Bronze

Competition Deliverables

Our project promotion video was submitted in September and our wiki page was completed on 27th October. And we are looking forward to show our poster and the presentation video in the Giant Jamboree.

Attributions

Affected by the COVID-19 epidemic, iGEM teams around the world are facing the dilemma of disrupted plans. Therefore, in this year's project promotion process, we mainly adopted a combination of online and offline methods, and made full use of the Internet and online meeting platforms to complete communication within and between teams.

We have sorted out our work and division of labor, and thanks for everyone who made efforts in the competition.

Click HERE to see our Attributions.

Project Description

Evolution is a slow process that continually occuring in nature, and this has brought about biodiversity. Disappointingly, such evolutionary outcomes do not achieve the optimal results that one would expect for biological production. This begs the question, is there a way to make evolutionary outcomes more compatible with the production of human needs? Then comes directed evolution and our team gives an innovated try on it.

Click HERE see our Description.

Contribution

We have added quantitative experimental characterization data to Part BBa_J23117, and this year, we have made a troubleshooting manual based on our own experimental experience and lessons. This manual contains a number of problems that are very likely to appear in the experiment, and also contains the solutions to some of the problems. We hope that such a manual can help more iGEM teams and students.

Click HERE see our Contribution.

Silver

Engineering Success

We have designed and characterized new Biobrick parts: to facilitate the evaluation of the on/off-target level of the dCas9, one part, which is the pBAD/araC upstream of RFP with inhibition unit containing target (BBa_K3365014) is constructed and the RFP is used as one of the reporter proteins.

Click HERE to see our Engineering.

Collaboration

Many hands make light work. Other than our independent competition process, we also got involved in collaborations with other teams and some communities. Through communication and interchange with different organizations, we not only learned their design ideas but also made friends with them, which we treasured a lot. For us, iGEM is not just a game, it is an oasis where all the synthetic-biology lovers begin their friendship.

Click HERE to see our Collaboration.

Human Practices

Want to see more? Please refer to the Gold Standard and go to Human Practices SJTU-BioX-Shanghai for more information.

Proposed Implementation

Our potential users are research groups and industries who wants to customize their proteins.We can coorperate with them. They can give us their protein, together with the solved protein structure. We use our easy-to-use directed evolution platform and rational design program to customize their proteins.

Click HERE to see what we’ve done.

Gold

Integrated Human Practices

Following the above steps, we finished our integrated Human Practices.

Want to see more? go to Human Practices SJTU-BioX-Shanghai for more information.

Improvement of an Existing Part

This year, we have greatly expanded the application scope of BBa_K1321333 and created BBa_K3365006.

Project modeling

We have proposed a complete pipeline from a certain target sequence to Cas9/dCas9 variants with lower off-target effect. Models both guide the experimental process and evaluate the result of directed evolution. Researchers can use our off-target predictor to detect and select off-target sites with high confidence in experiments. Molecular dynamics method helps to find residues playing critical roles in interactions between DNA and Cas9/dCas9-sgRNA complex. The discovery of these functional positions integrates rational design into the directed evolution experiment. A graphic interpretation is also adopted to measure the mutation distance between different variants. On the other hand, our kinetics model fits the relationship between mismatch condition and off-target probability. The explainable parameters about transition state energy for WT Cas9 and evolved Cas9 can provide reliable inference on the changes in targeting progression after directed evolution.

Click to HERE see our model.

Proof of Concept

Based on our implementation, we have more results to proof our concept.

Click to HERE see our Proof of Concept.

Partnership

SYSU-CHINA team's project and ours both focus on directed evolution and hope to solve practical problems so we discussed a series of issues related to directed evolution. In general, our cooperation is mainly in modeling, public education, part upload and wiki production.

Click to HERE see our Partnership.

Science Communication

In this summer, our team, SJTU-BioX-Shanghai, cooperated with the school’s public welfare association TECC to conduct social practice activities. Our project aimed to popularize science among teenagers in simple terms and strived to inspire their interests in synthetic biology.

Click to HERE see our Science Communication and Education