Team:OUC-China/Collaborations
Overview
As the old saying goes: a single man is weak and feeble, drifting like Robinson, only together with others, he can complete many careers. The same will apply in iGEM. Therefore, we are very glad to share our ideas with others and consider the interesting opinions of others. Cooperation enables us to progress together. The process by which we work with other teams is the following.
Design
A project which introduced virus detection attracted our attention in the projects sharing session. Virus detection is a nice application for our system because the logic gate that we designed can solve the problem of false negative or false positive, those problems always appear when we recognized the characteristic sequence of viruses. Therefore, we contacted ZJUT_China_B who designed this project, with the help of them, we finished our design of virus detection.
We communicated with professors earlier this year and they suggested us to use basal logic gates to construct more complicated logic gates. After consulting the reference, we planned to utilize sigma factors to make this advice come true. In Coastal Areas Meetup, we understood that NEU_CHINA planned to amplify the signal by using sigma factors. But this year, on account of the impact of the epidemic, we can only complete the RNA part of the experiment. Then we asked help from NEU_CHINA, their data supported us to finish our design of complex circuits.
Model
This year, NAU-CHINA wanted to take advantage of Bacillus subtilis to control lead-contaminated. According to their design, toehold switch was used to construct a suicide system for meeting the demand for bio-safety. They hoped to enhance trigger’s stability, and make triggers accumulate in vivo.
Coincidentally，we improved our trigger‘s stability based on sequence in the reference. We added the hairpin structure at the 5’end of the trigger sequence and used NUPACK to test if the secondary structure is normal. Finally, we obtained the desired sequences and shared them in CCiC. We added the hairpin structure at the 5’end of the trigger sequence and used NUPACK to test if the secondary structure is normal. Finally, we obtained the desired sequences and shared them in CCiC. After that, NAU_CHINA found us and wanted to get our sequence, and refined their system.
Experiment
We want to design multi-input logic circuit, so we need promoters with excellent performance, so do NEFU_China. Therefore, they sharing their experimental data, this data helps to implement our vision of multi-input logic gate.
HP
SMMU-China invented us to participate in a seminar with virus-related teams, we shared our popular science comics with them, these comics helped them to publicity the knowledge of virus, and we also worked with them on the production of the mini-program/manual.
Meet Up
Southern China Regional Meeting
Due to the impact of the epidemic, the first communication of this year was held online. In order to save time, only a few teams gave presentations of their project, while others shared their projects via video and text. In the free communication section, we discussed the influence of RNA stability on experimental results, which is the same as the inspiration we got from the previous interview, which is to improve the stability of RNA, so as to make our system more stable and lasting.
Figure 1. Southern China Regional Meeting
Eastern China iGEM Meetup
The Eastern China iGEM Meetup was hosted by Jiangnan University online, which aims to help participants get access to the latest iGEM trends and get some inspiration from each other to make their project better. The organizer also invited experienced instructors to give some suggestions. In this meeting, iGEM coordinator Zhang Nan shared some matters of HP activities that we need to direct our attention to, which provided great help for us to carry out our HP activities. We have conducted exchange and cooperation with ZJUT_China_B in this communication.
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Figure 2. Eastern China iGEM Meetup
Northeastern Coastal Areas Meetup
The Northeastern Coastal Areas Meetup was hosted by Jilin University and Jiangnan University. They hoped we participants can share projects, communicate with each other, put forward Suggestions, and make clear what to do next and how to do it. In this communication, there was a collision of ideas that greatly broadened our horizons.
During this meeting, we learned that both Team NEFU_China and we were both looking for promoters with good performance, so we conducted further communication and cooperation with them.
Team NEU_CHINA presented their idea of using the sigma factor for signal amplification at this meeting, and it happened that we also had the same idea, so after the meeting we got in touch with them for further cooperation.
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Figure 3. Coastal Areas Meetup
2020-Five Schools Alliance
The purpose of this meeting was not only to exchange insights in synthetic biology but also to receive feedback from different angles and to seek creative solutions to the challenges that each team was facing. Team BUCT-China, NUDT_CHINA, SMMU-China, and UCAS-China along with us presented our projects. During this meeting, we five teams got together to share our project ideas, current progress, and any challenges we have encountered and jointly sought solutions.
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Figure 4. 2020-Five Schools Alliance
CCiC
Conference of China iGEMer Community (CCiC) is a national-wide conference launched by several Chinese universities that participated in iGEM. It is the largest synthetic biology conference in China. Over the past six years, about 200 teams and 2,000 people have participated. Nowadays CCiC is more than a simple iGEM meet-up, but a national academic conference for all junior SynBio enthusiasts and a platform for senior SynBio leaders to pass on their passion to the next generation. During communication, teams can share their projects by making presentations and presenting their posters. iGEMers and the frontiers of synthetic biology were linked through seminars and lectures through CCiC.
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Figure 5. CCiC
Virus-related Seminar
In this seminar, several teams whose projects have something to do with viruses shared ideas. We discussed the issues related to virus detection in this seminar, and we introduced to them how our design can be applied to virus detection. By communicating with other teams, we helped each other improve the design of our projects.
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Figure 6. Virus-related Seminar
Team List
NEFU_China
We need many promoters with low transcriptional leakage and high dynamic range since we want to design multi-input logic circuit, However, because of the epidemic, we don’t have enough time to test all promoters. Coincidentally, NEFU_China also need promoters with the same characteristic, so we asked them for help and they shared their data with us, this data is very important to our multi-input logic circuit.
Worldshaper-Shanghai
We wanted to find teams whose parts are similar to us for cooperation, so we briefly introduced our project through iGEM China Community. Fortunately, Worldshaper-Shanghai contacted us and told us that their project is about visual detection with toehold switch. After a deep exchange and discussion throughout the whole season, we made a close cooperative partnership. We helped them in many aspects of the project, such as design, model, and wet lab, which promoted the improvement and progress of their project. What’s more, they were also inspired by our cartoons which we published in WeChat public platform, and thought about spreading synthetic biology in a lively and interesting way.
Click Partnership Page for more details.
NAU-CHINA
NAU-CHINA wanted to control lead-contaminated plow by using earthworm and engineered Bacillus subtilis. They built a safety mechanism for their system, which consists of a toehold switch and a toxic protein. The toehold switch functioned as an AND gate, controlling downstream gene expression when it’s still inside the gut of the earthworm. In order to make it function effectively as a security system, they need the trigger RNA to accumulate after being expressed. Our project happened to enhance the triggers’ stability. Our method is to add a hairpin at the 5 'end of the trigger preventing RNA degradation enzyme combined with the triggers so as to reduce the amount of degradation. They use the sequence of the hairpin which we provided to them.
The NAU-CHINA also learned that we used 3WJ Repressor to build the reverse toehold switch. They used this OFF-toehold switch to design a new genetic circuit that simplify their design and make their idea come true.
NEU_CHINA
Sigma factors play a very important role in signal transduction, and sigma factors are also very helpful for us to construct complicated logic gates. Unfortunately, because of the impact of epidemic, we can not finish the whole planning of experiment, but we understood that NEU_CHINA planned to amplify the signal by using sigma factor in Coastal Areas Meetup. After meetup, we carried out a series wonderful communication about the function and performance of sigma factors, both of us got a lot from this communication, NEU_CHINA is very kindly and they shared their data about sigma factors for us, these data are very significant for us.
ZJUT_China_B
ZJUT_China_B shared their project in Eastern China iGEM Meetup. They used homologous Cas13 protein and fluorescent probe to achieve visual virus detection. They detected viruses by identifying the characteristic sequence of viruses, which may have a high likelihood of false negative or false positive. Coincidentally, our project has a high ON/OFF ratio and a low leakage, therefore, we thought maybe our system can solve this problem, and then we designed the virus detection application.
Because ZJUT_China_B has relevant experience, with the help of ZJUT_China_B, we finished our design about virus detection. In addition, we shared the characteristic sequences of the Zika virus we found with the ZJUT_China_B, helping them enrich their library of virus characteristic sequences.
SMMU-China
SMMU-China has contacted us through the cooperation invitation email. After initial communication and project sharing, we found that both of our projects were related to the virus to some extent. Therefore, at the invitation of SMMU-China, we completed the manual about viruses, and we also finished a WeChat applet. At the same time, we shared our popular scientific comics on COVID-19 to enrich the content of the manual.
SCU-China
This year, team SCU-China's topic is related to fermentation, they planned to show different fermentation processes of wheaten food in different parts of China in the HP section. They invited us to show the most common wheaten food in Shandong province, and we shared how to make green onion pie with them.
UofUppsala
At the invitation of UofUppsala, we answered some questions about the impact of the epidemic, such as the current situation in China, the impact of the epidemic on us, and the problems we encountered in this situation and how we solved them.