Team:GCGS China/Partnership



1.With NDNF_China

In 2021 iGEM, we had in-depth and close cooperation with NDNF_China. During the process of doing the project, we helped each other and discussed many times from the initial project design to the midway project experiment, and also to the final product production. At the same time, we also shared experimental resources. We were working on a device that could detect the corruption of fish, and NDNF_China was building a system to better improve biosafety and help synthetic biology products out of the laboratory. After designing and refinement, we eventually developed a convenient and accurate system that could detect C4-HSL based on the original idea.

Who is NDNF_China?

NDNF_China design to build a hydrogel-based system Hidro, which can help a variety of modified microorganisms play a role in the natural environment safely, stably, and efficiently. This system has three main functions: 1)The dense shell can effectively prevent internal microorganisms from escaping to the outside environment. 2) The hydrogel material can provide nutrients and a stable living environment for internal microorganisms, and ensure the survival of microorganisms under adverse conditions such as acid and alkali, high temperature, and so on. 3)Barcode and toxic protein genes are added to the genomes of microorganisms wrapped in Hydra. Once escape occurs, the Cas12 system can be used for rapid identification and targeted killing. We hope that Hidro can help more Synthetic Biology products break through the limitations of the laboratory and play the expected role in the real environment

Why NDNF_China?

In April and May, our project was established to determine the content of fish corruption detection, mainly targeting the detection of quorum sensing signal molecules of Pseudomonas aeruginosa. In the project internal communication meeting of Lanjing about mid-May, we learned that the application scenario of NDNF_China for the Hidro system also considered that it could be used to detect food corruption, to create a device that is harmless to food and can detect food corruption at the same time. Several signature signals involving related pseudomonas aeruginosa and a variety of food spoilage have been studied. After the initial communication, we found that we can carry out in-depth cooperation.

How do we collaborate?

Our product, Fish Hola is dedicated to the detection of fish corruption, specialized for one kind of corrupting bacteria: Pseudomonas aeruginosa. The life activities of Pseudomonas aeruginosa are inseparable from its quorum sensing system, and the existence of QS signal molecules is the reason for its rapid decay. We expected to make a convenient, fast, and accurate product for the detection of QS signal molecules of Pseudomonas cuprum. Our idea mainly includes a common live bacteria detection system,which is based on transcription factors. One another is based on aptamer flow chromatography paper. The live bacteria detection system may face problems such as microbial escape, external environmental interference, and affect food health. Combined with the NDNF_China Hidro system, these problems can be well avoided and a stable and viable bacteria detection system can be created. Therefore, in addition to our self-constructed dipstick detection device, NDNF_China provides us with another product to detect corruption, namely, live bacteria detection based on transcription factors, which makes it possible to choose different detection products according to different operating environments.

How do we improve our project?

Helps from NDNF_China

Background information
The advisor of NDNF_China provided basic knowledge guidance for us in the early stage because they also had considered the detection of food corruption and the advisor did some research on the quorum-sensing signal of Pseudomonas aeruginosa before. That helped us a lot to have a deeper understanding of Pseudomonas aeruginosa ’s quorum-sensing system and the existing methods for detecting quorum-sensing signals, which helped us to have a better establishment on the detection targets and detection methods.

Product form
At the initial stage of the project, we planned to build a device that could detect C4-HSL from two directions of transcription factor and dipstick. However, due to the time problem and COVID-19 limiting condition, we could only successfully constructed the product test paper. However, in the preliminary research and experimental method design, we had read a reference that the author had successfully constructed a strain that used GFP as the reporter gene to detect C4-HSL. Therefore, we obtained the bacterium by contacting the author of the article. After received the bacteria, tests were carried out and we found that the bacteria successfully detected C4-HSL in the growing environment. As the test was successful, we shared the bacteria with NDNF_China. NDNF_China combined the bacteria with their project: Hidro to establish a live bacteria detection system based on transcription factors. This system can directly contact food to detect food corruption. NDNF_China shared the test data for this system with us, which improves on our original concept and it also can be used in different operating scenarios with the strip system. Each has its advantages and disadvantages. The test strip can be used for quick inspection with simple operation. The live bacteria detection system wrapped in Hidro can carry out real-time and long-term detection in the process of fish transportation, which can not only achieve the detection purpose but also will not affect the food itself.

The testing of C4-HSL receiver cells(left) and the biosensor combined with hydro system(right)

Helps we offered to NDNF_China

Modeling Advice
We provided many useful suggestions for NDNF_China in the modeling of caffeine-induced downstream gene expression. They followed our suggestion to add the consumption caused by the work of gene circuits to the consumption of caffeine digestion in the gut. At the same time, the model and parameters are also simplified.

Application scenario
NDNF_China had already designed the food corruption detect part in the early stage. In addition, the hidro system, as a carrier of bacterium, also had broader application scenarios. Due to the time limit of competition, NDNF_China could test more gene lines in a short time by cooperation with other teams, which makes the hidro system can be applied to more scenarios in a short time. As their corrupt detection thoughts were in the same direction with us, therefore, combined with the bacterial strains we offered, encapsulate with water gel, and cultured in the medium containing C4-HSL, biopsy last, observed by fluorescence microscope fluorescent signal, which suggested that the bacterial strain is normal operating at the same time, It also represented the formal realization of the product form of the idea.

Conclusion & Expectation

We benefited a lot from the cooperation with NDNF_China. With their help, we not only deepened our understanding of the project background but also enabled us to achieve each other's goals and complete the project. In the end, we worked together to create a system that could successfully detect fish corruption, fulfilling our initial idea and achieving the goals. That is a meaningful cooperation experience of 2021 iGEM!

See more about Proof of concept of NDNF_China and Partnership of NDNF_China

2.With GreatBay_SZ

In the year of 2021, we developed partnership not only with NDNF_China, but also with GreatBay_SZ. We cooperated and communicated with each other in the fields of laboratory sharing, product design and health education. GreatBay_SZ focused on finding a new way for art authenticity verification. They developed a system called barcoded microbial system: a scalable, safe, and sensitive system and insert designed barcodes into the genomes of Bacillus subtilis and Saccharomyces cerevisiae spores. The spores was added in stamps used as an untagible anti-counterfeit label. They believed that in a way their work would help in dealing with counterfeiting cases since a new method for authenticity identification of artworks is presented. The inspiration for the beginning of our cooperation is that we are both building a detection system. If we exchange our ideas and designing experiences, we could benefit from each other and gain a lot.

Why GreatBay_SZ?

First, we had several meetings with GreatBay_SZ members. During the first meeting, we introduced our project to them in the first step. We would use the aptamers that can be specifically bind to 3O-C12-HSL and C4-HSL found in papers and verify the function by some fluorescence method. In the process of the experiment, we also rationally designed the aptamers in order to make them have a better binding ability to our target molecules. Finally, we gained our aptamers with high affinity to targets. We utilized the aptamer based lateral flow method to detect 3O-C12-HSL and C4-HSL by constructing test strips. What's more, we would like to construct a system that can detect 3O-C12-HSL and C4-HSL based on transcription factor, namely the the receiver cell that can sense the autoinducer signal and characterized it by a reporter gene. Then, we realized our friend GreatBay_SZ uses the Cas12a detection method to develop an anti-counterfeiting system. Their spore detection technology uses the Cas12a detection method and would also detect the fluorescence signals. In the later part of our discussion, they also planned to construct a test paper-based test basis to the fluorescence-based test basis. Meanwhile, we could use their lab for the experiment in transcription factors. In a sense, we could offer help to each other in order to better accomplish our projects.

How do we collaborate?

After that we had an in-depth exchange with GreatBay_SZ. We offered some ideas for their test strips' creation based on our horizontal flow test paper. We helped them to improve and upgrade the test paper in a way that better designs conforming to the form of Cas12a testing. In their lab, we met together and construct text papers for our projects. At the same time, we used their lab to do some transcription factor experiments. Through this cooperation, their detection system was more convenient, and the most important thing was to reduce the cost of their products and increase the possibility of popularization of the spore anti-counterfeiting system. Furthermore, we also cooperated together in Human Practice, by sharing interview information and resources required for health education.

Helps from GreatBay_SZ

- Experiments Members of GreatBay_SZ taught us how to carry out some microbiology experiments, the configuration of agarose gels and the use of microscopes. When there were some problems presented, we discussed and solved them together. They helped us to analyse and check our experiment data. The inappropriate experimental methods and negligence in some details were pointed out. The whole process consisted of deeply connected partnership. We shared the experiment materials with each other too. Since anti-biotic and LB medium are universal for most iGEM teams, we shared them together. Moreover, we also shared the experiment apparatus to process our project. Both of our projects use PCR, so we have shared the lab's PCR apparatus to proliferate our aptamers, and GreatBay_SZ used PCR techniques to construct recombinant plasmids.

- Health education In October, GreatBay_SZ helped us in synthetic biology classes to middle school students at GCGS. The main elements of the program include an introduction to synthetic biology, molecular biology, bioethics, debates, etc. The reason for this education is that synthetic biology is a very cutting-edge new discipline in biology that needs to be better understood by a wider audience. In order to develop our partnership, we adhered to the principle of mutual benefit and provided assistance to each other. We hoped that more people, especially middle school students in our age group, would learn about the origins, goals, current developments, and future of discipline. Team members of GreatBay_SZ contributed to the teaching of our students. They were responsible for teaching "What is Synthetic Biology" to students.

Helps we offered to GreatBay_SZ

- Human practice-data sharing GreatBay_SZ learned about the urgent expectations of new detection methods the artists had in the art industry. In their investigations, fervent expectations include fast-speed detection methods. They were looking forward to meet the urgent needs for market demand. As GreatBay_SZ planned to make test strips in a cheaper and a more efficient way, we could offer them some experiences and information we have. We had investigated the prices of the text paper by making a phone call to the company which sells the test paper. We were also sharing HP data with them to facilitate their test-strips' design. The exchange of HP experiences helped them to improve their products. Together, we calculated the price of the current test papers that are sold on the market. Finally, we helped GreatBay_SZ in finding an optimal way to construct the cheapest test-strips .

- Product design In exchange, we also shared our thoughts about testing the concentration of Pseudomonas Aeruginosa and using test strips. The members of GreatBay_SZ discovered that our thoughts on capturing quorum sensing (QS) molecules can be used for reference in their project. As a result, we introduced our existing producing method for test papers to GreaBay_SZ. In this way, they could construct a more efficient detective system for spores. By further deep communication, GreatBay_SZ successfully reduced the cost of their products (test strips) and expanded the potential application scenarios for spore anti-counterfeiting systems. Screenshot below is the process of our communications about the test paper. (Green: member of GrearBay_SZ. White: GCGS member). We introduced our basic principles in strips'making and the result of our test paper experiments.

Conclusion & Expectation

We have benefited a lot from the cooperation with GreatBay_SZ. Not only enhanced our comprehension of our projects but also contributed to the accomplishment of our projects. In the end, we worked together to construct a new and general way of making test strips for our different detective system. We fulfilled our initial idea and achieved the goals eventually. That was a meaningful cooperation experience of 2021 iGEM! Also see GreatBay_SZ