Team:OUC-China/Human Practices
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
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.
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
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. BIG gave us some advice on our project and it really enlightened us华大基因
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海洋所
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.明月海藻
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 优度公司
3. Integrating project with a game——
"The principles of all fundamental scientific research are obscure for us amateurish people."
“The form of the game
…
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 -
The game introduction
The leading role ofFig. The logo of
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 nowThe 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.
The background of
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.
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