Team:Tokyo Tech/Human Practices

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.


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 systems 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.

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

All life-concerning studies have always undertook ethical problems, especially synthetic biology. Until what point is it allowed to perform an experiment, from where on should it be regulated. This decisions are difficult to make. As a team that works with life studies, iGEM_Tokyo_Tech2016 has also encountered this problem and has needed to consider it deeply. So our team organized a symposium, conversed with specialists in bioethics and exchanged ideas. Also, we utilized the knowledge we obtained in this symposium as the base for our ethic code.

[Read More]

Symposium

There are two ways of using synthetic biology: for technology development and for scientific research. This 2 points are fundamentally different. First, for technology development there is a clear purpose. So when thinking about this field, one has to take in account the engineering ethics, the validity and usefulness needed to be useful for our society; as well as the security, risk management and environment impact.

The goals technology development and scientific research look for are different, so the way of deciding on the ethics involved are also different. Basing our research on this thought we decided that it was closer to that one of technology development.

iGEM_Tokyo_Tech2016's ethic problem

For team iGEM_Tokyo_Tech2016's current project we are using a TA system to recreate the Snow White story. So, in the previously mentioned symposium, we thought of what kind of ethical problems would be faced if we applied the TA system in several other fields in the future. In recent years, the overuse of pesticides has brought the fear of the appearance of multiple-drug-resistant bacteria. Besides, the distribution of pesticides one by one is takes too much time and money. So we thought of mitigating the risk of appearance of this multiple-drug-resistant bacteria by implementing the protein-control mechanism our TA system, the Maz system, has. In order to apply this technic into farms and alike, we have to take it outside. So first we think on this topic. We must not use any pesticide or gene recombinant regulated by the law. Also, we have to think that our genetically modified organism's structure does not present any leaks. Furthermore, we also have to think on what kind of impact it has on the environment or if it does have any adverse effect in the human body. Nevertheless, the solutions to these problems are also progressing. For example, in order to prevent any leakage of genetically modified organisms, E. coli that are weak to dry environment or yeast that need specific nutrition are being used; since the first one would die without the help of an special equipment, and the later one would not survive even if it leaks. This way, we can ensure safety.

Until this point, we have considered the possible dangers that synthetic biology may present to us humans. But, on the other hand, we also have to deeply think about the organisms that are used for experimentation. We are using E. coli in our project. And while experimenting, we came to realize that, since E. coli is systematically different to humans, it is difficult to feel any kind of guilt while modifying it to work as you want it to work. However, if this was another living being how would we feel? Probably we would not be able to treat them as carelessly. We are probably unconsciously determining the weight of a life depending on the organism's specie. And we can also think that how lightly one can treat each living being depends greatly on each person. So what can we call an ethic code accepted by most of the people? We decided on writing our own ethic code based on the things we learned and thought.

Also, we thought that in order to decrease as much as possible the amount of organisms used in experiments, it's also important to use mathematical models. Originally, modeling was used to determine the most optimum amount of reagents or to find out the time needed for an experiment. But we also want to use it to spread the "reduce as much as possible the number of organisms used" thought.

Our synthetic biology research's code of ethics

We now publish the synthetic biology code of ethics for our project, that we obtained from what we learned during the symposium.

Preamble

The main goal of several studies to understand the living systems was the analytic approach of breaking down the components of the currently existing organisms in order to understand the function of each component and the interactions between themselves. However, after accumulating knowledge about the organism's components, now this components are reckoned as "parts", and are combined in order to design new living mechanisms or to construct artificial live systems, in other words we can now see it through the synthetic approach.

  • Respect each and every organism's life and show appreciation to the lives of those that become subjects.

  • 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.

  • Exert oneself in complementing the deficiencies of oneself and fellow researchers without missing on daily dialogue, but always respecting the others' position, like in the Asilomar Conferences. Specially, since cooperation between wet and dry teams is important, 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.

  • Take in consideration the environment by reducing the number of organisms used. At the same time, in order to have a general idea and to clarify the goal, perform some simulations using modeling.

  • 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

Even inside synthetic biology, gene modification is thought as a field that goes against the natural commandments. However it is not as if this logic is completely consistent because regarding ethical problems, it is not as if an absolute line has been traced. For example, the boundary of living and not living varies on the organism’s specie, and also the influence of culture and religion influence in people’s opinion. So the ethical problems are being complicated due to this reasons.

In this way, this seems to be a problem without a clear solution. Also, currently the general public seem to think of this problem as something the scientists should tackle on and that does not concern the. In order to change this concept, just like we did with our visits to our alma mater schools, it’s important that the scientists should be the first to actively educate others from the beginning by letting the public know the proximity at which this problem is, and also by making them understand that they are not unrelated to it. And, at the same time, just like we did when we performed some lessons for high school students, talking to a general audience can be a great gain for scientists, since there is a possibility that they notice some things that they had not been noticing by discussing with people other than fellow scientists.

We think that this is a problem that should be faced on, step by step. If each one of us think of what kind of ethical problems we may face, then by talking with your comrades you can realize the familiarity of this problems, and if the this circle gets to grow, then it should lead to a better understanding of this problem.

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.

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.






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.