We have developed two software, P2N and gDesign, which can be of great help to iGEMer and the scientific research community in the future. P2N is a codon optimization software developed by us, which uses the web crawler technology to obtain database information, so as to conduct codon preference analysis efficiently, quickly and accurately. By analyzing the confidence of codon optimization, we prove that such a program is reliable. gDesign is our guide RNA design tool used to service our Target-AID system. With the target-AID system, we can knock out any gene in E. coli genome, thus serving our Safety. This software can provide better Safety for future iGEMer, and create the method of CRISPR-screen for various strains of E. coli in the future.
Our Pro-LAC is a conceptually novel approach to detect RNA biomarkers in biological samples that elegantly combines chemical and synthetic biology. It uses an RNA-guided fusion protein, recognizing target RNAs with CIRTS (CRISPR-Cas Inspired RNA Targeting System), and making them detectable by proximity labelling. As far as we know, we are the first iGEM team to introduce CRISPR-like system into our project to achieve high modularity in RNA detection. We hope we can inspire future iGEM teams or other students to work on similar topics.
1.Competition deliverables: All the prerequisites of a complete iGEM project, including our wiki, presentation video and judging form have been successfully submitted.
2.Attributions: Sixteen members of our team have been working together very hard to achieve our goal. A big THANK YOU to everyone!
3.Project description: We focused on IBD, an intestinal disease troubling hundreds of thousands of people, developing a novel early diagnosis tool and a multi-probiotic therapy with a new delivery strategy.
4.Contribution: Our diagnosis approach is unprecedented by previous iGEM teams in its usage of proximity labeling combined with CIRTS. Also, we developed an awesome software which can greatly assist codon optimization and sgRNA design. Apart from that, we designed a brand-new diagnosis method - check it out if you are interested!
1.Engineering success: We successfully completely a number of GEM construction from the bottom up, expressing BSH, fusion protein and etc. Furthermore, we have testified all these components can function perfectly in vitro.
2.Collaboration: Our team collaborated with team QHSF on details of communication and education. We also worked together on parts with team Tokyo University.
3.Human practices: We visited a number of famous biotech companies in China, learning about the latest advances in probiotics industry.
4.Proposed implementation: Our Pro-LAC system has the potential of becoming a fast, household tool for IBD early diagnosis. We also envisioned our probiotics to be accepted as a part of IBD standard therapy.
1.Integrated human practices: We assessed our idea through communicating with doctors, patients, and attending the ChinaGut conference. The latter also introduced us to the technology used in our delivery strategy. We consulted professors and doctors in related fields on experiment design, whose advice led us to decide on conducting animal experiments. We also visited several companies to learn how our project can be implemented.
2.Project modeling: Our modeling contains four parts: Bacterial Adhesion Modeling, Intestinal Flora Simulator, Lateral Flow Modeling and Protein Degradation Modeling, which provide a useful and powerful system for IBD diagnosing and therapy.
3.Proof of concept: Each subproject has presented experiments like WB, antimicrobial experiments, labeling test and so on to proof the genetic system we have constructed should function as expected and has potential practical use.
4.Partnership: Tight partnership has been formed with team SZU-China, as we had shared experience with each other and tackled wet lab problems. We also teamed up with team THIS-China on other issues such as education and wiki.
5.Education and communication: We put up posters at China Gut Festival and participated in Northern China Meetup and CCiC8. We also visited a few high schools to lecture on our project and the basic ideas of synthetic biology.