Partnership

# Partnership

## Overview

It is hard to make a forest out of a single tree. That is why we focused on various ways for collaborations to occur, both online and offline. Compared with communication, long-term and in-depth cooperation is of more value. In the spirit of a globally connected iGEM community, we have established a deep cooperation partnership with the NUDT_CHINA and XMU-China throughout the season. Through various forms of collaboration, including mutual use of experimental instruments, joint education and publicity, exchanges of questionnaires and analysis, we are closely linked in modeling, video production, HP, experiment and other aspects, promoting each other and making progress together. We believe that the collaboration is helpful not only for a better understanding of the project but also to give full play to our respective strengths and optimize resource allocation. Our ultimate goal is to participate in undertakings that have a significant positive impact on both the teams that collaborate with us and the general public.

## XMU-China

August 2nd，2020

At the South China conference, XMU-China attracted us for our same target to move out toxic chemicals from agricultural products. This day, XMU-China and CSU_CHINA's teammates gathered online to discover an efficient way to cooperate. Based on our projects' introduction, we enhanced the understanding of each other. We made it possible to interchange ideas and information.

The screenshot of CSU_CHINA&NUDT_CHINA online meeting

In the experimental design, XMU-China devote themselves to degrading the glyphosate in tea, while CSU_CHINA's goal is to reduce the cadmium content in soil or water to obtain healthier edible rice. Coincidentally, all we need to do is to detect, degrade and prevent engineering bacteria from escaping. For this reason, we launched a series of discussions, including experiments, modeling and human practices. We chose some of the conversations and divided them into mentoring and being mentored to show.

Mentor:

In addition to binding cadmium ions, merR protein may also be interfered with by other ions, such as mercury ion. Then how to handle the interference of other ions?
The pMer is indeed a mercury promoter, but we can use a screening mutant to disconnect from mercury ions, but can specifically recognize cadmium ions.
The self-protection mechanism of Syncytial algae may transfer cadmium ions out. Do you need to knock out its external transport function to achieve cadmium enrichment?
Transferring out does play a protective role. If it is knocked out, the survival condition of the algae may be affected. We bring in a protein that transports cadmium inward. If its transport efficiency is high, the role of the transferring out protein can be ignored.
We have some questions about the Human Practices. When we interviewed stakeholders, they were reluctant to accept interviews because of some sensitive issues. Is there a right solution?
We encountered such problems when contacting sewage treatment plants and government agencies. We actively seek teachers' help, looking for related enterprises or departments cooperating with teachers to enhance trust.

Being mentored:

We want to convert the biological network into an equation, but the active oxygen network is getting larger and larger. How can we convert it into a simple equation?
It will be very troublesome if the massive metabolic system is listed one by one. The whole network analysis can see some metabolic flux analysis, which will be more convenient. And we generally use a few ODE.
When experimentally designing the detection part, will the extra-membrane detection be interfered with due to the escape of NADPH?
This problem does exist. We can draw the standard curve in the initial experiment, consider the error and eliminate it.

We gave some suggestions to XMU-China and obtained some new ideas through this activity, which is beneficial to our projects' promotion. How to ensure the safety of engineering algae has plagued us for a long time. To our surprise, XMU-China's design of the Toxin-Antitoxin ( TA) system uses MazE and MazF, exceptionally inspiring us.

In their MazE-MazF system, ATc in the culture environment is like a "protective umbrella". When the engineering algae is lying under the umbrella controlled by ATc, MazE is like a knight who resists MazF's toxic damage to algae. Suppose the algae escape from the safe environment that ATc exists. In that case, MazF loses its protective capacity, which causes the positive feedback caused by delta with ORF, making the toxin MazF like a "hungry wolf" to eliminate the "stray sheep" instantly.

The ppt of XMU-China

This delicate design inspired us. After consulting documents, we found that the TA systems are widely distributed in prokaryotes and archaea. The TA operon encodes a stable toxin and an easily degraded antitoxin to regulate bacterial metabolism. Given this, we combined our own components to modify, adding a light-controlled suicide system to enhance our engineering algae's safety. To learn more about our experiment, please click:
https://2020.igem.org/Team:CSU_CHINA/Description.

Moreover, our interchange also reflects in the sharing of instruments. We sent some samples of cadmium-absorbed algae to XMU-China. They helped us process them and measured the concentration of cadmium ions in our algae using their ICP-MS.

We also give each other a help in the modeling and human practices. We communicate with aspects below:

Team CSU→XMU XMU→CSU
Experiment group /

①XMU-China's design of the Toxin-Antitoxin (TA) system inspired us.

②XMU-China measured the concentration of cadmium ions in our algae using their ICP-AES.

Modeling group Providing our experience for the XMU-China in using molecular dynamics and docking methods to screening potential protein mutation points for better binding affinity. Received referenced papers one brick by one brick from XMU-China when we were modeling an amplification system designed by them.
Human practice group Inspiring XMU-China to ask for teachers’ help and change the way they ask questions when stakeholders were reluctant to accept interviews because of some sensitive issues. Sharing us a communicate skill when we had difficulties in talking with interested enterprises, which is talking like a customer.

This was an in-depth communication covering several parts of the experiment, model and human practices. In practice, we will inevitably encounter obstacles that hinder the process. At this time, mutual inspiration and exchange of needs will lead to a win-win situation. That is what we learned from this cooperation.

## NUDT_CHINA

### WHAT WE DID FOR THEM

Complete part of the experiment and modeling work for them

Assist them in getting in touch with medical professors

Design our joint textbook of synthetic biology

Help to extend the influence of their projects by conducting education propaganda together

### WHAT THEY DID FOR US

Complete part of the experiment and modeling work for us

Help us design survey questionnaires and conduct data analysis

Provide technical personnel for photography and video in the education lecture

Initial online meeting

August 19th, 2020

We reached out to Team NUDT_CHINA, which was also looking for a partner. On August 19th, 2020, both teams agreed on further collaboration on a video conference. Members of both sides got to know each other in the meeting and introduced each other's projects. At the meeting, questions and suggestions were raised after presentations. We carried out brainstorming, which significantly contributed to the projects' innovation and improvement.

The screenshot of CSU_CHINA&NUDT_CHINA online meeting

Joint textbook of synthetic biology

August 25th, 2020

To better convey the concept of synthetic biology and the significance of our team's project to the public, the art group and HP group of our two teams jointly compiled a textbook of synthetic biology. We have distributed this brochure during educational propaganda and offline visits. According to the feedback, our textbook does achieve a good publicity and science popularization effect.

Synthetic biology propaganda textbook jointly compiled by CSU_CHINA and NUDT_CHINA

Offline meet-and-greet party

October 8th, 2020

After several times online discussions, on October 8th, 2020, we finally grabbed the opportunity to hold the first offline meet-and-greet party as the pandemic was under control. More conveniently and interactively, we set the mutual assistance plan and exchanged our work for further discussion.

Group photo of CSU_CHINA and NUDT_CHINA team members at the offline meet-and-greet party

The results of the meeting's discussions on cooperation are shown in the table below：

Team CSU→NUDT NUDT→CSU
Experiment group

①NUDT_CHINA team members visited the laboratory of Central South University.

②we helped the NUDT_CHINA quantify their fluorescence images and visualized the data in the form of heat maps with the R programming language.

②The NUDT_CHINA performed the time-varying curves of cadmium enrichment in algae at different concentrations of cadmium for us.

Modeling group ①We wrote a C# program to fit a curve with provided function to get a best fitted freedom-degree for the NUDT model group. ①NUDT_CHINA shared their experience on curve fitting to help us get our population growth rate differential equation.
Human practice group

①Co-produced Science Communication textbook

②The NUDT_CHINA team went with us to the biology competition class of Yali Middle School to give a lecture on synthetic biology

①Assist CSU_CHINA team to distribute and fill out questionnaires

②Provided questionnaire design suggestions for CSU_CHINA and conducted statistical analysis of questionnaire results

Art group ①Created a joint textbook for synthetic biology education ①Provided technical personnel for photography and video

Laboratory visit

October 9th, 2020

To understand the specific instrument conditions of the laboratories of both sides and better decide which part of the experiment should be exchanged, we visited the laboratories of the other team on October 9th, 2020. A detailed description of the laboratory facilities and environment were given. During this visit, we discussed the issues to be solved in our respective experiments and set specific experimental projects and dates for our collaboration.

Joint education propaganda

October 12th, 2020

To further advance science education and promote our project's awareness, we worked with some members of the NUDT-CHINA to give a talk on synthetic biology to some middle school students at Yali Middle School, one of the best middle schools in Hunan Province, China. After a brief introduction to synthetic biology, the NUDT_CHINA conveyed the iGEM competition's meaning to the students.

Group photos of CSU_CHINA & NUDT_CHINA members and students from YALI High School

Experimental exchange

October 17th, 2020

As our access to the cadmium ion detection kits was limited, the NUDT_CHINA selflessly lent their atomic absorption spectrometer to help us measure the cadmium-uptaking levels of Synechocystis while in different growth states. In exchange, we helped the NUDT_CHINA quantify their fluorescence images and visualized the data in the form of heat maps with the R programming language.

Modeling cooperation

October 20th, 2020

Through discussions between the two modeling groups, the idea of compensating for the lack of experimental data through simulation experiments was accepted in order to solve the problem of incomplete model construction due to insufficient experimental data. NUDT_CHINA model team spent much time adjusting intricate parameters to fit their model. They shared their experience on curve fitting to help us get our population growth rate differential equation. We wrote a C# program to fit a curve with provided function to get a best fitted freedom-degree for the NUDT model group.

$$f(x)+C = α*∫\frac{x^{\frac{k}{2}-1} e^{-\frac{x}{2}}} {2^{\frac{k}{2}} ∫_{0}^{+∞} e^{-t} t^{\frac{k}{2}-1} dt} dx$$

Plot of curve fitting results provided by our modeling group