2020 iGEM ShanghaiTech_China team believes that the collaboration between different teams is important to make a good competitive atmosphere as well as to promote and perfect each other’s project. With such a belief, we have been actively involved in cooperation with other excellent iGEM teams.
ShanghaiTech_China & NJU-China
This year, ShanghaiTech_China and NJU-China have made deep collaboration online and offered a lot of help to each other 's project. The collaboration is of following:
What we offered:
1. We searched key parameters for NJU-China to build their model of the expression of siRNA. To control the expression of siRNA, they use the Tet-On inducible expression system, which is somewhat similar to the lactose operon in principle. As a result, they mimicked the prediction of the amount of synthetic mRNA by lactose operon, and added folding and cutting process, to predict the amount of siRNA synthesized by Tet-On inducible expression system. However, the kinetic and thermodynamic parameters of their siRNA expression model are difficult to find, so they ask us for help. After inquiring about many documents coming from our school library’s rich literature resources, we finally find appropriate parameters for them and allow them to carry through their prediction modeling.
2. We raised some questions about their design of siRNA delivery system. For example: “is there any possibility that exosomes cannot reach tumor cells hidden inside that leaves chance for tumor to recrudesce?” “Will strong expression of exosomes affect normal liver function?” These questions provide ideas for their in vivo confirmation experiment of siRNA delivery system next year.
What we obtained:
1 Although we have designed the 3D prototype of our hardware. Our team couldn’t bring it into a real object due to lack of 3D printing equipment and members who master this skill. NJU-China gave their hands in constructing the hardware by using 3D printing.
Figure 1. The outlook of CESAR.
2. NJU-China built a neural network for us to predict the binding of aptamers and proteins. We had proposed a neural network to predict the binding of aptamers and proteins. In the process of the binding, extracting all feature manually is very difficult, and we are not sure which one affecting the protein binding. Whereas, neural network, obtaining appropriate eigenvalues to study the corresponding parameters through deep learning framework, can better predict the binding capacity of a given protein. However, we did not have experience in developing corresponding network, while NJU-China had rich experience, so we requested them to help us build the neural network. Their work further perfected our CESAR by extending its application range. The neural network modelling also promoted our recognition to aptamer.
3. We took part in a virtual seminar on synthetic biology held by NJU-China and GenScript Biotech Corporation. In this seminar, questions about ethical issues and practical application of gene editing technology such as CRIPSR have been discussed, which is helpful to the application of our project.We learnt that, although CRISPR has made a great breakthrough in the efficiency and convenience of gene editing, off-target effect and ethical issues are still inevitable in the present. During this seminar, professors talked about development prospects for the detection and reduction of the risk of CRISPR as well as the ethical implications of CRISPR as a therapeutic approach. In our project, we applied CRISPR to the in vitro detection of resistance genes and antibiotics, avoiding the ethical issues that would arise from affecting the genomes of tested individuals.
Figure 2. Virtual Seminar with NJU-China
ShanghaiTech_China & ZJUT_China_B
We also had close cooperation with ZJUT_China_B. Their project this year is to design a detection device using the CRISPR/Cas13 system for rapid detection of multiple virus in one pot. The design ideas of our two teams have a lot in common, so we worked closely together during the project. We met on the Conference of China iGEMer Community (CCiC) in August, and then we had a brief communication almost every week to get to know the project progress.
What we offered:
Because of the epidemic, they had very limited time to do experiments in school. In one exchange, we learned that their LwaCas13a expression system based on BL21(DE3) was always contaminated with phages and lack of codon optimization to BL21(DE3). We helped trouble shooting on this problem and suggested the competent cells of Rosetta (DE3) Gami pLysS as a better chassis for soluble expression of LwaCas13a, so we helped them do the transformation and the transformed bacterial as well as the component cell was sent to them. They said this helped a lot, and they are considering expressing other related proteins in Rosetta (DE3) Gami pLysS in future.
What we obtained:
In return, ZJUT_China_B suggested to us that Cas13 has great potential to be used in our project because it not only can recognize RNA target, but also single-strand and double-strand DNA with T7 transcription. Therefore, if we added Cas13 to our own design, we could expand the detection range of our products. At the same time, they gave a plasmid expressing Cas13, which we really appreciated. However, due to the time limitation, we didn't realize this idea to our device, but their proposal did help us expand the project's potential.
ShanghaiTech_China & IISER_Bhopal
We collaborated with IISER_Bhopal from India through the video meeting.
What we offered:
Last year, the main goal of ShanghaiTech_China featured utilizing the intestinal probiotics who can synthesize and release N-palmitoyl serinol to promote the body insulin level, which will greatly benefit the patient suffering from diabetes. There is overlap between the part related to blood glucose monitoring and APP design which we’ve done last year and IISER_Bhopal’s project of this year. So they asked us about the APP design and blood glucose monitoring experiment. Then we held a video meeting and introduced the project contents of this year to each other. We invited Derun Li, the software engineer of the team in 2019, to introduce the Bluetooth module and glucose signal processing module in the APP to iGEMers of IISER_Bhopal. We also gave them some suggestions on real-time monitoring of blood glucose and APP design.
What we obtained:
After listening to our project, they thought that our design was very novel. The application of Cas12a in the detection of antibiotic resistance is not only very creative, but also a good solution to the social issues faced by many developing countries. Having been recognized by members of teams from other countries, we understood that our design has a worldwide application value and had more confidence in the development prospects of it.
The Seventh Conference of China iGEMer Community (CCiC)
In order to communicate and collaborate with more teams and receive suggestions from more professors and experts, we participated in the Seventh Conference of China iGEMer Community (CCiC). Different from CCiC in previous years, the Seventh CCiC was held online due to the epidemic. We shared our presentation video and poster, and also watched the displays of other teams. Then we received lots of feedback about our design. It was more important that we met many teams with whom we could develop cooperation. For example, team ZJUT_China_B, whose project has overlaps with ours, was the one we met at CCiC.