How we collaborated with NJMU-China through the year
Thanks to NJMU-CHINA iGEM team, we shared a close relationship with each other throughout the year. During our project we keep in contact with each other and help each other in many aspects. Both teams benefit a great lot!
1. Early stage of project: about plan and thoughts
At the beginning of the project, we firstly brainstormed to determine our project direction, got in touch with each other for online discussion, introduced and exchanged our inspiration and preliminary plan, and put forward opinions on the general idea respectively. Since both teams are in Nanjing City, Jiangsu Province, and our projects are all relevant to the intestine, so we came up with the idea of long-term cooperation between our two iGEM teams.
NJMU-China ——> Nanjing-China:
Since the project of NJMU-China focuses on the gut microbiome, they suggested that we may also discover the effect polyphosphate made on the gut microbiome after listening to our introduction. This idea inspired us to do the relevant modeling work at later stage of our project.
Nanjing-China ——> NJMU-China:
In the discussion, we heard that they hope to encode target protein--FOXP3 and tight junction protein directly in the gut. However, we thought that the protein is difficult to secret from the modified bacteria and make effect on the gut. Therefore, we suggested that they can try smaller molecules like siRNA and microRNA, which is easier to function outside the bacteria.
2. Early stage of project: experiment design and preparation
In the early stage of our team project, we discussed and helped each other better design the experiment.
NJMU-China ——> Nanjing-China:
After a thorough understanding of each other's projects, we entered the stage of experiment design. Designing our experiments, we encountered a challenge that we had no idea how to measure the degree of polymerization in polyphosphate. After reviewing several previous researches, we found that 31P NMR is a feasible method. However, GPC needs complex pretreatment of the sample which is time-consuming. Then NJMU-China suggested that maybe we can try Urea PAGE. This method was proved to be efficient in our later experiments.
Nanjing-China ——> NJMU-China:
In the stage of experiment design, we heard that NJMU-China was lack of an appropriate method to simulate the intestinal inflammatory environment. Since our PI used sodium nitroprusside (SNP) in his previous research, which is a medicine that is often used to realize the simulation of inflammation. We suggested that they may also try SNP in their experiments in vivo. Since SNP can release NO, our PI also suggested that they can view NO as an important signal of inflammation.
3. Early stage of project: modeling and prediction
NJMU-China ——> Nanjing-China:
Before our experiments began, both teams hope to do the protein structure simulation. Our team members in modeling group contacted NJUM-China’s modeling group. We co-learned the Autodock Vina and exchanged idea during the modeling process. As a result, we completed the simulation together.
4. Middle stage of the project: about publicity and popularization
In the middle stage of our projects, both teams prepared material for publicity and popularization and designed various activities to carry out propaganda and popularization.
NJMU-China ——> Nanjing-China:
We hoped to carried out face-to-face education activities in local middle schools. In order to give students an interesting lecture, we combined synthetic biology and intestinal health with easy-understanding examples. In our preparation stage, NJMU-China gave us plenty of interesting knowledge about the effect of the gut microbiome on the overall health, which aroused the interest of students in our education activities.
Nanjing-China ——> NJMU-China:
Brainstorming for publicity material together, we also helped NJMU-China prepare material and pictures about gut microbiota. Moreover, we also publicized NJMU-China’s iGEM project on our Official Account.
5. Middle stage of the project: about experiment improvement
NJMU-China ——> Nanjing-China:
At the mid-term meeting in Nanjing, we shared our experimental results with our partner team NJMU-China, they suggested we prolong culture time (almost two hours) and reduce the interval of measuring time.
6. Middle stage of the project: about modeling
NJMU-China ——> Nanjing-China:
Having abstracted a coherent feedforward loop composed of ions, active PPKs and polyP, we racked our brains to transform such a device from theory to practice. Thanks to the NJMU group concentrated on the gut microbiome, we gained the information that some researchers had applied bacterial transplantation to animals. Therefore, we began to think about letting our loop make a difference with the method of installing the bacteria factory in the user's intestine.
Nanjing-China ——> NJMU-China:
Knowing NJMU-China hoped to carry out modeling based on the GEO dataset, our team members with bioinformatics background suggested that effective early screening is a significant method to assist the treatment.
7. Middle and later stage of the project: about human practice
In the middle and later stage of the project, we and NJMU-China got together for brainstorm to think about how to expand the application of our projects to help more people.
NJMU-China ——> Nanjing-China:
We learned that Professor Xingyin Liu, the PI of NJMU-China, has been researching the gut microbiome for years and has abundant experience in the application of engineering probiotics. Therefore, we interviewed her about how to improve our product in order to gain expanded application. She suggested that we can try to improve our modified bacteria and apply it as the carrier that enter the human body, which can make a sustainable effect on the gut.
Nanjing-China ——> NJMU-China:
We added questions about the gut microbiome in our questionnaire to provide individuals’ understanding and suggestions on probiotics products and the gut microbiome, which is relevant to the application of NJMU-China’s product.
8. Middle and later stage of the project: about improvement and security
Nanjing-China ——> NJMU-China:
We collected relevant documents and policies about ethics about the application of modified bacteria in gut, which can help NJMU-China improve their project in the aspect of security and ethics.
9. Late stage of the project: about art design
The design groups of the two teams also exchanged ideas and conducted cooperation. All of them are biology majors, not familiar with web design, art design and other matters. However, through mutual help, we still try our best to make our publicity materials beautiful and perfect.
NJMU-China ——> Nanjing-China:
The design groups of the two teams designed a shared logo for both teams together, which combines our time logo with the focus of our project and represents the friendship of the two teams.
10. Late stage of the project: summary and meeting
In October, we had a concluding online meeting with NJMU iGEMers. At the meeting, we summarized our respective projects and our thoughts and reflections on partnership throughout the season, as well as our vision for the future. In the end, we took a photo together, which left precious memories and contributed to our deep friendship.
CLICK HERE
to see the partnership webpage of Team:NJMU-China.