HP Flowchart
Goal Setting
The meaning of improving the "genetic instability "in actual production
Why did we approach them?
When thinking about this year's project, we thought of the phenomenon of "genetic instability". In biological production, strains without the burden of expression of the target product will have a survival advantage over those strains that synthesize the target product, and may eventually replace them. This is a problem that has troubled related technicians in the industry for a long time. We hope to solve this problem by our method and want to konw whether our idea is meaningful for improving the actual production situation. To get some suggestions for this question, we consulted experts in the related fields and visited factories.
What did we learn?
In the communication with experts, we understood that genetic instability is indeed a difficult problem in both scientific research and industry.
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Researcher Huanqin Dai ( Institute of Microbiology, Chinese Academy of Sciences) replied “Strain degeneration is indeed an important problem in industrial production, especially in Streptomyces industrial fermentation”. |
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Researcher Weishan Wang (Institute of Microbiology, Chinese Academy of Sciences) approved the practical significance of our project, "It is a very meaningful work to find a solution to strain degeneration." |
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"Even in scientific research, the degeneration of strains is a common problem. In the field of production, this problem is particularly prominent due to its large scale." Prof. Jiang Zhong (College of life sciences, Fudan University) said. |
Visiting Sinovac
Moreover, Manager Zou of Sinovac R&D department put forward his own views on our experimental project. He agrees with that our project is very meaningful for the initial strain selection of vaccines and other microbial drugs. Our platform could be used in both factory and laboratory to help screen out strains that do not work properly.
In summary, it is necessary and meaningful to try to solve this problem, which encouraged us to carry out our project.
Associated with Prof. Peng Xu
Prof. Peng Xu , Guangdong Israel Institute of Technology; Editorial board member of international well-known magazines Metabolic Engineering and Current Opinion in Biotechnology.
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Why did we approach him? With the very basic idea learning from the guards in the natural community to build a general industrial production platform, we wanted to consult the related experts and fortunately we got in touch with the Prof. Peng Xu. What did we learn? Prof. Xu said, "This is generally achieved by applying social reward-punishment rules to eliminate cheaters and reward winners in a mixed cell population. We envision this will be a rapidly-evolving area." In the colony, bacteria will produce public substances together. But under the pressure of survival, some cheaters who don't produce but only use public substances will appear, which is obviously unfavorable to the whole flora. Therefore, a new role "guard" has emerged. The guard will use the quorum sensing system to kill cheaters to maintain the stability of the flora. |
Project preliminary goal setting
We understand that genetic instability is indeed a difficult problem in scientific research and industry. According to professor Xu, we finally decided to learn from the interaction of colonies in nature to solve this problem. Learning from the guards in the natural community, we intended to make use of E. coli to build a general industrial production platform with guards to kill the cheaters who didn't make contributions.
Project Refinement with HP
Associated with Prof. Quanguo Zhang
Prof. Quanguo Zhang, College of life sciences, Beijing Normal University
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Why did we approach him? Prof. Zhang studies evolutionary of model microbial systems to verify evolutionary and ecological theories related to the origin and maintenance of biodiversity. Besides, he studies the rules of adaptive evolution and its impact on population survival in rapidly changing environment. We asked him for professional suggestions, which helped us to improve our design. |
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What did we learn? We explained our project to Prof. Zhang that in order to prevent the guard from consuming too much resources and producing benefits, it was designed to perform the killing function and synthesize the target material at the same time. However, Prof. Zhang raised this question, "Guards have a heavier burden. How to maintain their work efficiency?" Different sizes of pathways have different degrees of effect on the survival of bacteria. This gave us inspriation to adjust our project. How did we refine our project? To address Prof. Zhang's concern, we changed the previous design so that the guard has the ability to produce the target substance and kill the cheaters at the same time. Also we adopted a toggle switch in the pathway. The guard stops producing the target substance while activating the pathway to kill the cheater to stabilize function and efficiency of the platform. |
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Associated with Prof. Sen Li
Prof. Sen Li,College of life sciences, Beijing Normal University; member of the the Chinese Society of Biochemistry and Molecular Biology
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Why did we approach him? Prof. Li has extensive research experience in the field of Biochemistry and Molecular Biology. He creatively proposed the concept of single chain antibody type molecular chaperone, and developed a set of single chain antibody oligopeptide chaperone system which can effectively help protein refold. He also systematically studied the effect of macromolecular crowding on protein folding and aggregation. We hope to learn more about antibody and improve our PmrBAC system. |
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What did we learn? In terms of PmrBAC system, Prof. Li said, "Generally, there are six binding sites in the binding region of monoclonal antibody. Our project has half of the binding sites of monoclonal antibody, so the binding ability with mCherry needs experimental verification. If the binding ability is not good, the last six binding sites can be replaced." Besides, Prof. Li provided us with a thinking direction, "Your pathway is too complicated that the bacteria’s work efficiency may decrease. Other ways can be selected to simplify this pathway." How did we refine our project? Following this idea, we finally simplified the pathway design so that researchers can choose to use different forms of cheaters monitoring (mutations, translocation, deletion, insertion or other variations) according to the characteristics of the target substance. Also, we validated the killing module to ensure that our modified receptor added with antibody worked normally. |
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Associated with Prof. Yao Yu
Prof. Yao Yu,Researcher, College of life sciences, Fudan University
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Why did we approach him? Prof. Yu is an expert in yeast genetics and keen on using simple microorganisms to study problems in higher biology. At present, Prof. Yu mainly focuses on the role of epigenetic regulation in transcription. He has undertaken courses such as "Principle and Application of Genetic Engineering", with a lively teaching style. We asked him for professional advice, which helped us to improve our design. What did we learn? Prof. Yu provided us with a new idea, "We can also try to reward 'workers' who have made contributions and make them grow better." How did we refine our project? Referring to Prof. Yu's opinions and some articles, we are also thinking about establishing negative feedback pathways among workers to help them grow better. Therefore, we designed a pathway that can senses survival pressure to adjust the yield of target protein. |
Project implementation
Associated with Yang Li
Yang Li, Chief of Research and Regulation Section, Academic Department, Yakult (China) Investment Co., Ltd.
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Why did we approach him? Yang Li is the Chief of Research and Regulation Section, Academic Department, Yakult (China) Investment Co., Ltd. He is mainly responsible for the management of probiotic-related research projects, as well as food-related regulations and standards. With 15 years of relevant work experience in the food and beverage industry, he has participated in the alternate work of national food safety standards and relevant academic teams organized by the National Food Safety Assessment Center. We asked him for relevant suggestions, which helped our product to be put into actual production. |
What did we learn?
During the communication, Chief Li told us about the production and quality control of live lactic acid bacteria beverages, and the scientific nature of probiotics. At the same time, he introduced the production process and quality and safety control points of probiotic beverages through actual cases. In the end, Chief Li approved the security of our platform and emphasized the importance of standardization because industrial application focus on quality and efficiency.
How did we refine our project?
Inspired by communication with Chief Li, we got the idea that our project needed to be standardized. Consequently, we planned to make a kit, which is convenient for factory users.
Visiting Beijing Fumate Biotechnology Co., Ltd
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Why did we approach it? Fumate Biotechnology Co.,Ltd. is a high-tech enterprise focusing on human intestinal microecology reconstruction and personalized health management of intestinal microecology. After years of technology and clinical research, in May 2020, Fumate Biotechnology Co., Ltd. established an international standardized enterobacteria bank in Beijing. We wanted to know whether our project is significant or not and whether our product could be applied in other fields. |
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What did we learn?
During visiting Fumate, Manager Zhang affirmed and encouraged our innovative idea, and proposed some directions that can be expanded. For example, our project could be applied in disease treatment. When the intestinal flora is imbalanced, we could use the suicide system to automatically regulate the number of bacteria, which is an area worth exploring.
How did we refine our project?
Enlightened by this visit, instead of the initial thought that killing all cheaters is always right in our project, we may try to expand the using of our platform to control the threshold of bacterial concentration.
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