Team:Tokyo Tech/Human Practices
Human Practice
Contents
Introduction
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. Currently, synthetic biology is unfamiliar to the public, and in most cases, they cannot comprehend it easily. However, using 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. What is more, our research about Toxin-Antitoxin system (TA system) and Quorum Sensing (QS) created "ACA Dwarfs" and "TA system ~Queen's Caprice~." Additionally, we are doing the experiments of E. coli mutants that secrete proteins extracellularly. It makes a giant step toward technological developments in economy in the future.
Overview
Through communicating with the public, it was shown that people tend to have an erroneous idea about genetic modification and E. coli, and they have almost no idea about synthetic biology. Additionally, there is some advice 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 how the outreach activities, the class we gave and the dialogues with experts had made changes to our project, and what we thought with advice from them and what we did in chronological order. Moreover, Snow White in Grimm's Fairy tales has been published a lot of versions so far. 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.
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 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 also 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. Further, we coordinated activities to achieve the protein production control using TA system. 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.
Education
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 of genetic modification, E. coli, and synthetic biology to have the public, especially the youth know them.
In order to let the general public, especially the youth, know more about the knowledge about E. coli and synthetic biology, we gave related classes to high school students as well as making teaching videos which can be viewed on YouTube.
Using the familiar story, Snow White, as a base for our project, many people got interested in synthetic biology and .
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.
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 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 this lectures 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 second episode: How to modify genes? What can we do by modifying the genes of E. coli?
Card Game
The public will not understand our project unless they experience it.
We made the card game containing two functions so that the public can understand the basis of our project, TA system and Quorum Sensing.
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.
Click here to download the kit with the rulebook that we developed through trial and error to play easily for everyone. If you get interested in this card game, you can print it out and play.
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 audience's satisfaction. We should not only talk about the results but also convince audience through our explanation.Hence, we should construct the whole concept, thinking what listeners will think after explanation about our project.
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 we should arrange the flow our project accordingly.
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 of the public even after iGEM.
Economy
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 future 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 of 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 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.
He showed interest in the fact that TA system inhibits cell growth of E. coli and resuscitates E. coli, and with those, the same applies to protein expression. While the dialogue, we got the positive opinion. It was that repeat protein production control probably takes a step to the technology which reduces the risk of 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 obtain protein production control.
ACA Rise and Fall Code"
The development of 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 production by Maz system, we developed a tool of 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-to-cell communication that one cell containing maz 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 decreasing the risk of the appearance of the multidrug-resistant strains.
Decrease the risk of the appearance the multidrug-resistant strains
These days, it is alarmed that there appears the multidrug-resistant strains due to excessive use of pesticide. But it costs spreading the pesticide one by one. Then, we suggest using the system of controlling the protein production by Maz system: the produce of the pesticide is usually repressed by MazF, but only when the substance delivered from the target living things (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 or illness. If the balance of intestinal flora is lost, it will lead illness or might 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 were toxic to E. coli, but it was solved by, for example, tagging ssrA or experimenting at low temperature (see AHL Reporter assay page and AmiE assay page).
2-3. Temperature-dependent Promoters
We indicated that temperature-dependent promoters were activated strongly at the specific temperature: gfp under Pcold, which is activated at 15℃ and under, was much more expressed at 18℃ than at 37℃; on the other hand, gfp under Pheat, which is activated at 42℃ and over, was more expressed at 37℃ than at 28℃. 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 expression-inducing 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 expression-inducing promoters communicated with each other. 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). 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.
Policy & Practices
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.
This page explains the changes that some events had made to our project in chronological order.
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.
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.
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.
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.
After having dialogue with expert, we obtained the comment that TA system has the potential to be linked to the development of effective technology.
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.
Then 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.
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 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.
Among the projects, the ones with approachable themes were quite popular.
Settle on "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 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.
Let's perform a play during the presentation!
Homecoming Day
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.
- Make videos about E. coli and synthetic biology for the public.
- Make an interesting card game for study.
Ochanomizu University Junior High School
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. One student offered the 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.
Snow White story has some versions. Based on our parts, we designed two gene circuits to represent different story versions.
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. 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 discussed with ourselves and set up an opportunity to have a dialogue with experts.
Expert Prof. Nakasaki
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.
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.
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"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
Aim of the Class: To raise students' interest and awareness of E. coli and to increase knowledge about synthetic biology and gene ligation techniques.
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.)
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.
Science Communicator Mr. Ogawa
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.
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 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 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 synthetic biology and got feedbacks.
Homecoming Day (May 21, 2016)
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 E. coli and genetic modification.
Reference
http://catalog.takara-bio.co.jp/PDFS/50_24-27.pdffile:///C:/Users/Mako/Documents/iGEM/MazF社会貢献性（single%20protein）.pdf
Snow White Versions
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.
