Partnership

We partnered with Gene Rate (iGEM Qdai).
We went beyond collaboration and worked with them toward a common goal to improve our mutual projects. Here is a step-by-step description of how our collaboration with them has had a wonderful impact on our 2022 project.

May - Discussion of each other's projects from the previous year-

We were both members of the iGEM Japan team community, and so we contacted each other through there. At the time, we had not yet decided on the content of our projects and were still thinking about what kind of project we wanted to do. We started by reading each other's wikis and exchanging ideas: the iGEM Tokyo Tech team was working on eradicating tooth decay, and the Gene Rate team was working on detecting gases through fluorescence. We pointed out areas for mutual improvement regarding the content of each other's projects and each team's wikis. It was a very useful exchange of ideas for future projects. We decided to meet twice a month to update each other on the progress of our projects.

June - Discovering a common goal (1)-

After several meetings with Gene Rate we had the opportunity to read the iGEM Tokyo Tech 2018 Wiki. This led us to decide to proceed with a project to predict the dengue virus epidemic. Meanwhile, the Gene Rate team's project seemed to have decided to produce methane gas from unwanted materials. The dengue virus is endemic in tropical and subtropical regions, and our project is specifically targeting areas where it is difficult to install large machinery. On the other hand, the Gene Rate team was looking for a solution to the resource problem. We thought that our projects might have a similar target audience, and that teams with similar end-users could collaborate on local research and problem solving.

July - Discovering Common Goals (2)-

By this time, our projects were becoming more solidified, and we were able to think about a partnership that was more in-depth in nature. During our bimonthly meetings, we asked the Gene Rate team for advice. We asked the Gene Rate team for advice on how to quantitatively analyze the fluorescence of cells. We had read each other's team's wikis from the previous year at our May meeting, so we knew that the Gene Rate team was working on a quantitative measurement of cell fluorescence in 2021. We had a meeting with our hardware team and the Gene Rate team's hardware team to exchange ideas about methods and modeling for quantitative analysis of cell fluorescence.

August - Survey of local conditions-

Photo1：Gene Rate x iGEM Tokyo Tech meeting

The first of our common goals

• Teams with similar end-users can collaborate on local research and problem solving.
  To solve this problem, the Tokyo Tech team talked to Dr. Kameoka of Kobe University, who is an expert on healthcare and economics in Southeast Asia. He gave us some useful advice.
• Methods that use large machines are not preferred.
• Those that can be implemented cost-effectively are preferred
• If either of the above can be achieved, there is a great possibility that needs will exist.

We received information that was useful for both teams. We also shared this information with the Gene Rate team and discussed "how hardware should be" in the project, which resulted in improved development of hardware for social implementation. We also shared with the Gene Rate team some papers on the current status and limitations of local medical care, as our project will be conducting an assay on dengue fever. The Gene Rate team shared with us some papers on the relationship between the country's economic situation and health care. They were very helpful for us to think about Imprementation and Proof of Concept.

September - Mutual Cooperation in Fluorescence Observation-

The second of our common goals

• To collaborate with each other on methods and modeling for quantitative analysis of cellular fluorescence
  To achieve this goal, we had frequent meetings with each other's hardware teams beyond the bimonthly meetings.
  In fact, the Gene Rate team's advice to the Tokyo Tech team was as follows
• There are many biological containment issues when dealing with synthetic organisms.
• When using light as a sensor, it can be difficult to quantify.
• When using fluorescence, it is difficult to create an independent sensor based solely on the organism.
• Propose equations that can be used as a basis for molecular modeling.

Based on this advice, the Tokyo Tech team has successfully improved Hardware and Software on fluorescence detection. The Gene Rate team also asked us to provide them with the data we had obtained from our experiments. We decided to provide the data obtained from our experiments. Our project is based on a paper by Dr. Suzuki of the National Institute of Infectious Diseases. In his paper, he analyzed the number of cells by luciferin luminescence, not fluorescence. In our project, on the other hand, we used fluorescence to correlate the intensity of fluorescence with the number of cells infected and recombined by Single-round infectious particle (SRIP). We compared the fluorescence of the original paper with that of our detection kit, especially that of EGFP, and provided the Gene Rate team with a summary of the differences.

Conclusion - With Gene Rate Team-

Figure1:Our partnership

• Based on our meeting with Dr. Kameoka, we provided information on the current situation in Southeast Asia and the values and references we used in designing our project.
• The Gene Rate team provided us with insights into resource issues and healthcare in Southeast Asia, and the papers they used as references.
• We summarized the differences between fluorescence and luminescence emitted by cells and provided the data to the Gene Rate team
• The Gene Rate team had developed hardware and software that could quantitatively analyze the fluorescence emitted by cells, and they provided us with data and advice to improve our hardware.
• As a result, we have successfully developed hardware that can actually measure fluorescence!

Figure2:Our Interaction