Moreover, it is familiar to the public and promotes a better understanding about <span style="font-style:italic;">E. coli</span>, synthetic biology, and our project.</p>
+
<p class="normal_text">Snow White is the story everyone knows, and people can understand the story pretty much. Moreover, it is familiar to the public and promotes a better understanding about <span style="font-style:italic;">E. coli</span>, synthetic biology and our project. </p>
 
    </div>
 
    </div>
 
</div>
 
</div>
Line 529: Line 955:
 
    <div class="practice_left integrated_human integrated_human_contents">
 
    <div class="practice_left integrated_human integrated_human_contents">
 
<a class="integrated_human_header" href="">Public Engagement / Dialogue<br />Suzukake Festival</a>
 
<a class="integrated_human_header" href="">Public Engagement / Dialogue<br />Suzukake Festival</a>
−
<p class="normal_text">At the school festival of Tokyo Tech, the public (parents and friends of students at Tokyo Tech, and people who hung around the festival) advised on our project in a poster session. We got the advice that we should put on a play to make our story easier to understand.</p>
+
<p class="normal_text">At the university festival of Tokyo Tech, the public (parents and friends of students at Tokyo Tech, and the other visitors of the festival) advised on our project in a poster session. We got an advice that we should put on a shortplay to make our story easier to be understood.</p>
 
    </div>
 
    </div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="32px" /></div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="32px" /></div>
 
    <div class="practice_left practices practices_contents">
 
    <div class="practice_left practices practices_contents">
−
<p class="normal_text">Let's perform a play during the presentation!</p>
+
<p class="normal_text">Let's perform a short play during the presentation!</p>
 
    </div>
 
    </div>
 
</div>
 
</div>
Line 541: Line 967:
 
<a class="integrated_human_header" href="https://2016.igem.org/Team:Tokyo_Tech/HomecomingDay">Public Engagement / Dialogue<br />
 
<a class="integrated_human_header" href="https://2016.igem.org/Team:Tokyo_Tech/HomecomingDay">Public Engagement / Dialogue<br />
 
Homecoming Day</a>
 
Homecoming Day</a>
−
<p class="normal_text">This is an annual event held at Tokyo Tech with everyone related to Tokyo Tech and local people, where we aimed to get feedback from them by introducing our activities with a poster. However, we were not able to tell the public science and technology easily, and they had trouble understanding baseline knowledge.</p>
+
<p class="normal_text">This is an annual event held at Tokyo Tech with everyone related to Tokyo Tech and neighboring residents, where we aimed to get feedback from them by introducing our activities with a poster. However, we could hardly tell the public science and technology easily, and they had trouble understanding fundamental knowledge. </p>
 
    </div>
 
    </div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="32px" /></div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="32px" /></div>
 
    <div class="practice_right practices  practices_contents">
 
    <div class="practice_right practices  practices_contents">
 
<ul class="normal_text"><li>Make videos about <span style="font-style: italic;">E. coli</span> and synthetic biology for the public.</li>
 
<ul class="normal_text"><li>Make videos about <span style="font-style: italic;">E. coli</span> and synthetic biology for the public.</li>
−
<li>Make an interesting card game for study.</li></ul>
+
<li>Make an interesting card game for study.</li></ul>
 
    </div>
 
    </div>
 
</div>
 
</div>
Line 554: Line 980:
 
<a class="integrated_human_header" href="">School-visits<br />
 
<a class="integrated_human_header" href="">School-visits<br />
 
Ochanomizu University Junior High School</a>
 
Ochanomizu University Junior High School</a>
−
<p class="normal_text"><span style="font-weight: bold;">The classes's goal was to obtain feedback on our project from junior high school students and to get our project valued with their own evaluation axes.</span> One student offered the following comment.<br />
+
<p class="normal_text"><span style="font-weight: bold;">Aim of the lesson was to obtain feedback on our project from junior high school students, and to get evaluations of our project on the basis of their criteria. One student offered a following comment.
 +
<br />
 
"Don't other characters appear in the story?"
 
"Don't other characters appear in the story?"
 
</p>
 
</p>
Line 561: Line 988:
 
    <div class="practice_left practices practices_contents">
 
    <div class="practice_left practices practices_contents">
 
<p class="integrated_human_header">At the beginning, the characters were three: Snow White, the Queen and the Prince. To make our story closer to the original one, we added the Magic Mirror to the story.</p>
 
<p class="integrated_human_header">At the beginning, the characters were three: Snow White, the Queen and the Prince. To make our story closer to the original one, we added the Magic Mirror to the story.</p>
−
<p class="normal_text">Snow White story has some versions. Based on our parts, we designed two gene circuits to represent different story versions.</p>
+
<p class="normal_text">There are some versions of Snow White story. Using our parts, we designed two gene circuits to represent different story versions.</p>
 
    </div>
 
    </div>
 
</div>
 
</div>
Line 569: Line 996:
 
    <div class="practice_left integrated_human integrated_human_contents">
 
    <div class="practice_left integrated_human integrated_human_contents">
 
<a class="integrated_human_header" href="">School-visits
 
<a class="integrated_human_header" href="">School-visits
−
Tokyo Metropolitan Nishi High School</a>
+
<br>Tokyo Metropolitan Nishi High School</a>
−
    <p class="normal_text"><span style="font-weight: bold;">The classes' goal was to raise student's interest in iGEM through the explanation of the possibility of genetic modification, gene recombination techniques, and synthetic biology. The other goal of this class was to get feedback on our project from high school students. In the class we focused on the explanation of our project at the time.</span> One student gave the following opinion.</p>
+
    <p class="normal_text"><span style="font-weight: bold;">Aim of the lesson was to raise student’s interest in iGEM through explanation of possibilities of genetic modifications, gene recombination techniques, and synthetic biology. The other aim of this lesson was to get feedback on our project from high school students. In the lesson, we focused on explanation of our project at that time. One student gave the following opinion.</p>
 
    <p class="normal_text">"Certainly, representing Snow White Story is interesting, but can you make your project work for society?"</p>
 
    <p class="normal_text">"Certainly, representing Snow White Story is interesting, but can you make your project work for society?"</p>
 
    </div>
 
    </div>
Line 577: Line 1,004:
 
     
 
     
 
    <p class="normal_text">Can we make something socially beneficial?</p>
 
    <p class="normal_text">Can we make something socially beneficial?</p>
−
<p class="normal_text">We discussed with ourselves and set up an opportunity to have a dialogue with experts.</p>
+
<p class="normal_text">We discuss by ourselves, and set up opportunities to have dialogues with experts.</p>
 
</div>
 
</div>
 
    </div>
 
    </div>
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<div class="practice_right integrated_human integrated_human_contents">
 
<div class="practice_right integrated_human integrated_human_contents">
 
    <p class="integrated_human_header">Expert Prof. Nakasaki</p>
 
    <p class="integrated_human_header">Expert Prof. Nakasaki</p>
−
    <p class="normal_text">During the dialogue, He said that repetition of protein production control probably takes a step to the technology which reduces the risk of the multiple-drug-resistant bacteria emergence.</p>
+
    <p class="normal_text">During the dialogue, he said that repetition of protein production control probably takes a step to the technology reducing risk of the multiple-drug-resistant bacteria emergence.</p>
 
</div>
 
</div>
 
<div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="54px" /></div>
 
<div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="54px" /></div>
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<a class="integrated_human_header" href="">School-visits<br />
 
<a class="integrated_human_header" href="">School-visits<br />
 
Kanagawa prefectural Atsugi High School</a>
 
Kanagawa prefectural Atsugi High School</a>
−
<p class="normal_text">Aim of the Class:
+
<p class="normal_text">The classes' goal was to raise students' interest and awareness of <span style="font-style: italic">E. coli</span> and to increase the knowledge about synthetic biology and gene ligation techniques.</p>
−
To raise students' interest and awareness of <span style="font-style: italic">E. coli</span> and to increase knowledge about synthetic biology and gene ligation techniques.</p>
+
<p>The class got the result of an advance in knowledge and enhancement of the students' interest toward genetic modification (However, we could have got better results.) </p>
−
<p>The class got the result of an advance in knowledge and enhancement of students' interest toward genetic modification (However, we could have got better results.) </p>
+
 
    </div>
 
    </div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="54px" /></div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="54px" /></div>
 
    <div class="practice_left practices practices_contents">
 
    <div class="practice_left practices practices_contents">
−
<p class="normal_text">So far, iGEM team Tokyo_Tech has "tell the public synthetic biology" in various ways with the familiar theme. However, we have not been able to affect all of the people. We thought that the reason relied on our way of communication. Therefore, we decided to ask a science communicator, who is an expert of telling science to the public.</p>
+
<p class="normal_text">So far, iGEM team Tokyo_Tech has "told the public about synthetic biology" in various ways with a familiar theme. However, we have not been able to influence all of the people. We thought that the reason relied on our way of communication. Therefore, we decided to ask a science communicator, who is an expert on telling science to the public.</p>
 
    </div>
 
    </div>
 
</div>
 
</div>
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<div class="practice_wrapper">
 
<div class="practice_wrapper">
 
    <div class="practice_left integrated_human integrated_human_contents">
 
    <div class="practice_left integrated_human integrated_human_contents">
−
<a class="integrated_human_header">National museum, nature and science, Tokyo<br />
+
<a class="integrated_human_header" href="https://2016.igem.org/Team:Tokyo_Tech/Human_Practices/National_museum">National museum, nature and science, Tokyo<br>
−
Science Communicator Mr. Ogawa</a>
+
Science Communicator Mr. Ogawa</a>
−
<p class="normal_text">He told us that only representing the research cannot attract audience's interest, and cannot get shrewd feedback. Also, he suggested that our story should have a clear conclusion to tell people something.</p>
+
<p class="normal_text">He told us that only representing the research cannot attract the audience's interest, and cannot get shrewd feedback. Also, he suggested that our story should have a clear conclusion that can tell people something.</p>
 
    </div>
 
    </div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="32px" /></div>
 
    <div class="practice_center"><img src="https://static.igem.org/mediawiki/2016/2/27/T--Tokyo_Tech--Apple.png" width="32px" /></div>
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<h2 align="center">Summary</h2>
 
<h2 align="center">Summary</h2>
 
<p class="normal_text">We "went beyond the lab" and developed our project through human practice activities.</p>
 
<p class="normal_text">We "went beyond the lab" and developed our project through human practice activities.</p>
−
<p class="normal_text">We have not just reflected the opinions from the dialogue with the public and experts about our project. Firstly, we investigated and discussed the issues on our own. Secondly, in the light of the application of our project, we did the experiments and modeling. Finally, we succeeded in the creation of "ACADwarfs" and "TA system～Queen's Caprice～". Furthermore, we are doing the experiments to make <span style="font-style: italic;">E. coli</span> mutants secreting protein extracellularly. The products will probably lead to further developments of our project. </p>
+
<p class="normal_text">We have not just reflected opinions from dialogues with the public and experts about our project. Firstly, we investigated and discussed about the issues on our own. Secondly, in the light of the application of our project, we did experiments and modeling. Finally, we succeeded in the creation of "ACADwarfs" and "the growth and death wave by toxin-antitoxin on agar medium." Furthermore, we are doing experiments to make <span style="font-style: italic;">E. coli</span> mutants secreting protein extracellularly. The products will probably lead to further developments of our project.</p>
 
<p class="normal_text">Achievements as mentioned above indicate that we have succeeded in the integrated Human Practice.</p>
 
<p class="normal_text">Achievements as mentioned above indicate that we have succeeded in the integrated Human Practice.</p>
 +
       
 +
                        <div class="tokyo_tech_clear"></div>
 
 
 
 
−
<h3><a href="https://2016.igem.org/Team:Tokyo_Tech/Collaborations#may_festival">Suzukake Festival (May 14 & 15, 2016)</a></h3>
+
<h3>Suzukake Festival (May 14 & 15, 2016)</h3>
 
<img src="https://static.igem.org/mediawiki/2016/8/81/T--Tokyo_Tech--May_Festival.png" alt="May Festival" width="200px" style="float: left;" />
 
<img src="https://static.igem.org/mediawiki/2016/8/81/T--Tokyo_Tech--May_Festival.png" alt="May Festival" width="200px" style="float: left;" />
−
<p class="normal_text" style="float: left; width: 550px;">The Suzukake Festival, the school festival on the Suzukakedai campus, was held on May 14-15, 2016. We introduced iGEM and our projects to the visitors to let them know synthetic biology and got feedbacks.</p>
+
<p class="normal_text" style="float: left; width: 550px; margin-left: 10px;">The Suzukake Festival, the school festival on the Suzukakedai campus, was held on May 14-15, 2016. We introduced iGEM and our projects to the visitors to let them know about synthetic biology and we received feedback.</p>
 
 
−
<div class="clear"></div>
+
<div class="tokyo_tech_clear"></div>
 
 
−
<h3><a href="https://2016.igem.org/Team:Tokyo_Tech/HomecomingDay">Homecoming Day (May 21, 2016)</a></h3>
+
<h3>Homecoming Day (May 21, 2016)</h3>
 
<img src="https://static.igem.org/mediawiki/2016/6/69/T--Tokyo_Tech--Homecoming_Day.jpg" alt="PHOTO" width="200px" style="float:left;" />
 
<img src="https://static.igem.org/mediawiki/2016/6/69/T--Tokyo_Tech--Homecoming_Day.jpg" alt="PHOTO" width="200px" style="float:left;" />
−
<p class="normal_text" style="float: left; width: 550px;">Homecoming Day is an annual event held at Tokyo Tech. We introduced iGEM and synthetic biology to alumni. We realized that it is hard to explain our research themes and goals to the public clearly. Therefore, we decided to make videos about <i>E. coli</i> and genetic modification. </p>
+
<p class="normal_text" style="float: left; width: 550px; margin-left: 10px;s">Homecoming Day is an annual event held at Tokyo Tech. We introduced iGEM and synthetic biology to the alumni. We realized that it is hard to explain our research themes and goals to the public clearly. Therefore, we decided to make videos about <i>E. coli</i> and genetic modification. </p><br /><br /><br /><br /><br /><!-- fit imgae -->
 
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    <div id="reference" class="container_contents">
−
<h2 align="center">Reference</h2>
+
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+
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http://catalog.takara-bio.co.jp/PDFS/50_24-27.pdf<br />
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file:///C:/Users/Mako/Documents/iGEM/MazF社会貢献性（single%20protein）.pdf
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+
 
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 +
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<div id="Snow_White_Versions" class="container">
 
<div id="Snow_White_Versions" class="container">
 
<div id="Snow_White_Vesions_header" class="container_header">
 
<div id="Snow_White_Vesions_header" class="container_header">
−
<h1><span>Snow White Versions</span></h1>
+
<h1><span>4. Snow White Versions</span></h1>
 
</div><!-- /Snow_White_Versions_header -->
 
</div><!-- /Snow_White_Versions_header -->
 
<div id="Snow_White_Versions_contents" class="container_contents">
 
<div id="Snow_White_Versions_contents" class="container_contents">
−
<p class="normal_text">The remaking of fairy tale "Snow White" by the Brothers Grimm has enjoyed a lot of versions since it was published in 1812 in the first edition of their collection Grimms" Fairy Tales. Some elements are common in any Snow White stories. However, because authors add their original elements or features to the story, it becomes unique. We chose other two versions, "Mirror Mirror" and "A Snow White Christmas" and designed their genetic circuits.
+
<p class="normal_text">The remaking of the fairy tale "Snow White" by the Grimm Brothers has enjoyed a lot of versions since it was published in 1812 in the first edition of their collection Grimms" Fairy Tales. Some elements are common in any Snow White stories. However, because the authors add their original elements or features to the story, it becomes unique. We chose other two versions, <a href="https://2016.igem.org/Team:Tokyo_Tech/Snow_White_Versions">Mirror Mirror" and "A Snow White Christmas"</a> and designed their genetic circuits.
 
</p>
 
</p>
 
<div align="center"><img src="https://static.igem.org/mediawiki/2016/7/74/T--Tokyo_Tech--HP_kairo1.png" width="400px"/></div><br>
 
<div align="center"><img src="https://static.igem.org/mediawiki/2016/7/74/T--Tokyo_Tech--HP_kairo1.png" width="400px"/></div><br>
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Latest revision as of 01:58, 3 November 2016

Human Practices

1. Overview

At the beginning of our iGEM activities, we felt that people seem to be unfamiliar with synthetic biology and its social contribution. In order to solve these issues, we chose to show our concepts through Snow White, one of the most famous stories around the world. Besides, we held many outreach activities, dialogued with experts, and created a model called "3E": education, ethics, and economy. We also designed some ideas based to our research (Toxin-Antitoxin system etc.) for society.
We contributed to raising public awareness of synthetic biology and improving our project through science communication.

2. 3E

We approach the social meaning of our project from three aspects: Education, Ethics, and Economy. Education plays an important role to raise scientific literacy as one of the most fundamental activities in daily life. Ethics is indispensable when you are engaged in synthetic biology. Economic profit is produced by technological application of synthetic biology. To approach the social meaning (of our project) from these aspects, we worked on many activities. This page shows all of our human practice activities.

Overview

After exchanging opinions with the public in school festivals (including May festival, Suzukake festival and Homecoming day), we found that the majority of people do not know much about synthetic biology. We thought that attributes to the lack of opportunity to stimulate their curiosity. Therefore, using a familiar fairy tale, Snow White, as a main theme, we designed our project. We also gave classes and made YouTube videos to raise the awareness. After the classes we gave, students improved their awareness of genetic modification and E. coli. Furthermore we created a special card game for the public in order to let them study science independently and delightfully. It can be used as a new type of educational tool and requires the basic knowledge about Toxin‐Antitoxin system(TA system) and Quorum Sensing(QS).

School-visits

In order to enhance the understanding of youths, we decided to conduct some School-visits. As a result, we gave lectures to 269 middle and high school students from 6 schools. Furthermore, these activities were good opportunities to learn how our project can impact the general public.

The detail of each school visit is organized on our wiki, so you can use it as a reference if you come to get involved in this kind of activity.

If your mouse is over photos you can see the explanation. You can see the details when you click the photo,


There is not only one story for Snow
White, but there exist several ones.

We designed a circuit in order
to recreate the story using our
own parts!

Does no other character apart from Snow White, the Prince and the Queen appear?

We decided to include the Mirror in the Story!

It is interesting to recreate the story of Snow White, but is there a way to apply Tokyo_Tech’s project into medicine or agriculture?

Could we use the TA system for any contribution to society?

“I was surprised to see how you can use E. coli to make this kind of playful experiments!” It changed my impression that E. coli equals food poison, and now I fell some kind of respect for it.

We usually hear the term gene recombination, but never how it’s done. It sounds hard!

I was surprised that it wasn’t as hard as I thought. It looks like it could be used in several fields. I’d like to try it too.

We included the opinion of the students in our card game and improved it!

What kind of lecture should we perform in order to let students understand better the gene recombination technics.

Let’s ask the Science Comunicator

As a result of incorporating what we learn after talking to the science communicator in our lectures... we obtained even better results!

Video

"It is difficult." "I don't get it." "What are you doing?"

These are words that the public told us about our activities, which means that the public did not understand our activity well. Therefore, we made intelligible videos to improve this situation.

The first episode: What is E. coli?
https://youtu.be/VJre_GtDRo4

The second episode: How to modify genes? What can we do by modifying the genes of E. coli?
https://youtu.be/nJtvFeMDbac

The third episode: "Snow White"
https://youtu.be/BCej9LzkYlc

Card Game

The public will not understand our project unless they experience it.

So we made a card game containing two functions so that the public can understand the basis of our project, TA system and QS. Click here to download the kit with the rulebook that we developed through trial and error so everyone can play easily. If you get interested in this card game, you can print it out and play it yourself.

Card Game Rule

Card Game Parts

Expert [Ogawa Tatsuya]

We noticed that the ways of manifesting and expressing our project are important when we explain our project to the public.

He gave us the advice that we should insert a punch line in our project to summarize our project to the audience's satisfaction. We should not only talk about the results but also convince the audience through our explanation. Hence, we should construct the whole concept, thinking what listeners will think after explanation about our project.

Summary

We raised the public's attention of genetic modification, E. coli and synthetic biology through our activities. Since we found our activities are influential to many people, we want to continue these to inform the utility of synthetic biology to the public even after iGEM.

Overview

There always exists ethic problem about research of life science. Especially synthetic biology, there are a lot of problems in this field. The judge about the boundary between the research allowed and the research restricted is extremely difficult. However, as researchers of life science, iGEM 2016 team Tokyo_Tech must take into account the problems arising deeply. In this case, we organized a symposium where we can discuss with the experts and exchange opinions with them. Moreover, we start to think about our ethic code of synthetic biology, basing on the things we learned from this symposium.

[Read More]

Symposium

We discussed with 6 researchers who is working on synthetic biology in this symposium. Then we learned that which one should be deal with between ethics of technology and ethics of science is decided by the thing that between developing technology and scientific research, which field your study is most likely to belong to. We have interests in this thing , so when we think about ethic code, we make it based on this.

Firstly, the reason why the ethic of technology and the one of science are different is because the goals of studies are different. The goal of debeloping technology is mainly application in the society, as a result, it is necessary to include appropriateness of method, usability, security and management of risk. On the other hand, researcher do the scientific studies due to the spirit of inquiry, therefore, it is necessary to include appropriateness and completely mutual criticism among researchers. We aim to make our project be applied to developing technology which is usable to society, therefore, we think about our ethic code referencing the ethic of technology. However, thinking about the ethic directly is difficult, so at the first step, we want to think about ethic related to what kind of problems in our project.

iGEM_Tokyo_Tech2016's ethic problem

As what we said in Future work, we are thinking that whether TA system can be applied to DDS and to decreasing risk of mutidrug-resistant bacteria appearing . In the temporary society, according to the law, taking out the designate genetically modified organism is restricted. Additionally, research institutes are focus on the construction whether it can leak genetically modified organism or not. However, the solution to the leak of genetically modified organism are being developed. And the utility of E. coli which will extinct even without being dealed with to become weak under the dry condition.

We thought about the danger of synthetic biology to our human being so far, on the other hand, we also need to take account into the creature used in experiments. We are using E. coli in our project this time.when we actually did the experiment, E. coli is systematically different with human being, so we hard to have a sense of guilty even though we make them work to meet our own needs. However, how about the other creatures? Their lives are likely to be decided by species when we didn’t even realize it.

In addition, in order to decrease the amount of creatures used in experiments as possible as we can, using modeling is important．In the past, modeling is used to decide the most suitable amount of reagent and time. We apply it to enhance consciousness that we try our best to decrease the amount of creature utilized.

Our ethic code of synthetic biology

It is becoming possible currently that Through machine learning about construction elements of creature, we regard construction elements as spare parts , design some creature functions and create artificial intelligence. Although through this people will get profit, the other creatures will be faced with new dangers. In order to prevent creatures from dangers, people who work on synthetic biology should follow the things shown below.

  • We should respect every life and be grateful to every life utilized in experiment.

  • We should concern about the influences on life environment of utilized sample and testee.

  • We should be aware of our position as a researcher and never utilize any specimens escaping from the law in gene modification experiments and etc; and we should never perform any fraud of experimental results, unauthorized reproduction or any other kind of plagiarism that would put in doubt one’s dignity.

  • We should always respect the others' position, and try our best to make up for deficiency mutually like in the Asilomar Conferences. Specially, since cooperation between wet and dry teams is important, we need to share information daily and never fail to communicate in order to improve the understanding of each other.

  • Compared to the analytic approach, the synthetic approach has to take in consideration more topics including technology and ethic. So it is not something easily achievable. Take in account that not everything is going to go as expected.

  • Through reducing the amount of creature utilized, we need to concern about environment, give a whole impression and do simulation to clarify the goals.

  • When "designing" biomolecules or biological systems, we should take into account the use of artistic activities to make our project easier to understand to the general public.

Final remarks

Because there is no clear boundary, it is hard to find clear answer of ethic problems such as genetically modification. For example, the boundary of living and non living creature depends on species. Moreover, there are always different opinions because of culture and religon. All the things above are the reason making ethic problems become complicated.

On the other hand, as reality, ordinary people tend to think towards questions that it is scientist who should take into account theses problems, and have nothing to do with the problems. In order to change the way they are thinking, it is important to have the opportunities that we can get information from scientists in symposium and lectures given to high school students. We need to let ordinary people know that ethic problems do have relation with them, which is also merit for scientists. when we were giving the lecture to high school students, we know something new through the conversation among ordinary people, which is different when we talk with scientists. Everyone can feel the ethic problems closing to their daily life through thinking about what kind of questions will happen and discussing with each other. Moreover, by popularizing this, there is a goal that all the actions taken are right after thinking about life ethic.

Reference

1. Nudeshina, Jiro Ph.D. To what extent should research on life be free? -dialogue with scientists (in Japanese) Iwanami Shoten Publisheres, Tokyo, 2010

2.Makoto Masuda. [Internet].Japan: Gouseiseibutsugaku－sonokanouseitokadai－ [cited July 18th, 2011]. Available from http://www.tbr.co.jp/pdf/sensor/sen_a216.pdf

3. TA Note 07 [Internet]. Japan: Seimeikinounokozotekikenkyunogenzyotosya　kaitekikadai：nihonniokerugouseiseibutsugakutoha？(Present state and social problems on structural research of life function: What is ‘Synthetic Biology’ in Japan?)　[cited October 7th, 2016] Available from http://i2ta.org/news/i2ta/ta-note-07.html

4. The Institution of Professional Engineers, Japan [Internet]. Japan: Gizyutushi- rinrikoryo [cited October 7th, 2016] Available from www.engineer.or.jp/c_topics/000/000025.html

5. Japanese Association of Certified Social Workers [Internet]. Japan: Rinrikoryotokoudoukihan [cited October 7th, 2016] Available from: http://www.jacsw.or.jp/01_csw/05_rinrikoryo/

6. Japanese Nursing Association [Internet]. Japan: Kangosyanorinrikoryo [cited October 7th, 2016] Available from: http://www.nurse.or.jp/nursing/practice/rinri/rinri.html

7. John R Pringle, James R Broach,Elizabeth W Jones. The Molecular and Cellular Biology of the Yeast Saccharomyces. Vol. 3. Cell Cycle and Cell Biology. US: Cold Spring Harbor Laboratory Press; 1997.

Overview

In order to use our project in society, we decided to approach it from a big perspective, economy. Our project includes a basic research, so, we thought that we should work on our project in terms of economy, instead of more specific fields such as environment and medicine, to make our project flexible to the upcoming technology. Among many elements of our project, in this page we focus on TA system.

We had a dialogue with experts to think our project from an economic perspective. This dialogue was the biggest turning point of our project.

Expert [Nakasaki Kiyohiko]

Prof. Nakasaki is a professor on the department of international development engineering at Tokyo Tech. He is researching about bio-refinery, prevention of plant disease by functional compost and DNA sensor of compost maturity. One of his research aims to produce chemical materials efficiently such as L-lactone and ethanol that is biodegradable plastic materials.

 

He showed interest in the fact that TA system inhibits the cell growth of E. coli and can even "resuscitate" it. And also in the protein expression that comes with this mechanism. During the dialogue, we were given with the positive option that continuously repeating the control of protein production can lead to a technology which reduces the risk of the appearance of multiple-drug-resistant bacteria. Therefore, from the view point of economy, we set a goal to control protein production.

After this dialogue, we have done two things to implement the protein production control.

  1. ACA Rise and Fall Code
    The development of a software which adjusts the number of ACA (Adenine-Cytosine-Adenine) sequence in the DNA.

     

  2. The experiments of creating E. coli mutants which secrete protein extracellularly

    "TA system ~Queen's Caprice~"

    These resulted in big success to obtain protein production control.

 

Moreover, we had a dialogue with Prof. Nakasaki about the application of the technology of TA system. The subjects for the dialogue were mainly DDS (Drug Delivery System) and risk reduction of the multi-drug-resistant bacteria emergence. These lead to technological development in the future, so the details on them are shown on Future work.

Future Work

Overview

We consider the possibility of the protein production system is controlled by Maz system and signal transfer mechanism. To improve the performance of controlling the production by Maz system, we developed a tool for increasing or decreasing the number of ACA sequence, which is the specific site cleaved by MazF homo dimmer. Maz system.

  1. Controlling the protein production

  2. Selectivity of the target mRNA

  3. System of communicating with outside

Combining i. and ii., it is expected that the target protein is obtained effectively and with favorite rate. Furthermore, adding iii., we could design an automatic and advanced information-processing system. In other words, we could design an oscillatory cell-cell communication in which one cell containing man system, receives an extrinsic signal (Maz system is controlled by the type of the signal), then the cell produces the substance which affects other cells.

To increase the selectivity of repressing the protein production by Maz system, we develop a tool of increasing or decreasing the number of ACA sequence named "ACA Dwarfs." This application makes our future work much more realistic than other iGEM teams (see Model page).

Furthermore, a lot of vital phenomena are oscillatory. So we could apply this oscillatory system to DDS (Drug Delivery System) or to decrease the risk of the appearance of the multi-drug-resistant strains.

  • Decrease the risk of the appearance the multi-drug-resistant strains

    These days, the possible appearance of multi-drug-resistant strain due to excessive use of pesticides is alarming. But spreading a pesticide one by one costs money, so we suggest using the system of controlling the protein production a by Maz system: the production of a pesticide is usually repressed by MazF, but only when the substance delivered from the targeted organism (for example: pheromone), MazF is contradicted by MazE and the pesticide is produced. This oscillatory model can decrease the possibility of the appearance of the multidrug-resistant strains because the pesticide is produced at intervals.

  • DDS(Drug Delivery System)

    Introducing maz system to human cells and orchestrating the human original signal transduction system and Maz system, we design the mechanism that the cell secrets drug depended on the internal condition. For example, when a maz system introduced cell receives the blood glucose level increase, the cell synthesizes the insulin.

  • Our TA systems and QS might be applicable to control the Intestinal Flora

    1.Introduction

    These days, Intestinal Flora draws a lot of attention because it will greatly affect our health. If the balance of intestinal flora is lost, it will lead into an illness or might even change your personality. It is assumed that intestinal flora consists of communication systems among various bacteria. However, no such communication systems have been found. So, it will contribute to the society to clarify the mechanism of intestinal flora and to find a way of controlling it.

    Our project focused on the cell-cell communication through TA system and QS, and proved the initial step to explain and control the system of the intestinal symbiosis.

    2. The results of our project

    2-1. TA System Assay

    We used Maz system, which is a kind of TA system. MazF (Toxin) inhibits translation by cleaving ACA sequence in mRNA and MazE (Antitoxin) releases MazF inhibition. We showed that Maz system could regulate cell growth when mazE and mazF were alternately expressed in E. coli (see TA system assay pages).


    2-2. AHL and AmiE Assay

    We indicated that QS of Pseudomonas aeruginosa genesand V. fischeri, and amiE, which selectively degrades AHLs, could work in E. coli. Sometimes, these genes are toxic to E. coli, but this was solved by, for example, tagging ssrA or experimenting at low temperatures (see AHL reporter assay page and AmiE assay page).


    2-3. Temperature-dependent Promoters

    We indicated that temperature-dependent promoters were activated strongly at a specific temperature: gfp under Pcold, which is activated at 15°C and under, was much more expressed at 18°C than at 37°C; on the other hand, gfp under Pheat, which is activated at 42°C and over, was more expressed at 37°C than at 28°C. We can say that we can control the expression of the gene under these temperature-dependent promoters by changing temperature.


    2-4. Modeling

    We simulated our final genetic circuits containing the genes of TA system, QS and temperature-dependent promoters. The simulation showed that the circuits could perform favorably by improving some parts (see Model page and Rhl system assay page).

    3. Discussion

    In conclusion, we proved that the genes of other bacterial QS and temperature-dependent promoters worked in E. coli and that E. coli original TA system gene under inducible promoters regulated the growth in WET experiments. From these results, the simulation showed that E. coli containing TA system gene and QS gene under various inducible promoters communicated with each other.
    Besides, by simulating that the genetic circuits worked properly with the three types of inducible promoters, we suggest that intestinal bacterial growth is controlled by nutritional condition, temperature and intestinal bacterial density. The three types of promoters were the sugar-dependent promoters (PBAD, Plac), the temperature-dependent promoters (Pcold, Pheat) and the AHL-dependent promoters (Prhl, Plux and Plas). Our project therefore helps to understand the symbiosis of intestinal flora. Furthermore, we are quite sure that we could engineer the E. coli or other bacteria which have function of regulating the symbiosis.

3. Policy & Practices

During promotion of our project, we had dialogues with the public and experts. Based on the opinions from them, we developed our project. Keeping from our narrow view, this led to success in creation of a well-rounded project with connection between the public and experts.

This page explains changes that some events had made to our project in chronological order.

Integrated_Silde_Figure

In the school festivals, we did poster presentation. Through diverse dialogues with the general public about our preliminary idea of several projects, we found out that the public preferred the Snow White project, one of the preliminary projects. As we figured out even though contents of Snow White project are difficult to understand, the public still showed great interest in it because it brought a sense of familiarity to the most. And this obviously leads to the public's deeper understanding of Snow White project than the others. Thus, we selected Snow White as our project.

Then, in the classes we gave to high school students, we were asked the reason why there are only three characters in the story. Accordingly, we found suitable characters and environmental factors to add into the story.

Another question from the students is that representing the story is interesting, but how our project can contribute to the society. Because this comment actually inspired us a lot, we started to focus on the consideration of the prospect of our project. After having dialogue with experts, we obtained a comment that TA system has a potential to be linked to development of effective technology. However, at present, there exits problems when using a TA system to control the protein production. We cannot selectively produce only desired protein because other proteins would be also produced at the same time. Then, our dry lab used JAVA to develop software named "ACADwarfs" adjusting number of ACA base sequence as a solution to the problem.

 

In this way, we integrated Human Practices to out project. However, we have done much more activities for Human Practices and show them in detail, below.

 

 

Human Practices

Integrated Human

Our Project

Practices

Public Engagement / Dialogue
May Festival

At the university festival of University of Tokyo, the public (parents and friends of students at University of Tokyo, and the other visitors of the festival) advised on our project in a poster session.

Among the projects, the ones with approachable themes were quite popular.

Select "Snow White" from prospective projects

Snow White is the story everyone knows, and people can understand the story pretty much. Moreover, it is familiar to the public and promotes a better understanding about E. coli, synthetic biology and our project.

Public Engagement / Dialogue
Suzukake Festival

At the university festival of Tokyo Tech, the public (parents and friends of students at Tokyo Tech, and the other visitors of the festival) advised on our project in a poster session. We got an advice that we should put on a shortplay to make our story easier to be understood.

Let's perform a short play during the presentation!

Public Engagement / Dialogue
Homecoming Day

This is an annual event held at Tokyo Tech with everyone related to Tokyo Tech and neighboring residents, where we aimed to get feedback from them by introducing our activities with a poster. However, we could hardly tell the public science and technology easily, and they had trouble understanding fundamental knowledge.

  • Make videos about E. coli and synthetic biology for the public.
  • Make an interesting card game for study.
School-visits
Ochanomizu University Junior High School

Aim of the lesson was to obtain feedback on our project from junior high school students, and to get evaluations of our project on the basis of their criteria. One student offered a following comment.
"Don't other characters appear in the story?"

At the beginning, the characters were three: Snow White, the Queen and the Prince. To make our story closer to the original one, we added the Magic Mirror to the story.

There are some versions of Snow White story. Using our parts, we designed two gene circuits to represent different story versions.

School-visits
Tokyo Metropolitan Nishi High School

Aim of the lesson was to raise student’s interest in iGEM through explanation of possibilities of genetic modifications, gene recombination techniques, and synthetic biology. The other aim of this lesson was to get feedback on our project from high school students. In the lesson, we focused on explanation of our project at that time. One student gave the following opinion.

"Certainly, representing Snow White Story is interesting, but can you make your project work for society?"

Can we make something socially beneficial?

We discuss by ourselves, and set up opportunities to have dialogues with experts.

Expert Prof. Nakasaki

During the dialogue, he said that repetition of protein production control probably takes a step to the technology reducing risk of the multiple-drug-resistant bacteria emergence.

School-visits
Kanagawa prefectural Atsugi High School

The classes' goal was to raise students' interest and awareness of E. coli and to increase the knowledge about synthetic biology and gene ligation techniques.

The class got the result of an advance in knowledge and enhancement of the students' interest toward genetic modification (However, we could have got better results.)

So far, iGEM team Tokyo_Tech has "told the public about synthetic biology" in various ways with a familiar theme. However, we have not been able to influence all of the people. We thought that the reason relied on our way of communication. Therefore, we decided to ask a science communicator, who is an expert on telling science to the public.

National museum, nature and science, Tokyo
Science Communicator Mr. Ogawa

He told us that only representing the research cannot attract the audience's interest, and cannot get shrewd feedback. Also, he suggested that our story should have a clear conclusion that can tell people something.

We learned how to tell science to the public from a science communicator. From his talk, we noticed that we should design the whole project considering what the public will think after explaining our project.

In addition, we decided to make our project more attractive, through clarifying our project's goal and setting a clear conclusion.

Summary

We "went beyond the lab" and developed our project through human practice activities.

We have not just reflected opinions from dialogues with the public and experts about our project. Firstly, we investigated and discussed about the issues on our own. Secondly, in the light of the application of our project, we did experiments and modeling. Finally, we succeeded in the creation of "ACADwarfs" and "the growth and death wave by toxin-antitoxin on agar medium." Furthermore, we are doing experiments to make E. coli mutants secreting protein extracellularly. The products will probably lead to further developments of our project.

Achievements as mentioned above indicate that we have succeeded in the integrated Human Practice.

Suzukake Festival (May 14 & 15, 2016)

May Festival

The Suzukake Festival, the school festival on the Suzukakedai campus, was held on May 14-15, 2016. We introduced iGEM and our projects to the visitors to let them know about synthetic biology and we received feedback.

Homecoming Day (May 21, 2016)

PHOTO

Homecoming Day is an annual event held at Tokyo Tech. We introduced iGEM and synthetic biology to the alumni. We realized that it is hard to explain our research themes and goals to the public clearly. Therefore, we decided to make videos about E. coli and genetic modification.






4. Snow White Versions

The remaking of the fairy tale "Snow White" by the Grimm Brothers has enjoyed a lot of versions since it was published in 1812 in the first edition of their collection Grimms" Fairy Tales. Some elements are common in any Snow White stories. However, because the authors add their original elements or features to the story, it becomes unique. We chose other two versions, Mirror Mirror" and "A Snow White Christmas" and designed their genetic circuits.