This year, we've done a lot of works that make useful contribution for future iGEM teams.

New Documentation To Existing Part

In many situation，the inducible promoters with low transcriptional leakage and high dynamic range are very important. Since the project needs, we tested a lot of inducible promoters. After a series of experimental tests, we selected Tet promoter and Lux promoter with good performance for our project. And this data is also useful for future teams.

Figure 1. The Fluorescence Data of Promoters

Document Troubleshooting

In the middle of our experiment, we found that white flocculent precipitations appear after 6-8 hours of shaking the culture of E. coli and the culture medium becomes clear. Phage infection occurs accidentally not only in the fermentation factories but also in the lab, and it might get worse and worse without appropriate treatment. By coincidence, 2019 OUC-China team also met this problem. As the same, we also thought this phenomenon appears, which is because our E.coli strain encountered a phage infection. By using the booklet that they received last year, we easily checked that the death strain was not caused by phage. Then, we asked our PI for help. They also have met this problem and they think that may be caused by plasmid losing. We transformed E. coli again and this problem was solved.

Figure 2. The white flocculent in E. coli culture

Data Standardization Applets

Data standardization is a basic work of data analysis. Different evaluation indicators often have different dimensions and dimensional units, which will affect the results of data analysis. In order to eliminate the dimensional influence between indicators, data standardization should be carried out to solve the comparability between data indicators. After the standardized processing of the original data, each index is in the same order of magnitude, which is suitable for comprehensive comparative evaluation.

When we analyze the data after the experiment, we found that the fluorescence amount and threshold of different logic gates were very different. After consulting the literature, we found that there was also such a difference in the representation of the previous logic gate experimental results. Considering nowadays，with the development and popularization of computer science, more and more scientific research works benefit from it. In our project, our modeling work was also done with the help of software. Therefore, we want to design a small software to uniformly characterize the fluorescence amount of logic gate. By inputting the experimental results of different logic gates, this program can calculate the coefficient of fluorescence amount of each logic gate, and give the fluorescent light threshold of the final judgment logic gate 0/1.

Click SOFTWARE to learn more details.

Figure 3. The results of logic gate analysed by our small applet.

Bronze

√ Register for iGEM, have a great iGEM season, and attend the Giant Jamboree.

√ Completed all required deliverables: successfully created our team wiki, poster, video, filled out judging form and presented at the Giant Jamboree.

√ Created our attribution page.

√ Documented our project inspiration and description.

√ Added quantitative experimental characterization data to parts BBa_K2904111 (Ptet) and BBa_R0062 (Plux).

√ Document troubleshooting that would be helpful to future teams. The solution of white flocculent in E.coli culture was found.

√ Build a data standardization applets.

Silver

√ Created many new BioBrick parts that are related to our project works as expected.

√ Collaborated with many iGEM teams.

√ Successfully participated in Human Practices to validate our work is responsible and good for the world. And get many suggestions from professors.

√ Explained how we would implement our project in the real world. Thought about some of these issues for the Safety Form.

Gold

√ Successfully expand on our silver medal activity and demonstrate how our team responded to our human practices reflections, research. According to the professor's suggestion, we made some improvements to our project.

√ Created a new BioBrick part named BBa_K3328000 that has a functional improvement of an existing BioBrick part BBa_K2150031.

√ Successfully modeled our project. Calculated the 3WJ scoring function, designed new sequences for our project and used the ODE model to predict the logical gate expression.

√ Successful expanded upon our Silver medal work for Proposed Implementation and developed a proof of concept for our project, which reflects our project as a whole, not just a single aspect or component.

√ Collaborate throughout the year with Worldshaper-Shanghai on a set of shared objectives related to both of our projects. Compared to the Silver Medal Collaboration criterion, we successfully worked together throughout the season (not a single interaction). It was a perfect partnership.