Difference between revisions of "Team:OUC-China/Human Practices"

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Human Practices

Silver

Safety

1.Biosafety considerations and investigation for our project
Having identified our project, we discussed the bio-safety of our project with professor Liang who have worked for years on nucleic acid detection and bio-sensor. We discussed with professor Liang on the safety and feasibility of our project . For the safety of our project, our experimental strain is E.coli DH5 Alpha, a very common strain in biological experiments. As long as we do experiments according to microbial and molecular experimental operation specification., there will be no safety issues. For the feasibility of our project, designing different structures of hairpin and enzyme to regulate the expression of the gene of interest is very useful for the future work.

2.Biosafety Project
Because the track of our project is foundational advances, the downstream product have nothing but fluorescent proteins which act as reporter to characterize our experimental results. What’s more, nonpathogenic bacteriaE.coli DH5 Alpha is employed as the main chassis for our prior design on the DNA sequence, stem-loop and enzyme. As a matter of fact, when using hairpins and csy4 enzyme to tune the expression of genes, it is relatively safe for industrialized applications and scientific research. In our project, all the parts we have utilized are selected from Risk Group 1, none of which are with a Red Flag. As for microbial organisms, the microbial organisms has no chances to escape from our laboratory because we use ultraviolet sterilization after finishing our experiments. Furthermore, all the equipments used for recombination strains will be sterilized by High-Pressure Steam Sterilization Pot.

3.Biosafety lab work
Our cautiousness about experiments makes it even impossible for classis to escape. Every week, we do a thorough laboratory cleaning, including spraying alcohol and disinfectant to sterilize. Every day we check all the instruments and strains in our lab. Due to lack of enough nutrition, recombinant strains cannot survive outside the lab. And we are certain that everything we do is under our control. Every week, the teacher responsible for laboratory safety checks our safety work every week.

Fig1. We have strict safety regulations and safe operation

4.Biosafty education
We organize a summer camp to help students who have just entered university or are about to enter the university to know about biology, teach them basic microbial experimental operations such as butterfly specimens, microbial painting, and plasmid extraction. More importantly, we explain the safety of laboratories to them before entering the laboratory, raising their biosafty awareness. No experiment carries no risk to the experimenters, so we must learn to protect ourselves. Before each experiment, they are educated to be equipped with some necessary facilities, such as latex gloves, nitrile gloves, goggles, lab coats to protect them from biotic and abiotic hazards. Undoubtedly, safety is always in the first place for us.
See more details about safety in our safety page

Fig1. We have strict safety regulations and safe operation

Establish links between project and stakeholders

1. Integration with labs
The purpose of our project is to regulate the expression of a target gene with the help of miniToe structure which is composed of endoribonuclease Cys4 and hairpin. Initially, we just want to realize the regulation of gene expression. By establishing dialogues with labs, we found the limitations of our thoughts. Enlighted by Professor Liang in Ocean university of China and Professor Du in Institiue of microbiology, we changed our initial thoughts and extended the expression gradient of target gene by model prediction and mutation of hairpins and Cys4. For further application, we applied our minToe to polycistron with the help of model.
See more details in our Gold & integrated human practice.

2. integration with biosafety companies
The best way to further verify the practical application of our project is to investigate in the biological company who are good at transforming basic research into practical results . We go to some relevant local biotech-companies to interview stakeholders and tell them about our project, such as BGI, Qingdao Bright Moon Seaweed Group Co. LTD, Qingdao youdu biotechnology Co. LTD. From their perspective, these companies give us some opinions and references. After learning about the design of our project, they applauded our ideas and proposed some application of our project on production. Enlightened by the investigation, we ensure our ideas of applying our system to polycistronic expressions and put it into practice.
See more details in our Gold & integrated human practice.

Fig. We went to biotech companies and it really inspired us.

3. integration with other iGEM teams
In ccic(Conference of China iGEMers Community), we communicated with other teams about our project. XJTU-China came to exchange their ideas with us. We found that we two teams can be integrated. Having realized polycistron system, we integrated it with their project. In the process of human practice, we establish a platform with stakeholders for long term cooperation and feedback. Our project is a great example of fundamental research being transformed into application. So we share our experience with other teams and documented for future iGEMers. Apart from that, we share our experience with other teams who also do some fundamental advances and form a fundamental research group with other five teams.
See more details in our Gold & integrated human practice.

Meet up

1. co-organizer of ccic, Conference of China iGEMers Community
Served as a co-organizer, OUC-CHINA tried their best to help the organizers Shanghaitech hold the conference successfully. For the conference preparation, We are responsible for contacting each team, sending a questionnaire to them and investigating the commands of each team for the meeting. Then we organized and summarized all information of 62 teams. At each key time we remindeded each team to submit project summary, team logo then sorted out according to the track. As an old team, OUC-China actively participate in After iGEM activities and share our team heritage and experience with other teams.
As a part of the joint iGEM session, OUC-China joined the CCiC Executive Committee and worked with the members of the Executive Committee, organizers, sponsors to plan the conference and contribute to the CCiC heritage.
Shanghaitech https://2018.igem.org/Team:ShanghaiTech/Collaborations

We are the co-organizer of CCiC

Gold & integrated

Introduction

“How do fundamental research results transform into applications that benefit human?” “How do you apply social feedback to a project? “How do you turn an obscure basic research into an easy-to-understand form?” There are some questions that the OUC-China team has been considering.
Through communication, we found that this problem has also been plagued by other teams. In order to transform the basic research results of our team into practical applications, we communicated with many stakeholders, visited related biotech companies, asked professors in related fields, and created a game based on our project in order to make people understand some principles and knowledge of biology while playing games and entertainment. In the process of spreading our project, it is difficult for many amateurish people to understand these principles, especially when we mentioned some biological terms, such as “CRISPR”. With the help of our game and the game brochure, the obscure principle became vivid and interesting to them, which was really a good feedback for us. Apart from that, we teamed up with five other iGEM teams to set up a basic research results transformation team to jointly research local biotech companies and explore a fixed model for the transformation of basic research results, hoping to give a reference to the future iGEM teams.

Integration

Interaction with some stakeholders

By establishing models and molecular predictions, OUC-China constructed a toolkit and named it MINITOE FAMILY. The toolkit can regulate the expression level of targeted gene in a gradient form. 1.integration with labs
"Your hairpin mutant is very conservative. Only a pair of base mutation will not achieve your idealized effect. You can try more bases modifications." Professor Liang, who studies nucleic acids for about twenty years, gives us some advice on hairpin mutation.
Having accepted his suggestion, we expand the range of base mutations, from a pair of base mutation to two or more pair of bases mutation, from bases mutation on the stem to base mutation on the loop. Indeed! Expanding the range of mutations shows us a better expanded expression gradients, which forms a useful toolkit ”miniToe family” by combining different hairpins with Cys4 mutations. Initially, professor Liang doubt if crRBS and RBS can be separated after interaction with Cys4. He is concerned that the cleavage of Cys4 and steric hindrance are not sufficient to break the hydrogen bond between base pairs. But his concerns have been broken by the expression of fluorescent gene.

Fig. We expanded the range of mutations to get a better expanded expression gradients

“A great idea! It will be better if you can regulate the expression ratio of more than one gene. So your application range can be wider.” said Assistant researcher Du of the Institute of Microbiology, Chinese Academy of Sciences.
Du ever changed the intensity of RBS to achieve different expression levels of the target gene. So we take the train to Beijing and consult him some opinions about our project. He gives an example of our project application. The traditional way is to knock out a gene then observe different performance of the organism, Your experimental results can be used to explore the effect of different gene expression levels on the function of organisms. Indeed! … Inspired by Teacher Du, we consider applying the MINITOE structure to the regulation of gene expression in polycistron expression systems.

Fig. Du said, ”Your project can be used to explore the effect of different gene expression levels on the function of organisms”

Fig. We were enlightened by Professor Du and applied our miniToe to polycistron

2. Integration with biotechnology companies and research institutes
Given that all basic researches aim at application and benefiting for human beings, we suppose that visiting the biotechnology companies to investigate the prospect of our project is a great idea. We went to the BGI, Qingdao Youdu Biotechnology Co. LTD and Qingdao Bright Moon Seaweed Group Co. LTD to integrate our project with social reality and communicate with technical staff in these companies. In this way, we can know about the current social needs and improve our project accordingly. At the same time, we established a long-term relationship with them. On the one hand, they can provide us an effective way of converting foundational research to actual application, on the other hand, we will inform them of the latest results in the lab, by which we can promote each other and make progress together.
2.1 BGI
Firstly, we visited BGI research institute. BGI is the world's largest genomics research institute that applies scientific research results in the fields of medical health, agricultural breeding and resource conservation. It is committed to promoting the transformation of genetic science and technology, so as to bring benefits to human. We introduced our project to BGI researchers and visited the company's laboratory and breeding area. The researchers in the gene editing laboratory evaluated our project and proposed new application directions for our project, suggesting that we can apply the genetic circuit to the anabolic design of engineered bacteria and combine it with some industries such as fermentation engineering. At the same time, they told us that their lab was also trying to apply gene-editing techniques to the genetic breeding of Marine economic fish, which may also provide us with some ideas. We are very grateful to BIG for their valuable advice. And now we have been keeping in touch with BGI and they also encourage us to combine our project with their labs.

Fig. BGI gave us some advice on our project and it really enlightened us

2.2 Marine Institute, Chinese Academy of Sciences
Inspired by BGI researchers, we arrived at the Marine animal molecular developmental biology and evolution laboratory of the institute of oceanology, Chinese academy of sciences. The main research direction of the laboratory is the development of gene resources and germplasm improvement of mariculture fish, which provides breeding materials and new breeding methods for the breeding of improved species of blue agricultural mariculture animals. Under the guidance of the researchers, we visited the laboratory and learned about the history of the laboratory as well as the results of the innovative research on Marine fish germplasm. We asked the teacher if our project could be combined with genetic breeding, she gave us some suggestions. At present, they use traditional genetic technology in model organism zebrafish to explore the function of target gene. We wondered if our project can be applied to their labs. The researchers said we could have a try and it is an innovation to apply our system to another model organism. Indeed! Applying our system into another model organism is an opportunities as well as a challenge. The researchers also encouraged us to have a try and combine our fundamental research with industry, which was and affirmation of our project. They are very willing to apply our projects to their labs in the future.

Fig. We went to Marine Institute and communicated with researchers

2.3 Qingdao Bright Moon Seaweed Group Co. LTD.
In order to find more ideas, we came to Qingdao Bright Seaweed Group Co. LTD. It is a leading enterprise in the Marine biological industry of Shandong province, and the largest seaweed biological products enterprise in the world. We visited the seaweed science museum and the state key laboratory of algae active substances, learned about the alginate and seaweed polysaccharide industries. In the process, we have come up with a new idea that we might be able to use our system to regulate the expression of one or two enzymes that are needed for the processing and production. The company's research and development staff agreed with our idea and suggested that we should design a complete biological treatment scheme and explore its cultivation conditions to realize the better integration of our system with industry. We learnt a lot from the journey of Qingdao Bright Moon Seaweed Group Co. LTD, which was a great progress for us.

Fig. We form a long-term cooperation relationship with Qingdao Bright Moon Seaweed Group Co. LTD.

2.4 Qingdao Youdu Biotechnology Co. LTD.
Youdu Biotechnology Co. LTD is mainly involved in the beauty industry, which has many production lines and beauty brands, which is a new and dynamic biological enterprise. We visited its factory, laboratory and production line of the enterprise, and preliminarily knew about the material selection, physical and chemical experiment and downstream product operation. We introduced our project to the researchers in the laboratory, who gave us a high evaluation of the project and affirmed our idea of applying the system to the regulation of anabolic circuits to better integrate with the real industry. Since engaging in the beauty industry, they suggested that we may be able to not only use our system to produce the enzymes that are needed to process raw material, but also directly produce some ingredients, which can be added to skin care products. And our polycistron system can even attempt to mix two materials proportionally in production. In addition to using E·coli as our engineering cells, we may also be able to apply the system to other chassis, such as yeast, to explore the most convenient way to apply it to factory production. We will also keep in touch with Youdu for the long term and hope that our system can really achieve industrial integration.

Fig. Qingdao Youdu Biotechnology Co. LTD applauded our polycistron system

In the process of interaction with biotech companies, we have gained a lot and integrated it with our project. We organized our biotech companies research reports into documents and shared our experience with other iGEM teams. Having known that our project is about basic research, Tianjin University contacted us and we set up a fundamental research results transformation team together with several Chinese iGEM teams, ZJU, SJTU, XJTU, JLU, NUDT. We are glad to share our experience with them. Finally, we have finished a joint report on the transformation of basic research results, hoping future iGEM teams to learn something from it.

3. Integrating project with a game——< CSY4 GO!>!

"The principles of all fundamental scientific research are obscure for us amateurish people."
"The form of the game < CSY4 GO!> is Interesting!"
…
In the process of human practice, we tried to explain our projects to some people. But we found that they felt it very difficult to understand, especially some amateurish people. In order to let more people better understand the principles of biology in an interesting and effective way, we spent lots of time designing a game - < CSY4 GO!>, which is a good combination with our project.

The game introduction

The leading role of < CSY4 GO!> is a little cute enzyme named Csy4 which is the main target of our project. Naturally, Cys4 is very active and able to protect the host from being harmed. We enumerate the functions of Csy4 from six parts--Immune, Secretion, Transport, Constitute, Recognition and Catalyze. Our game < CSY4 GO!> is based on these six parts. When we start the game, there will be six situations for players to choose, each situation includes one interesting story which is showed in the picture. Then the players can control Csy4 to cleave RNA chain in the right order and right place. The player’s operation simulates the process of Csy4 protecting host from external damage. In that way players can not only enjoy our game < CSY4 GO!> but also learn about some functions of Cys4. Once the game starting, RNA chain will roll with the background at a certain speed, so the players must move fast enough to make sure Csy4 won’t touched by the top of screen.

Fig.1 The logo of < CSY4 GO!>

Purpose of designing the game

As is known to us, the mechanism of endonuclease Csy4 in microorganisms is difficult to observe with our eye straightly. But now < CSY4 GO!> solves this problem successfully. The game presents a microscopic view of the world with a more vivid picture. In this way, we can tell the story of Csy4 as well as the CRIPSR system to more amateurish people, thus achieving the goals of propagandizing our project and synthetic biology.

The designing process of our game

1.The game started:
At first, we planned two game blueprints. The first one is controlling Csy4 to specifically cut RNA, which can explain the principle of Csy4.To make the game more interesting, we created the second one. The second is to control Csy4 moving on RNA chain. To get the destination, they need to cleave on the certain site and keep falling.

Fig.2 The background of < CSY4 GO!>

Have discussed in our team, we created the general design of our game. Given that no professional programmer in our team can take charge of this work, we asked for Mingjie Shen who has the experiences of programming mini-games to help. In our first blueprint, we character Csy4 the ability of cleaving the RNA by recognizing certain three base site instead of cleaving RNA by recognizing the hairpin.
Once the game started, there will be some golden coins suspend on the screen, and several kinds of RNA structures which are shown in pictures and rolling at the bottom. We hope players can play the game by putting the RNA structures on the proper position, and use the certain keys to cleave the RNA and fall down, gathering golden coins and arrive the destination at bottom.
Many different cleave sites random are generated from four different kinds of ribonucleotide. At the beginning, Csy4 only have the ability to recognize and cleave several sites. Players should get the ability to cleave at new site by passing more game levels or buying in the store using the money gathering during game.

This is our initial design about the first blueprint.
In this part, we enact the game rules:
a.Csy4 cleaves the RNA by certain cut site instead of special structure.
b.Csy4 starts at one side of the screen, it’s supposed to go to the diagonal side.
c.Players should use RNA to help Csy4 reach the end.
d.The golden coins gathered during the game can be used to buy more skills (active cleave sites) to cut the RNA
e.There will be several levels. Pass a level can also get a new ability.
After discussing with Mingjie Shen about some details, we started our design!

2. The first step of our game:
During programming, we designed 6 RNA in different structures carrying one or two sites on it, players can chose the certain sites and cut it to help Csy4 fall. And Csy4 is designed as a little cute white devil in the game.
The game was divided into 6 parts on the basis of the properties of proteins: Immune, Secretion, Transport, Constitute, Recognition, Catalyze. The difficulty among those parts from Immune to Catalyze is in gradient.
We also designed other widgets we need in the game.
In this part, we've done:
a.Designed the 6 kinds of RNA with specific structures.
b.Designed the cartoon character of Csy4.
c.Give the gradient difficulty in game.
d.Designed other widgets in game.

Fig.3 Six kinds of RNA with specific structures

Fig.4 The cartoon character of Cys4

Fig.5 The dynamic effects of our role

3. Meet some troubles
While programming, we found that the RNA rolling sidebar is hard to re. And it’s difficult for most of players to control the movement of Csy4 and arrange the certain RNA at the same time. So we modified the game rules -- delete the rolling sidebar and immobilize RNA to lengthen the path and make the rolling background picture come true.
In our original vision, Csy4 can only move horizontally. It can not jump or fall down at both ends of the RNA. Referring to the RNA picture we showed in ‘The first step of our game’, which is difficult to program such a flexible path, so we redesigned RNA and make Csy4 jump.

In this part, we’ve done:
a.Modified the RNA structure.
b.Modified game rules:
c.Delete the rolling sidebar.
d.Roll the background picture.

Fig.6 Some small icons that we designed in our game

4. The game rudiment
We've finished most of programming in this part. When testing, it works well. We finally decided to name it < CSY4 GO!>. Although the shop part of the game is still missing (including the gold coins that expect to be shown on the screen), and the game levels are not in the gradient difficulty. In order to make the game better integrated with biological elements, we took the prototype of biological environment as background picture.

Video. Know about how to play this game in this video.

In this part, we've done:
a.Named the game.
b.Finish most of the programming except the shop and the gradient difficulty game levels parts.
c.Designed background picture of the game.
d.Users can operate the game smoothly.

Click here to see our background picture in the game

Fig.7 We took the prototype of biological environment as the background picture of our game design.

Fig.8 If you win the game, Csy4 will be cheerful and appear "Congratulations!" Fig.9 If you lose the game, Csy4 will be disappointed.

Comic brochure about our game < CSY4 GO!>

To make people have a better understanding of both the game and our project, we designed six comic pictures represent the six game levels separately. The picture will be shown before the game starts to help players understand situations clearly. The comic pictures not only help in driving the storyline but also enhance the enjoyment of the game. They are so cute and straightaway that can be really helpful in engaging the audience.
There are the pictures and the story in six game levels:

① Immune：when the virus invade our bodies, the cells are on the verge of death or destruction. Consequentially, the cells have their own ways like compounding certain protein to defense the virus. However, when the cells can't bear the heavy load, we can ask Csy4 for help by cutting certain mRNA to improve the protein army.

Fig.10.1 Immune

②Secretion：our body is constitute by thousands of cells, and what’s fantastic is those cells don’t live alone but have their unique method to communicate with each other closely. There is a kind of method which is relied on the secretion protein. When we want to construct the connect between two cells, we can use Csy4 to create certain secretion protein, help them send the messages to each others.

Fig.10.2 Secretion

③Transport：Hey! Have you seen the huge one lying there with a bag of potato chips? It is always eating, eating, eating…… It so fat that the normal size carrier is not big enough for it. It seems like we have to Built a carrier for it Professionally. Csy4 can be help.

Fig.10.3 Transport

④Constitute：Warning! Warning! Cellular components are destroyed! ……In the short, precise life cycle, cells just like a space ship wave in the universal but have their certain destination, It’s normal for it to fix and replace the damaged components, but when the cells are given the task that its predecessors never had which means when it’s in the bad situation there is no certain method can be find to solve the problem at that moment, Csy4 can be helpful.

Fig.10.4 Constitute

⑤Recognition：Some cells when you look at them are nothing special but actually have the vitally important task. One day, Clark Kent walk down the street as usual, not recognize there is a world waiting for he to save it. He has no response to cosmic signals…… Csy4 can be helpful, let’s change the signals that make it easy to understand. Well, it seems we did it.

Fig.10.5 Recognition

⑥Catalyze：Enzymatic reactions are common, one of the most important in them is the metabolism of energy, our bodies’ move, cellular activities and so on rely on it. Sometimes, It’s necessary to enhance the reaction to provide more energy. Here, we can ask Csy4 for help.

Fig.10.6 Catalyze

Game MANUAL -- COMIC MANUAL
The game manual contents 3 parts -- abstract of < CSY4 GO!>, abstract of Csy4 and story and pictures of comic. Manual was designed to look like an envelope. You can see it in the short video.
（视频1）
Our creative design of comic picture:

Fig.11 Game MANUAL -- COMIC MANUAL

Feedback

We showed the game to people from all age groups. After playing the game, they can clearly describe what the pictures want to say and even understand how Csy4 works exactly. Based on the responses we received from participants in our game, we believe < CSY4 GO!> is succeeded in achieving our goals. We also gave some speeches based on our game at game brochure at local schools. In lectures, the students were fascinated with the wonderful figures and the principle of our project and biology, which really broadened their horizons. Furthermore, by using our game brochure, we found that it is easier for those people who know nothing about biology to understand the main meaning of our project. That is a huge success for us!

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