Overview
Collaboration is not only a process of mutual sharing, but also can bring us new reflections and improvements. In-depth cooperation between any module and other teams is indispensable. We are committed to communicating with different teams on different aspects and gaining extensive knowledge in various fields. We believe that continuous communication and cooperation can bring better results to the project.
FBA
FBA Freshwater Bioremediation Alliance
Freshwater Bioremediation Alliance was composed of Nanjing-NFLS, XJTLU-China, NPU-China, UM_Macau, FAFU-China, GXU-China, and Nanjing-CHINA. We had similar backgrounds and had many similarities in experiments and HP. It aims to solve problems through mutual communication and provide help to other environmental tracks.
Biosafety Meetup
Overview
Overview
The spread of dangerous biological factors will endanger human health and social stability. From the perspective of the research object of synthetic biology, both the modification of known organisms and the creation of new organisms have safety uncertainties. Therefore, we need to control the existence and spread of genetically modified strains involved in the project. Among them, the setting of the suicide module is particularly important, which can effectively control the self-elimination of bacteria after the completion of the task, and control the possible gene pollution problem from the source.
Time of Attendance: September 2, 2022
Participants: NPU-CHINA、XJTLU-CHINA、CAFA-CHINA、FAFU-CHINA、GXU-CHINA、Nanjing-CHINA、Nanjing-NFLS
Form of Participation: Online conference
The Meeting Content：Each team designed different control modules for their respective projects and shared their content during the meeting. The project of the GXU-China team is "Photoregulated wastewater treatment bacterial preparation based on Bacillus subtilis", in which the experimental part aims to convert NH4+, NH2OH, NO2-, NO3- plasma into N2 to remove it from the water body through the "metabolic pathway of heterooxy-aerobic denitrification and nitrogen removal". Considering that the intermediate NO could be oxidized to NO2 and thus be harmful to the organism, the team designed the denitrification pathway. As a safety concern, NO can be reduced to nitrogen by two enzymes, NOR and NOS, so as to achieve harmless treatment. In addition, the team engineered a suicide mechanism that induced NucA expression by green light irradiation can be inactivated as early as possible by raising the temperature. So as to prevent it from leaking and causing harm to the environment. Chen Lekang of Nanjing China Group introduced the prevention of leakage, the scheme of leakage, and the operation of the finishing device, respectively. The team plans to design a completely sealed MFC device with only an electrical connection to the outside world, preventing the leakage of bacteria and silver ions.
At this meeting, our team shared the contents of leakage prevention, leakage plan, termination of device operation, and laboratory safety. To prevent leakage in gene-edited organisms, we used toxin genes to construct a genetic circuit that kills bacteria: araC+pBAD+B0032+mazF. araC-pBAD is an arabinose-induced promoter, B0032 is a ribosome binding site, and the araC-pBAD promoter can be tightly controlled by arabinose. When arabinose was added to a petri dish, it induced the promoter to express the toxin gene mazF and killed the modified E. coli.
In the construction of the early technical route, we did not consider the construction of the suicide module, so we could not establish the basis for the development of bacteria in reality. Through this meeting, we learned the basic construction methods and precautions of suicide module. At the same time, we also put forward a feasible plan. Due to the time problem, this plan has not been well implemented. So we switched gears, redesigned the suicide module, and enlisted the help of the team at Jilin University.
Model Meetup
Overview
Through the channel of FBA, we learned that the XJTFC team has many similarities with our team in building the model, so we held an online meeting in order to solve our common demands.
Meeting Time: August 22
Conference Members: NPU-China and XJTLU
Meeting Format: Online meeting
The Meeting Content:
We discussed the design and problems of mathematical modeling with iGEM team members from Xi'an Jiaotong-Liverpool University. We mainly studied the growth and strain release of E. coli. Jeff Zheng shared two aspects: the growth of E. coli in the Philippines, cellular automata and strain release. We observed very slow growth during the first three days of culture, and partial aggregation of thallus was observed during the first one to two days of degradation. However, the degradation rate of phenanthrene increased slowly and steadily during this period, and the aggregation of microorganisms caused the deviation in the extraction determination of phenanthrene. This may also be related to the detoxification reaction of microorganisms; that is, when microorganisms themselves encounter toxic substances, such as phenylene, the microorganisms will actively flee from this environment to protect themselves.
Communication Record:
NPU-Wei Shiqi: When you analyze the data, do you consider a biological explanation? such as characteristics, growth curves, and so on.
XJTLU-Liu Jiayi: We do. We've been working on a number of papers describing bacterial growth models, and hopefully the resulting models will fit a curve better. The biological perspective can not only show mathematical models, but also explain the biological process of the experiment itself. According to the model obtained so far, it fits well with some literature data.
XJTLU-Liu Jiayi: We observed that you are trying to make a model about the direction of the neural network for the growth of E. coli in the Philippines. What is the default input layer and output layer?
NPU-Zheng Jiefu: As for neural networks, there are not many factors that can be used at present. Only one incubation day and one concentration index can be used as a reference. If you build a neural network, the results may not be very accurate.
XJTLU- Liu Jiayi: If the neural network is successfully built, what is the source of the input and processed data? Did you find a certain amount of data in the literature?
NPU-Zheng Jiefu: At present, we prefer to use the known experimental data. If more data can be measured in later experiments, we can directly use neural networks to explain the variation of experimental data, which may better explain our modeling results.
The Harvest
In the exchange and sharing meeting, the students of XJTLiverpool iGEM introduced the specific content of their project and shared the growth curve fitting of E. coli in wastewater. They chose the logistic model to fit the data, but the logistic model can only explain the exponential growth phase and the stable phase of growth. Therefore, they used the decay rate coefficient to better fit the change of E. coli numbers during the death stage, and introduced new parameters to improve the model. Their experimental content is similar to ours, and we are just looking for biological principles and formulas that can be used, so we also tried to fit our experimental data with their basic model and the method of adjusting parameters in the latter stage, and explained the biological meaning.
Jilin_China
After the FBA biosafety meeting, we started building suicide modules to ensure that the strains released into the environment would be successfully killed. Due to time, we didn't have the energy to build a complex regulatory system. Finally, we got inspiration from the 2020 team at Jilin University and made effective contact with their team leader to guide us on how to use the relE gene to kill bacteria. However, due to the epidemic, Jilin University adopted strict epidemic prevention policies, so the express delivery could not be delivered normally, and we could not get the relE gene in time. Therefore, we have to obtain the target gene by a gene synthesis method. But when the epidemic improved, we received the plasmid from Jilin University the first time.
Meet up
NPU-CHINA regards collaboration as a significant part of enhancing a team’s comprehensive ability. Cooperation with others can achieve win-win results, and every member of our team cherishes every opportunity to collaborate with other teams, for we can share information related to the project with everyone, communicate with each other about innovative ideas in module design and other aspects. Due to the impact of the epidemic, we have missed many opportunities for face-to-face communication with universities outside the province. Fortunately, we have made a combination of online meetings and offline discussions, which allows us to talk to more excellent teams.
Meetup held by iBowu-China
Date：June 26, 2022
Format: Online meetings
Participant：Representatives of the 20 teams, iGEM ambassadors in Asia, Curtis and Bill, etc.
Content：
This is the first time that we have participated in a communication meeting between teams. For the first time, we felt that, in addition to us, there were so many young people who were also interested in synthetic biology who were using their own wisdom to create the first flowers on the scientific research road.
At this meeting, we shared the design concept of the project and the improvement we think this project can bring to the surroundings. Project ideas from different fields and modules collide with each other, enriching the understanding of all participants. with OUC-China, We preliminarily exchanged some questions about experimental safety, which laid the foundation for our future research on safety.
Harvest
At this meeting, iGEM Asia ambassadors Annika and Bill shared their experiences and achievements from the IGEM competition. We were impressed by the statement that iGEM was more than just an academic competition, but also involved team cooperation and exchange; team cooperation included not only the division of labor and cooperation within the team, but also mutual cooperation between different schools and teams. This seminar makes us clearly realize that this is a collision of excellent thinking from all directions, different fields, and different disciplines. It also makes us understand that in this competition, constant communication and reflection, learning from each other is particularly important. Only by constantly questioning others and being questioned can we gradually improve and learn from each other to do something.
Meetup held by NPU-CHINA, Jilin-CHINA, GXU-CHINA and Jiangnan-CHINA
Date：July 16-17, 2022,
Format: Online meetings
Participant：Representatives of the 27 teams, etc.
Content:
Chen Xianzhong, Dean of the School of Biological Engineering at Jiangnan University, opened the meeting. He pointed out that communication between different teams from all over the country can provide infinite possibilities for the future, and he warmly affirmed the scientific research of each team and encouraged each team to enrich their work through this opportunity.
At this meeting, a series of innovative ideas were shared by the team of Zhejiang University on the project design of cultural relic protection and restoration, the sewage treatment idea of Bacillus subtilis proposed by the Guangxi University team, and the construction of a microbial circulation system shared by ShanghaiTech University.
Harvest:
Through this meeting, we further confirmed that constant communication is of great significance to the improvement of the project. At this meeting, the official staff of iGEM also brought us additional harvest. We learned more detailed process information and matters needing attention in the competition. We also went a step further with ShanghaiTech-China to explore whether E. coli could survive on Mars. They inspired us to think about how to expand the time and space of our project.
Meetup held by Northwestern University
Date：July 23, 2022
Format: Offline meetings
Participant：Representatives of the 7 teams
Content:
We are constantly looking for offline communication opportunities. We talked about the ideas and designs of each team in the conference room of Northwestern University, exchanged freely, and explored the mysteries of synthetic biology together.
At the meeting, all teams pooled their wisdom and opened their minds. Through PPT presentation, each team presented their respective projects from the aspects of project background, experimental design, modeling, HP, and future prospects, and put forward the advantages, disadvantages, and doubts of the team project.
We stated that the strong motivation of each member, as well as the simplified project goal, is the essential element of a team. We also discussed the limitations that we were currently facing and how we planned on continuing to improve our design, opening the door to the more knowledgeable members of the public to talk to us and share their ideas.
Harvest:
We have learned from Nie Jiang of CCIC that the academic and completeness of the background presentations should be emphasized, and that the team's design should be continuously improved based on the application of the current environment. In the communication, we realized the deficiencies of the current project in terms of basic design and safety performance, and reached an agreement with other teams to help each other in the subsequent project improvement. In addition, we agreed with other teams to further enrich the content of Human Practice and agreed to hold a series of meaningful activities together.
Future Expectations
Due to the pandemic, a lot of communication can only be done online. We decided to have further communication with these teams even after the competition to help build an engineering system that can safely and effectively apply biotechnology. In addition, we will also promote our projects and share more related knowledge about synthetic biology to increase the public's understanding of the subject. We believe that through our continuous sharing, this love and passion will be passed on, just as we have received it, from one generation to the next.
CCIC
Conference of China iGEMer Community(CCiC)
Time of Attendance：From August 18 to August 22, 2022
Sponsor: Shanghai University of Science and Technology
Participants: A total of 1224 participants including teams and individuals
The 9th China International Genetic Engineering Machine Competition (iGEM) Team Exchange Conference CCiC, hosted by University of Shanghai for Science and Technology, is a national summit independently initiated by Chinese iGEM teams, with a record number of participants of 1224. The theme of this CCiC conference is "Life Meets Everything". The participating teams will share and explore the role of synthetic biology in different fields of scientific research and industry, and show the power of synthetic biology to participate in life and change life.
The Meeting Content
Due to the epidemic and other irresistible factors, we only participated in the online meeting of this CCiC conference. We shared the design concept, background information, and biology module of our team project, and presented our project results in Human Practice, Social Practice, and Digital Modeling to the audience and judges. The judge question session with the team communicates with students from different research directions to discuss the project security module settings of suicide, and we also research some similar issues with other teams of students discussing the issue of blue-green algae cell mathematical model building. Through these exchanges, we further improved the detailed design of our project, enriched the content conformation of other modules in addition to the experiment, and put forward the experiences and insights gained in our experiments for the design problems of other team projects.
The Harvest
During the CCiC conference, a total of 6 occasions of special lectures in the field of biology were set up, and professional researchers from different laboratories, such as Wei Wensheng, professor of the School of Life Sciences of Peking University, and Chen Zibo, researcher of the Life Programming Laboratory of Westlake University, were invited to share and exchange information. In the Shenzhen Institutes of Advanced Technology of Synthetic Biology, Chinese Academy of Sciences researcher at the institute of Chen Ye "gene route design and build positive" speech, we further understand the principle of synthetic biology engineering, and the project for us to reflect on the design of genes, which later in the experiment for us to consider to improve the construction of gene vectors produced a certain influence.
This conference issued a total of 2 awards and 6 individual awards. Our team in the Best Presentation was nominated for the Best Presentation.