Team:Nanjing-China/Partnership

Thanks to NAU-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!

NAU-CHINA&Nanjing-China in December,2019

1.Early stage of project: about plan and thoughts

At the beginning of the project, we initially determined 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, there were exchanges and cooperation between the departments before, so we came up with the idea of long-term cooperation between our two iGEM teams.

NAU-CHINA→Nanjing-China:

After listening to our introduction, the NAU team suggested that the application future of our project could also be extended to building materials and other aspects (wooden houses in some areas with dense forests often contribute to the spread of mountain fires). We reached an agreement that the products could be made into fire retardant coatings. Moreover, this inspired us to contact the fire retardant coating production company for later practical research.

Nanjing-China→NAU-CHINA:

We asked whether NAU had any preliminary ideas on the engineering bacteria used in the project. After discussion, they thought that the environmental dominant bacteria should be used, with strong secretion capacity. In the following period of time, we widely consulted papers in this field and finally suggested them to use Bacillus subtilis, because as a Gram-positive bacteria, it not only has strong secretion capacity, but also is the dominant bacteria in the environment and earthworm intestinal tract.

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.

NAU-CHINA→Nanjing-China:

When using Citrobacter freundii to prepare polyP, we found that the production of polyP in several experiments was low. After discussion with NAU team, they proposed that kanamycin's activity would be rapidly reduced when stored in a 4 ℃ refrigerator, which would lead to contamination of miscellaneous bacteria in the process of cultivating engineering bacteria. After replacing new kanamycin, the polyP production of engineered bacteria increased significantly and returned to the normal level.

Nanjing-China→NAU-CHINA:

NAU hopes that Bacillus subtilis could secrete phospholytic enzymes in earthworms and perform suicide function in vitro. However, the efficiency of phosphate solubilizing enzymes used is not high. We had a discussion on how phospholytic enzymes could effectively play its role in the intestinal environment of earthworms. Consequently, they changed the enzyme system under our suggestion. We reexamined the neutral enzyme systems with phosphate solubilization effect, and finally determined to use phytase PHY (yCd).

3. Early stage of project: modeling and prediction

NAU-CHINA→Nanjing-China:

In the early stage of the experiment, our team hoped to simulate the docking of polyP and GFP by modeling. Considering that the speed of using autodock software is slow and our need to get some results quickly for subsequent modeling, we consulted the modeling group of NAU. They introduced autodock to us. With the help of this software, we get some initial docking results, which helps the modeling group to lay a good foundation for the subsequent model construction.

4.Middle stage of the project: about publicity and popularization

Due to the special epidemic situation of Covid-19 this year, we discussed with each other online about effective ways to carry out propaganda and popularization based on the special situation. We decided to use the existing media platform to transfer the offline publicity content to online as much as possible. Although the form has changed, we still popularize the ideas of iGEM and synthetic biology to public.

NAU-CHINA→Nanjing-China:

In the publicity for iGEM competition, NAU intends to distribute the monthly magazines to four different middle schools and promote their project on their official account. We accepted their suggestions and operated our own official account to publicize Nanjing-China's iGEM project.

Nanjing-China→NAU-CHINA:

In terms of the popularization of synthetic biology, we plans to cooperate with the enrollment platform of the school to carry out online lectures for senior high school students. They introduce team projects and the application of synthetic biology, and release live broadcast through different video websites to expand the influence. This inspired the cooperation between NAU and other communities in the school to teach children online and show the charm of synthetic biology with simple and understandable knowledge.

5.Middle stage of the project: about experiement improvement

In the process of the project, each team encountered some problems. However, we fully cooperated, and students from the experiment group and modeling group of the two teams to explore solutions to the problems.

Nanjing-China→NAU-CHINA:

The NAU team designed the pathway and explained to us the mechanism of handling lead. Our students in the experiment group proposed how to ensure the full contact between the transformed phosphate and lead, and how to control the binding ratio. The NAU students also thought that this problem was very important. With some professors’w opinions and the calculation of the modeling group, we found that it was not necessary to make full contact for precipitation, which ruled out a doubt for the NAU team.

NAU-CHINA→Nanjing-China:

When our team tried to combine polyphosphate with spidroin, we found that the direct combination of polyphosphate and existing recombinant spidroin was difficult in order to form the organic-inorganic hybrid material we expected. So as to meet the electrostatic interaction with polyphosphate, we discussed with the students of NAU. With their help, we mutated the N-terminal and C-terminal amino acids of natural spidroin into positive amino acids, and constructed the expression vector of mutant recombinant spidroin, then induced expression and conducted purification experiment.

6.Middle stage of the project: about modeling

Nanjing-China→NAU-CHINA：

Due to the lack of experiments, data acquisition has always been a problem for NAU modeling group, especially for data such as DNA transcription rate and mRNA translation rate. With the recommendation of our modeling group, they applied https://www.denovodna.com/ the website which calculates the relevant data, to improve the accuracy of model data acquisition, laying the foundation for the later model establishment.

7.Middle and later stage of the project: about human practice

We and NAU got together for brainstorm to think about the stakeholders that might be involved in the team project on both sides. We explore the issues that need to be consulted and discussed with the relevant units. After discussion, the HP groups of the two teams think that we should consider and carry out our HP work from four aspects - Who will benefit? Who will use our projects / products? Who cares most about our project? Who are the policy makers?

NAU-CHINA→Nanjing-China：

The NAU team proposed that we should carefully consider the requirements or expectations of relevant enterprises and companies for our products, and guide us in the next step of investigation. We finally determined the interview questions and return visit to the enterprise. We also planned to focus on the feasibility, practicability and advantages of the project

Nanjing-China→NAU-CHINA：

Our team considered the stakeholders involved in NAU's projects and suggested that NAU connect them to make a “stakeholders cycle ", which is for health for peasants where stakeholders are connected closely.

8.Middle and later stage of the project: about improvement and security

Nanjing-China→NAU-CHINA：

The NAU team discussed with us the biosafety issues in the process of optimizing the pathway. We proposed our worry about the impact of Bacillus subtilis metabolites on soil quality or crop production after suicide. The NAU team thought that it would not have an impact, and had a discussion with us. After our investigation and research, both teams reached an agreement on the safety of the project.

Nanjing-China→NAU-CHINA：

After that, we discussed the problem of improving the pathway again. In view of the problem of not initiating suicide during the laboratory culture of engineering bacteria in the NAU project, we believe that continuous transcription of switch RNA is a kind of pressure for engineering bacteria. The NAU team took our advice and made adjustments. They added IPTG induction system to express CI protein and inhibit the transcription of switch RNA in laboratory culture environment to ensure that there is no pressure during the cultivation of Bacillus subtilis.

NAU-CHINA→Nanjing-China：

We talked about the recent experiments to NAU-CHINA. After learning that we have carried out in vivo experiments on binding polyP and GFP, they asked us whether we have also done in vivo binding experiments, and reminded us that we should pay attention to their in vivo binding conditions. We did carry out these experiments later and showed that +36GFP and polyP could be synthesized simultaneously in vivo and directly combined in bacteria.

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.

NAU-CHINA→Nanjing-China：

For example, the design groups of our two teams had a communication when learning how to make web pages. The students of NAU design group helped us solve the problem that there may be blank on both sides of the navigation bar when the page scaling is different. We added a blank div with white background outside the navigation bar with the ratio of 100% to achieve the desired effect.

Nanjing-China→NAU-CHINA：

Our design team also gave suggestions to NAU when they designed the team logo. We helped to improve the color and shape of the logo with respect to their project content and finally helped them design the team logo.

10. Late stage of the project: summary and meeting

In October, we had a concluding online meeting with NAU 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:NAU-CHINA.