Difference between revisions of "Team:Tokyo Tech/Human Practices"
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<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> | ||
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| − | <li><p class="normal_text"><a href="https://2016.igem.org/Team:Tokyo_Tech/Model# | + | <li><p class="normal_text"><a href="https://2016.igem.org/Team:Tokyo_Tech/Model#key_achievements">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> | ||
Revision as of 14:56, 19 October 2016
Human Practices
Contents
1. Overview
At the beginning of our iGEM activities, we felt that people seem to be unfamiliar with the 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 hold many outreach activities, dialogued with experts, and created a model called “3E”: education, ethics, and economy. We also designed some ideas base to our research (Toxin-Antitoxin system etc.) for society. We improved our project by feedback of these human practice activities.
We could improve the public conscious to synthetic biology and our project mutually by communicating with people.
2. 3E
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 E. coli, 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.
Overview
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, E. coli and synthetic biology is less well known. Therefore, we gave classes and made YouTube videos to have the public, especially the youth, know them. Using the familiar story of Snow White as a base to our project, many people got interested in it because of the story, but thanks to that they also got interested in synthetic biology. As a result, more and more people got interested in synthetic biology and E. coli because of the plot of Snow White we used which is familiar to the most. Moreover, after the classes we gave, students improved their awareness of genetic modification and E. coli. Furthermore 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.
School-visits
During the May Festival, the Suzukake Festival and the Home-Coming Day, when we talked to the general public, we found out that the E. coli is being rather misunderstood. So in order to solve this misunderstanding, and to provide more people with a more accurate information about E. coli, 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.
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.
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. Moreover, the third episode is dubbed into Japanese, English, Chinese and Spanish so that more people will be able to understand.
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 Quorum Sensing. 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.
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.
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 not 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 firsty step, we want to think about ethic is 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.
・We should respect every life and be grateful to every life utilized in experiment.
・Always take in consideration the impact the used samples and subjects have in the environment, and thoroughly exert oneself in the risk control and bioterrorism prevention against human beings and other life forms during the experiment.
・Be aware of your position as a researcher and never utilize any specimens that depart from the law in gene modification experiments and alike; and 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.
・Just as we did for the high school students with our visit to our former schools, or what we did for other high school students and college students with the symposium we organized, spread this field by letting the general public have a better understanding of synthetic biology; and, at the same time, dialogue with them.
・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, take in account the use of artistic activities to make your 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 big 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.
ACA Rise and Fall Code
The development of a software which adjusts the number of ACA (Adenine-Cytosine-Adenine) sequence in the DNA.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.
controlling the protein production
selectivity of the target mRNA
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 Quorum Sensing and TA systems 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 Toxin-Antitoxin system (TA system) and Quorum Sensing (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.
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
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.
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!
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.
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.
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.
We got the positive opinion that TA system probably leads to a valid technology in the future.
However, there are two problems with protein production control using TA system.
(i), You cannot produce target protein selectively; you produce other needless protein simultaneously.
(ii), Repetition of protein production control leads to sustainable production in one system. However, to take protein from E. coli, you have to destroy E. coli, which makes sustainable production impossible at present.
We continued the activities to find the clue of two critical problems. We worked on them (i) from a view of modeling, (ii) from a view of experiments, and finally found solutions for the problems.
-
"ACADwarfs"
The development of the software which adjusts the number of ACA (Adenine-Cytosine-Adenine) sequence in the DNA.This makes it possible to adjust the inhibition of each protein, that is, you can produce a bigger ration of target protein when MazF works. Moreover, we designed the Java code so that many people can use it.
The experiments to make E. coli mutants that secrete protein extracellularly and "TA system ~the Queen's Caprice~"
UV irradiation has being performed to make the mutants that secrete protein extracellularly.
Using "ACADwarfs" gets the higher grade target protein, which realizes high performance material production system. Additionally, preventing mRNA cleavage of target protein and cleaving mRNA of unnecessary protein can establish sensitive protein labeling.
Furthermore, our research leads to DDS (Drug Delivery System) and reduction of the multi-resistant-bacteria emergence. It should be developed in the future, so the details on them are shown on Future work.
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.
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 “ACA dwarfs” 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)
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)
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.
Reference
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.
