Team:SEFLS Shanghai/Collaborations

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Collaborations

Collaborations

Collaboration with HUST

The first part is about the information exchange session in HUST (Huazhong University of Science and Technology) on Jul 26. Xinyi Wang, who is currently in Wuhan, attended this meeting representing our team. Firstly, HUST-China introduced their program, whose topic is the utilization of banana straw.

During the speech, Hao Qiu, the leader of HUST-China, mentioned that there may be some problems when the gene is imported from a eukaryotic cell to a prokaryotic cell when he explained the reason why they chose Pichia Pastoris instead of E. coli as the baseplate cell. Xinyi Wang was curious about the problems he mentioned, as we had a step in our experiment importing the gene from Y. lipolytica to E. coli.
Therefore, Xinyi Wang asked him to explain the problems in detail. He let his program instructor, Prof. Xie, to answer this question. Prof. Xie gave us a very detailed explanation, listened carefully to the speeches delivered by the iGEM teams in high school division, and gave his comments.

Professor Xie is giving his comments

Then Xinyi Wang introduced our program thoroughly, including our title The Microorganism Factory of Squalene, the introduction of our team members, what squalene is, why we produce it with transformed E. coli, the process of squalene production using microorganisms, the feasibility and challenges and our contact info.

Wang is introducing our project

And then, other teams also introduced their programs. Worldshaper-Wuhan team focused on the detection and processing of arsenic in water. XHD-WS-Wuhan A team focused on the diagnosis of lung cancer in the early stage. XHD-WS-Wuhan B team focused on the detection and recycling of lead in the environment. They mainly introduced their experiment plan, their current stage of experiment and their social practice.

We learnt a lot from this session, for example we knew the achievements in lab of other teams, understood how they engaged with the public, and received valuable comments from Prof. Xie. The advance of the stage of other team's experiment, the diversity of their methods to conduct social practice, the comments of Prof. Xie on the innovation of our program and the careful design of the experiment plan of HUST-China team all triggered our thoughts. By attending this meeting, we built friendly relationship with the members of other teams. For example, I finished the questionnaire of other teams.

Table of Content

Project Introduction (First)

ShanghaiTech Mentorship

Offer suggestions based on the project (First)

Give some advices on integrated human practice (First)

GC-MS (First & Follow-up)

Suggestions on Modeling (Second & Follow-up)

Suggestions on Giant Jamboree Presentation (First)

Present the game they made, suggestions from SEFLS_Shanghai, help them to publicize and give feedback (Second & Follow-up)

First Meeting with ShanghaiTech

Giant Jamboree is approaching day by day, we still have some experiments to finish, and we are worry that it's impossible to establish a mathematical model that is enough practical. To solve these problems, We sent email to contact the university teams for their help.

We thought that the college students would ignore a group of young high school students they didn't know. Unexpectly, we received their reply soon. In order to contact NYU_Shanghai, we emailed the university admission office, which is not related to iGEM at all. To our surprise, the admission officer replied us and helped us to get in touch with the team.

Discussing with several teams online, we finally decided to collaborate with ShanghaiTech. After a period of keeping in touch online, we had a meetup with ShanghaiTech iGEM team on Sep. 28 near Century Avenue. Both teams sent 6 members to attend this meetup, which means that both teams pay great attention to this event.

After the members arrived, our team leader briefly introduced the project, including the project background, experiment plan and human practice plan.

ShanghaiTech offers a number of suggestions after listening to our introduction:

1. If the current cost of producing squalene from microorganisms is higher than that from sharks, industrialization will be difficult, because large companies will still prioritize the cost over environmental protection. But industrialization can be put in the future plan with detailed description.

2. We can work on arousing people's awareness of shark protection rather than mass production, so as to prove that our project has practical significance.

3. Our interviewees can be professors and researchers with professional background, who can give more valuable feedback on the technical problems of our project. For example, when students at ShanghaiTech studied an immune protein that regulates human intestinal flora, they interviewed professors from Shuguang hospital, ShanghaiTech and Harbin Institute of Technology to improve the experiment design according to their suggestions. We can consult professionals about the specific detail of the experiment.

4. Will squalene synthesized by microorganisms be less active than that obtained naturally? (We mistakenly thought that small molecules, unlike proteins, didn't need to be considered for their activity.)

5. Limited by the limited experimental data, the mathematical modeling may not be accurate after certain improvement, but it doesn't matter. It is ok to reflect the trend.

6. It is better to have a clear navigation bar on the Wiki and a separate experiment record.

One problem we have encountered so far in the experiment is that the transformation of the large plasmid failed. Regarding this, they gave the following suggestions:

1. In plasmid construction, we should adopt restriction enzyme digestion instead of homologous recombination, which often lead to mutations. If we adopt homologous recombination, we should sequence the plasmid.

2. We may try to use DH10B electroporation competent cell.

The advisor of ShanghaiTech iGEM team is a junior who went to Boston to attend Giant Jamboree last year, so he gives a brief introduction of what it will be like in Boston:

1. Arrive in Boston one day in advance. By then, we should be well prepared and we can test the equipment.

2. Check the presentation schedule. There will be six judges sitting in the first row and two to three hundred audience in the back. We will have 20 minutes to deliver the speech, and 5 minutes to answer the questions from the judges. The presentation time should be limited to 18 minutes in regular practice. It is recommended that at least 2 students deliver the speech together on the stage. We can also prepare a short video clip to show then.

3. It is impossible for the judges to ask all the questions in 5 minutes, so they come to ask questions during the poster session. Therefore, at least one person should stand by the poster to greet the judges and to answer their questions.

Thinking of the various opportunities and challenges that we will encounter there, we are both nervous and excited! We must make full preparation in this October.

Then, the two teams confirmed cooperation:

1. ShanghaiTech has a gas chromatography-mass spectrometer, which can be used to characterize the squalene obtained in shake-flask fermentation.

2. ShanghaiTech iGEM club members are willing to help us in mathematical modeling.

3. SEFLS_Shanghai is mentored by ShanghaiTech.

After 2 hours of discussion, we felt a bit hungry. We took some dessert, and the atmosphere was easier.

Then, ShanghaiTech introduced their project this year. The title is INSULEN: An Intelligent N-palmitoyl-serinol System Utilizing Light-controlled Enterobacterium for diabetic therapy. Type 2 diabetes (T2D) has become an increasing public health problem worldwide. Its existing treatments, including insulin/GLP-1 injections and other drugs, are inconvenient and expensive. N-acyl amides are a family of small molecules secreted by resident enterobacteria to relieve T2D.

ShanghaiTech_China team aims to engineer a smart enterobacteria system that can be fed in glucose values to control the production of N-acyl amides for diabetic alleviation. Using E. coli as a demo, they cloned the synthase for N-palmitoyl serinol, the most potent group in N-acyl amides, into the E. coli expressing plasmid under a light-controllable promoter. Then, they designed a software and LED device that can accept glucose signals from T2D patients to control the synthase expression, which leads to the production of the therapeutic molecule. Together, with INSULEN, they offered a convenient, cheap and smart way to battle against T2D and proved it in principle.

ShanghaiTech engaged with the society in various ways. They introduced their LED device on the roadshow, taught the middle school students about synthetic biology, produced animation introducing microorganisms with Tianjin University, and developed a video game relating to their project.

In addition, ShanghaiTech showed us their PPT for presentation in Boston. We all amazed at their PPT and video.

Finally, we took photos together and built a wechat group. Members of ShanghaiTech followed our official accound and invited us to a activity that is like a mini Jamboree.

Having listened to ShanghaiTech's advice, we discussed again to arrange the tasks that we have to finish later.

We learned a lot this afternoon. We solved some problems, improved our project, knew how to finish our experiments and do the modelling. We also studied ShanghaiTech's great project and learnd what we will face in Boston. We are really grateful to ShanghaiTech's patience and guidance. We will do our best to finish our project and collaborate with more teams in the next month.

Second Meeting with ShanghaiTech

During the meeting with ShanghaiTech on September 28, we introduced our project and problems we encountered. ShanghaiTech not only gave us suggestions, but also introduced their project. The two teams confirmed the collaboration friendly, and keep in contact online.

On Oct. 7, ShanghaiTech first presented the modeling their project: They built a population model. In the perspective of experiment, they genetically edited E. coli and introduced them into the stomach, where they compete with the existed E. coli. Therefore, students from ShanghaiTech wanted to discover changes in the population of E. coli strains during competition. They established a mathematical relationship according to the logistic function of population growth. In the case of two kinds of E. coli, the number change rate dN/dT= r*N1*(1-n1 / nm-n2 /Nm). They have also conducted experiments, using a visible spectrophotometer to measure the growth rate of a single species of E. coli over time, finding that the growth of a single species of E. coli was consistent with the logistic function.

Through their presentations, we had a general idea of mathematical modeling in the biology project. Then, we introduced our project and let everyone think about how to apply modeling to our project.

For our experiment, both sides proposed various modeling schemes, such as discovering the process of speed determination, the relationship between simulation time and squalene production, etc., but we found that these schemes were either too complex, lacking experimental data at the present stage, or not helpful to the experiment. Shanghai_Tech pointed out that the purpose of modeling is to make predictions when experiments are difficult to conduct. Finally, after discussion, we decided to establish the relationship between the volume of container and the yield of squalene, thus predicting the yield of squalene before the first feeding in fermentation tanks or even in industrial production.

In short, we need to engineer squalene production in, for example, a 3mL tube, a 20mL conical flask, or a 50mL conical flask. Then we can regress the relationship between volume and yield, predicting the squalene yield of engineering bacteria in the 5000mL fermentation tank.

Then, Shanghai_Tech introduced and demonstrated the game they have designed. Although the game is in the demo stage, the picture is excellent, and the content is rich. The background of the game is based on bioengineering, and players should complete the task requirements by building their own bioengineered bacteria. Students from SEFLS asked questions based on game, and they answered them. It was finally agreed that Shanghai_Tech would add elements related to squalene into the game and create a level for out project, while SEFLS would promote the game and give feedback.

Finally, team members from both SEFLS and the Shanghai_Tech enjoyed snacks and took a picture together.

Follow-up

After two meet-ups we started to carry out the collaboration.

On October 10, our advisor sent the squalene sample to ShanghaiTech University to have it analyzed using GC-MS. The sample was kept in the protection kit under 4 degrees Celsius. We have sent the sample condition to the lab in advance, which we think might be helpful for the operation. The lab assistant there helped us to set the condition and operate the machine. However, the condition we set was inaccurate and result was not qualified to use. The lab assistant tried other conditions to help us to improve the analysis result. After a few times of trial, the result was much better than the former one, able to be analyzed the existence of squalene and used in our wiki.

Since October 9, we started our discussion on Modelling. We conducted experiments as we have planned. And on October 15, we finished the experiment, got the result and statistics and sent them to ShanghaiTech to start modeling. However, the initial suggestion they gave could not be used because they missed some important details when designing the model, so the model didn’t fit the experimental statistics. As a result, we improved the basic model, combining their suggestions, and designed an improved model. Although they provided useful suggestions, we independently designed the model and wrote the report. The result of the model was quite helpful for prediction. Thanks to the help of ShanghaiTech, we could start to do Modeling, because we once thought that this could be a hard task.

After ShanghaiTech presented their game at the second meet-up, we started to publicize the game to other students.

Once the game was loaded in the classroom, we were at once surrounded by other students, who wanted have a look on the delicately-designed game with excellent picture and rich content. We presented the game and explained to them how to play it. They were all so excited to have a try. After trying this game, we asked them to give feedbacks. After collecting the feedbacks, combining ours, and we summarized the feedbacks and listed them:

1) There are some bugs in the game that need to be fixed

2) The game should ask the players to operate more other than just designing their own engineered bacteria.

3) As for high-school students, some contents are to hard for us to understand.

Collaboration in Education: with OUC-China

One evening in September, we saw the collaboration requests posted by OUC-China and IIT Madras on iGEM's website. OUC-China designed a comic book and invited other teams to translate it into other languages or to use their comics to teach students. As our team members are all proficient in foreign languages, we initiated the collaboration and translated their comic book into Japanese. In addition, with OUC's permission, we introduced their well-made comic book to our biology teacher at school, who is the class teacher of Class 1 Grade 6. She does need something to ignite six-grader's passion for biology. Therefore, she permitted us to teach her kids using this comic book every Monday noon. She thinks that this comic book is a perfect supplementary textbook for her course.

Collaboration in Education: with IIT Madras

The collaboration request from IIT Madras is to translate their education video clip into foreign languages. This time, we makes it from English into Chinese, French, German and Japanese. We posted this video via our own social accounts: WeChat Official Account and Bilibili. We also posted the video they made on our publication platforms. In addition, we sent our works to help them spread their video in different languages.

Left to right: Japanese, Chinese, German, French