Team:OUC-China/Human Practices
Bronze
1. Project inspiration and description
Riboswitch is RNA-based regulatory tool that specifically modulates the expression of a gene or operon. It holds great potential as regulatory element in various applications (e.g. bioenergetics, biofuels, therapy, bioremediation and biochemical engineering). However, by referencing the project of Paris_Bettencourt in 2015 and other study about riboswitch, we found that it can’t be regarded as a modular device. The three problems below make the riboswitch quite hard to design and employ to the application.
○First, due to the context-dependent performance of riboswitch, its structure is easily damaged by the GOI, leading to the failure of responsive to ligand, so it can’t be a plug and play device.
○Second, existing riboswitch only has simple response curve. It’s restricted by the limited dynamic range and cannot achieve multi-level regulation. So riboswitch function is expected to enhance.
○Third, because the ligand of riboswitch is often hard to degrade in the experimental culture system, it often makes the system away from your prediction. So it’s not easily toggle between the on and off state.
Inspired by past literature and iGEM projects, we know that it's time to make modular riboswitch. This year, we proposed a principle to make modular riboswitch-”RiboLego”. Through our approach, riboswitch can be considered as a modular device whose function is enhanced and varied. So this project is an useful application of synthetic biology.
For more details, see the Project Inspiration and Description page.
Silver
1. Attach importance to bio-safety
Figure 1: Why our work is responsible for the world?
1.1 Ensure the safety of our project
Having identified our project, we assessed any risks and discussed the bio-safety of our project. We used E.coli DH5AlphaZ1, a very common strain in biological experiments as our chassis. In our project, all parts we have utilized are selected from Risk Group 1, none of which are with a Red Flag. The downstream products have nothing but fluorescent proteins which act as a reporter to characterize our experimental results.
1.2 Ensure the safety of our lab
We work at a neat lab named “Lab for Micro-innovation and Enterprise”, which is a BSL-2 laboratory. Before working in the lab, we are supposed to be trained, not only for the general lab safety rules, but also for the standard experimental operation avoiding unnecessary damage. 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. What's more, the teacher responsible for laboratory safety checks our safety work every week. And we are certain that everything we did is under our control. As for microbial organisms, the microbial organisms have no chances to escape from our laboratory because we use ultraviolet sterilization after experiments. Furthermore, all equipment used for recombination strains will be sterilized by High-Pressure Steam Sterilization Pot.
Figure 2: We have strict safety regulations and safe operation.
1.3 Enhance bio-safety awareness of the public
By reaching out to the communities, we found that numerous public misconceptions remained about bio-safety issues in synthetic biology. So we made good use of our WeChat public platform where we published some articles and comic books about bio-safety. All these articles are rather approachable and most of them received positive feedbacks. We hope that it may help more people enhance bio-safety awareness.
Figure 3: Publish article in WeChat platform.
1.4 Educate students basic laboratory safety rules
Safety is always in the first place for us, especially for the laboratory staff. So we have the obligation to help students who are about to enter the laboratory to understand the potential risks of the laboratory and the basic laboratory safety rules. No experiment carries zero risk to the experimenters, so they must learn how to protect themselves. In order to popularize bio-safety issues in the lab with middle school students and freshmen, we organized an activity about bio-safety in the lab. Students have an opportunity to visit our lab, learn basic lab skills and raise their biosafety awareness.Before teaching them basic microbial experimental operations, they were educated to be equipped with some necessary facilities, such as latex gloves, goggles and lab coats to protect them from biotic and abiotic hazards. Through this activity, their bio-safety awareness has been significantly improved!
Figure 4: We taught them basic microbial experimental operations and on the right is their work.
2. Explore the values of fundamental research
Figure 5: Why our work is good for the world?
2.1 Establish links with biotechnology companies
This year, the track which OUC-China selected was Foundational Advance. Given that all basic researches aim at application and benefiting for human beings, the biggest problem we have to face is how to transform our basic research into useful and beneficial application. To verify our project is useful for the world, we communicated with some biological companies who are good at transforming basic researches into practical results.
We visited some relevant local biotech companies such as Qingdao Bright Moon Seaweed Group Co.LTD and Qingdao youdu biotechnology Co.LTD. We introduced our project to the stakeholders and also gathered many good suggestions. More importantly, they applauded our ideas, held great promise potential application of riboswitch and proposed some application of our project on production. Enlightened by the investigation, we ensured our project is good for the world and optimized our project deeply!
2.1.1 Qingdao Bright Moon Seaweed Group Co. LTD.
Invited by the researchers, we arrived at Qingdao Bright Moon Seaweed Group Co. LTD and visited State Key Laboratory of Bioactive Seaweed Substances. It is a leading enterprise in the Marine biological industry of Shandong province, and the largest seaweed biological products enterprise in the world. Many researchers work in the biological company, developing marine cosmetics, marine food and other high-tech products which are sold all over the country. So it’s necessary to ask them how to explore the value of basic research. During the process of communicating with them, the company's research and development staff praised our project and said that our worry about its usefulness were misplaced. They agreed with the potential applications of riboswitches, which could be greatly expanded if they were developed as modular components. In addition, they encouraged us to improve the regulatory capacity of riboswitch. Finally, to our delight, they mentioned that they would like to apply riboswitch to production.
Figure 6: We went to the labs of Qingdao Bright Moon Seaweed Group Co.LTD and learned about their current researches.
2.1.2 Qingdao Youdu Biotechnology Co.LTD.
In order to find more ideas, we came to Youdu Biotechnology Co.LTD, which is mainly involved in the beauty industry and has many production lines and beauty brands. As a new and dynamic biological enterprise, Youdu has many novel ideas and is dedicated to the transformation of basic research. We introduced our project to the researchers in the laboratory, who gave us a high evaluation of the project and suggested that we should create more Tuners to diversify the functions of riboswitch. In the future, we will also keep in touch with Youdu for a long term and hope that our system can really achieve industrial integration.
Figure 7: Qingdao Youdu Biotechnology Co.LTD applauded our system.
Summary
In summary, we learned about the current social needs and established a two-way dialogue with biotechnology companies. 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 and progress in the lab, by which we can promote each other and make progress together.
2.2 Communication and cooperation
After communicating with biotechnology companies, we also wonder whether other teams and labs focus on the values of basic researches and how they transform it into useful application. So we took part in many conferences. Fortunately, our team was invited to the 5th Synthetic Biology Young Scholar Forum. By communicating with Professor Zhang, we received positive feedback. He praised our project and said that the modular riboswitch approach we proposed can expand the RNA device toolbox, which will be of great use to the biochemical engineering. We were inspired greatly by the fantastic ideas from successful cases and also benefit a lot from the conversations.
Figure 8: We participated in the 5th Synthetic Biology Young Scholar Forum.
Furthermore, we had the honor to visit Marine Institute, Chinese Academy of Sciences. 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. The researchers also encouraged us to combine our fundamental research with industry, which was an affirmation of our project. They are willing to apply our projects to their labs in the future.
Figure 9: We had the honor to visit Marine Institute, Chinese Academy of Sciences.
In order to communicate and cooperate with other iGEM teams better, we participated in the China regional iGEM Exchange Meeting (CCiC), an influential symposium. We publicized our project and related activities better and deeply! At the same time, we understood the forefront of the field of synthetic biology. Besides, some suggestions inspired us to optimize our project.
Figure 10: we participated in the China regional iGEM Exchange Meeting (CCiC), an influential symposium.
In addition to the conferences above, we also participated in many small seminars organized by iGEMers. Undoubtedly, these are very meaningful and valuable!
For more details, see the Collaboration.
2.3 Transform basic research results into application
Finally, by engaging with companies and experts, we successful narrow the gap between foundational research and society. All basic researches aim at application and benefiting for human beings, so we summarized our preliminary preparation, research methods, research results and experience and wrote a complete survey report. We hope our report will help further iGEM teams to explore the values of their projects.
Click the report, you can get more information.
Gold
1. Create many tools derived from the project
1.1 RiboFold
This year, OUC-China proposed an approach to design modular riboswitch rationally. However, when we tried to explain our projects to more people, we found that it’s difficult to fully understand, especially for some amateurish people. In order to let more people understand the principles of biology in an interesting and effective way, we are creating a game - RiboFold meticulously. The game aims to allow users to build more riboswitches by adding sequence of expression platform while keeping the structure of the riboswitch intact. It will offer you the aptamer region of riboswitch and four buttons which respectively represent four bases. By continuously clicking the buttons, users can add the bases and complemented the expression platform of riboswitch. At the same time, the changed structure of riboswitch will appear on the screen. We believe that our game will offer the users an opportunity to randomly change the structure of riboswitch and construct more riboswitches. They can understand that the structure of riboswitch is so fragile that can easily influenced by the its sequence. And by playing our game, more people can understand our project very well! We will continue to improve it in order to achieve the best presentation effect!
1.2 Comic book
Ocean University of China published a comic book on synthetic biology in 2017. In 2018, the E. coli SPACESHIP comic book series began to cooperate on the iGEM official website and achieved high praise. This year, OUC-China continued the style of last year and added the new content. We have draw three more chapters, respectively including Riboswitch, Quorum Sensing and Safety.More foreign teams are willing to help us diversify the language of the comic book. At the same time, we cooperate with many domestic and foreign teams, and we are very honored that they are willing to use our comic book to promote the science of synthetic biology. It is worth mentioning that these teams also give us some good feedback about the effects of comic book E.coli SPACESHIP. we hope everyone to actively participate in science popularization, achieving the purpose of improving the depth and breadth of science popularization, strengthening the inheritance of synthetic biology.
Figure 11: This year, we continued the style of last year and added the new content og comic book.
Click Chapter 4,5 to get more information about our comic books!
Click Chapter 6 to get more information about our comic books!
1.3 ideal lab
A huge challenge came this summer - our team's laboratory was relocated and revamped! So we need to think about how to arrange the layout of new lab. We published an invitation to cooperate on iGEM's official website and looked forward to receiving some pictures and descriptions of the iGEM team's existing laboratories, which will provide us with ideas on how to design laboratories. Inspired by other iGEM teams, we successfully designed our own synthetic lab!
What synthetic biology pursue is modularity and standardization, so an advanced laboratory is a must for synthetic biologists. Although existing laboratories are capable of conducting synthetic biology research, it still has many disadvantages such as inconvenience and taking time and effort. Therefore, we began to think about what synthetic biology lab will look like in the future and what improvements will be made on the existing basis. We began to collect the ideal laboratory drawings from the smart and active iGEM team, and we look forward to them becoming “the greatest inspiration for humanity” and “ The future of synthetic biology laboratories." Many teams have participated in our collaborative projects, which inspired our ideas.
1.4 VR&Mini-lab: the real life of lab
During reaching out to the communities, we found that many people were interested in microbial and molecular experiments but had no chance to come in the biological lab. iGEM encouraged us to spread synthetic biology to the public by developing new tools. It’s also our responsibility to get more people to experience lab life. With reference to the results of the questionnaire and use VR technology, a great synthetic biology laboratory was built! It’s a golden opportunity for amateurish people to get in touch with laboratory. We have carried on the sharing and the propaganda in the school, has obtained the extremely high praise! We look forward to sharing with you on site this collection of many of our passion and wisdom of VR creation! And expect some feedback. We also recorded a video about VR and it will tell you something about our great idea! We also recorded a video about VR and it will tell you something about our great idea!
Figure 12:The lab scene in VR.
In addition, considering the availability and portability of the equipment, we have also created a mini lab to make it easier to share lab life with the public. We look forward to anyone who is interested in microbiology and molecular experiments to join us! We shared our microlab with the iGEM team and they gave us great advice and feedback!
For more details, see our vedio.
1.4 Software
By introducing stabilizer and tuner, riboswitch can normally regulate GOI. To expand riboswitch function, more tuners was designed. In practical production applications, when using riboswitch, synthetic biologists should select an appropriate tuner to regulate the expression of GOI, achieving their all kinds of goals. With the development and popularization of computer science, more and more scientific research works benefit from it，"Cloud-based" biology has become a necessity.To make it easier for biologists to design modular riboswitch with our principle, we developed a software. When user offer the original riboswitch, the natural gene , GOI and desired expression level, the complete sequence will come up in a short time. It turns out that our software can achieve the desired effect. We've exposed the code in the wiki, and we're looking forward to helping future iGEM teams design the riboswitch and asRNA they need more easily and accurately.
For more details, see the Software page.
1.5 Experiment manual
Invited by our teachers in Experiments Center, we edited an experimental manual including some basic microbiological operations and molecular operations independently. Our teacher wants to set up an experiment course with this experiment manual. We hope that our experimental operations will provide a reference to other students. We are very willing to share to realize the inheritance of iGEM.
For more details and get the PDF, see the Experimental manual.
Figure 13:The cover of the lab manual.
1.6 WeChat Platform
OUC-China has built up a WeChat public platform, a worldwide platform with billions of users for documentation, communication and popularization. To engage with the public and help them attach importance to synthetic biology and bio-safety,we published some articles. Fortunately, all these articles are rather approachable and most of them received positive feedbacks.
Figure 14: We make good use of our WeChat platform to spread the values of iGEM.
1.7 OT-2 video
This year, we were very lucky to get an ot-2! It's just a really cool robot that can help you do a lot of basic experiments under control, even if you're not in the lab. In order to express our gratitude to Opentrons and share ot-2's operation method and experimental process with more iGEM teams, we made a tape of video with great sincerity, which included our experiments with ot-2 controlled by program and detailed explanation of the whole process! I promise this is very fun! Video here!
2. Communicate iGEM values
Before spreading synthetic biology around the public, we successfully constructed the above educational tools. So we make good use of them to engage with the public. We hope everyone can actively participate in science popularization. By these effective tools, it’s easy to narrow the gap between synthetic biology and the public and achieve the purpose of improving the depth and breadth of science popularization, strengthening the inheritance of synthetic biology.
3. Get more inspiration and optimize our project
3.1 More tuners are expected
During our journey of human practices, we visited some new and dynamic biological enterprise. After visiting the factory , laboratory and production line of the enterprise, we introduced our project to the researchers in the laboratory, who gave us a high evaluation of our project. They affirmed that riboswitch would become a popular and attractive tool in real industries, because by responsing to ligand, riboswitch can regulate gene expression without dependence upon protein. However, due to limited dynamic range, the use of riboswitches is often restricted. The researcher said that the original riboswitch had a single response curve, which cannot meet the needs of industrial production. So we were encouraged to improve riboswitch function and make riboswitch response curve diverse.
Inspired by the biological company, we established model and designed different tuners to construct many modular riboswitches based on the original one. In fact, when the same amount of ligand is added, different tuners can make the modular riboswitches regulate different expression levels. In the process of interaction with biotech companies, we gained a lot and integrated it with our project. Finally, we successfully expand riboswitch function!
For more details, see the Model page.
3.2 How to control the on-off state of Riboswitch
Because small molecule, such as inducer and ligand, is often hard to degrade in the experimental culture system, we cannot change the state of our system, which will cause some problem and make the system away from our prediction. So we focused on the problem and consulted Professor Wang, who studies aptamer for many years. She said that comparing to the thermodynamic switch, the kinetic switch could not easily toggle between the on and off state. She inspired us to think deeply and find an esay and effective way to change the on-off state of riboswitch in a short time.
By referencing many studies and comparing different approaches, we chose antisense RNA, a well-studied category of RNA regulators that has been used extensively in engineered systems to achieve our goal. Our idea was praised by Professor Li Yun who study non-coding RNA. With the help of her, we successfully achieved this goal!
Figure 15: Inspired by Professor Li Yun, we utilized asRNA to regulate the on-off state of riboswitch.
For more details, see the Results page.
