Collaborations | SHSBNU_China

Overview

In this year's project, we actively established communication with other iGEMers. In Beijing area, due to irregular COVID-19 case outbreaks, most teams didn’t have the opportunity to organize meetup events. The challenge weakened the connections and communications between team at the starting stage. Having noticed the needs for a meetup, we jointly held a meetup with iBowu_China team. It is necessary for two team to work on the organizing this event together because about twenty teams, including high school teams and college teams, signed up for the meetup the first week we released the call. The success of the first meetup and warm feedbacks we received inspired us to immediately plan a series of follow-ups, an in-person meetup in August and an in-person Jamboree style meeting in October. In terms of labs, we contacted the Peking team to verify their experimental results. We reached out to BNDS_China, a high school team in Beijing, who built up connection with us through the meetups, to collaborate on wet labs. We also contact team Tsinghua, a Beijing area college team for advice and help on the modeling in our project.

We Held iGEMer Meetup Twice, Including Online and Offline, with Our Partnership Team iBowu-China

[June 26: First meetup]

This year, we collaborated with iBowu_China to hold a large-scale meetup.
The first meetup was held on June 26. A total of 20 teams participated in our discussion online. The participating teams include both China and even U.S. participants, and attracted more than 10 university teams. We also invited iGEM Asian ambassador Heng Shi (Annika Shi, 20’ BFHS) for comments and discussions. By that time, this meetup was largest meetup in China.
The meetup was thoughtfully organized with extensive discussions within the organizing committee, formed by team members from both our SHSBNU_China team and iBowu-China team.

First of all, we made extensive publicity and promotion before the meetup. Wechat official account is the most popular and most frequently checked social media in China. We created the promotion article together with iBowu-China leaders and released the article to the public. CCIC is the non-profit organization in China for connecting and communicating with all iGEMers, headquartered in Beijing with members from past iGEM competitions. Their official account is almost followed by every iGEM team in China. We asked for their help to promote this event and CCIC kindly offer the help. We noted down every step of what is going to happen on the meetup day, discuss the possible problems with our advisors and instructor and made backup plans for all scenarios, like last minute withdraw, network connection issue, delay of presentation and so many more. We started a special Wechat group to host every participating team’s delegate for communications and support.

Secondly, during the meeting, we focused on the team project presentation, and we provided time for audience questions and discussions as well. It was worth noting that after the meeting, we arranged a dedicated time for concentrated discussions between the participating teams, to conduct experimental design or communication on collaboration possibilities. Many teams found partners on our meetup and gained more support and help.
Thirdly, we invited the iGEM Asian Ambassador and hope to learn from her experience and advice.
Finally, we recorded the whole process of the meeting and provide the video of presentation and Q&A to every participating team for their reference. We also uploaded these videos on the open video channel Bilibili. So far, all the videos have been played more than 1000 times.

[August 26: Second meetup]

After the first meeting, we received a lot of feedback. Among them, we were surprised to see that many teams felt very helpful to this meetup, and they hoped to have more opportunities to participate in the discussion. Therefore, we actively coordinated with our partner iBowu_China, and finally the second Meetup was successfully held on August 26, exactly two month later. This meeting was an offline roundtable discussion, and we named it iGEM Beijing Regional Roundtable Meetup.
• A Squad from 10+ Different High Schools
• A Union across China and US Schools
In this meeting, we finally communicated with our partners face to face, which was more efficient. We cheered and applauded each other's progress in the experiment, and provided each other with resources and help. Many students became good friends in this meeting.

Experimental Collaboration with Peking to Test the Effect of AcrB

We Got the Similar Result with Their Original Data

This year, we collaborated with iGEM team Peking to test their experimental result in our lab. In their project, AcrB is a drug resistance protein that can excrete antibiotics from bacteria to achieve drug resistance. The aim of the verification experiment was to measure the effect of AcrB.
According to their proposal, we prepared several materials, including LB medium, E.coli, 96-well plates, ampicillin, chloromycetin and so on.
We transfected the empty vector and AcrB expressing vector into E.coli respectively, to perform control group and experimental group.
At first, we prepared of chloramphenicol liquid medium: 25 ug/ml chloramphenicol was added into the liquid LB medium, and the total amount is about 3-5 ml (Chl is a screening marker for plasmids).
Then we divided the medium into 5 parts and add ampicillin to the following concentration:
Group 0: 0 ug/ml
Group 1: 0.6 ug/ml
Group 2: 1.2 ug/ml
Group 3: 1.8 ug/ml
Group 4: 2.4 ug/ml
Next, the medium was transferred into 96-well plates, and 4 replicates were set in each group of 5 media, of which 2 were inoculated with Control E. coli strain and 2 were inoculated with experimental E. coli strain. The specific formula is: add 125 ul medium + 4 ul bacterial solution to each well, mix and vibrate for 16 h. At last, we measured the OD600 of each hole and record the data, which was shown in the table:

The result turned out be helpful to team Peking and they confirmed it agreed with their earlier results, which was a successful experimental collaboration.

Experimental Collaboration with BNDS-China

• BNDS-China tested expression of our plasmid with part BBa_K4255014 and obtained colored delphinidin
• SHSBNU_China offered BNDS-China M9 medium and precast protein electrophoresis gel.
On September 23rd, we contacted BNDS_China, i.e, Beijing National Day School to seek experiment collaborations, and the BNDS_China team helped us verify the production from daringenin to delphinidin. Our production yield has not been satisfying and we hope the BNDS team verification in their lab would help clarify whether the selected production conditions need further optimization. Finally they successfully produced yellow delphinidin, and the synthesized quantities was similar to our results judged by the color saturation, while the color is much shifted to the red side of the spectrum than ours.

In August we tried to improve our experimental measures, adding some stable substances such as glutaric acid, sodium ascorbate, etc., and replaced our LB medium with the M9 medium. We sent our M9 medium to team BNDS_China so they can try them for bacterial culture. Meanwhile, we found that BNDS_China have not been able to find a good protein electrophoresis gel. We recommended they use a precast gel from BRD, a biotech company that we got our gel from. Their subsequent experiments also used this brand of precast gel, and the effect has been greatly improved.
BNDS_China team also raise some questions and suggestions:
1. IPTG price is high and they recommended to replace IPTG with crystal violet induction system. This system is cheap, highly sensitive, odorless and its concentration can be easily monitored by the color.
2. In terms of convenience, it is best to premix the ingredients, so that it is much more convenient to use. When the vial is inducted to change m9, the amount of medium is relatively different, resulting in a very thick bacterial liquid. BNDS_China students verified the feasibility of the crystal violet induction system in last year's IGEM experiment, and according to previous experience, its effect is significantly better than IPTG.

Modeling Collaboration with iGEM Team Tsinghua

• SHSBNU-China received guidance and advice from Tsinghua team

SHSBNU_China team has encountered some problems in project modeling and had been seeking for help on understanding the Hill equations applied to fluorescence reactions. Team of Tsinghua University kindly offered their help. We got in touch during the meetup we co-hosted in August, and team Tsinghua leader warmly responded to our question in the meetup Wechat group. Later, we set up a modeling communication Wechat group. We asked for advice on various details, about making plots and solving equation in Matlab. We told them that we wanted to use modeling methods to speculate on the reaction results of the sensor and its fluorescence concentration and sent them the model from the reference paper we followed. They helped us organize and analyze the equations, walked us through key points of the equations and we successfully completed the modeling.

1 Team Tsinghua helped us sort out what can be used as variables and how to input equations. And taught us important Matlab codes, although our final equation is not actually scripted in Matlab and therefore there is no illustration to show their help.

2 When the plotted curve of our model does not meet our expectations, team Tsinghua guided us to modify the form of the equation so the plotted curve is more consistent with our expectation. The new forms are also easier to understand.

3. Guided us to understand the first order linear non-homogeneous differential equations and showed us the principles of how to calculate the optimal measurement time of the sensor.

Meeting with iGEM Team Sesame_shenzhen

On September 3, we had an online meeting with Sesame_shenzhen team. Sesame_shenzhen mainly studied synthesizing hypouricemic probiotics using a biological approach. The colony of bacteria they designed can capture uric acid of food in the intestine. A decrease in the uric acid content of food in the intestine can lead to the uric acid in the blood to reverse osmosis into the intestine, so as to avoid directly using the medicine in the blood. We introduced our project to one another, and asked questions about the projects.

Sesame_shenzhen suggested that we can switch the spectacle lens coating to a disposable eyewear cloth, and dip the cloth into the delphinidin, making it adhere to the cloth. This approach is both less costly and more easy to operate. We used their approach as reference and implemented it into our process of the dyeing of contact lenses.

They designed a great suicidal system for the plasmid. Since probiotics will be secreted out of the body along with the secretion after digesting the uric acid, and since the uric acid content outside human body is fairly low, the suicidal system will start preventing the genetically modified probiotics from large-scale reproduction and pollution to the environment in turn. However, flaws do exist in their suicidal system.

Students from our team asked them some questions on safety, such as how they measure the uric acid content outside the body, and how they prevent the probiotics from dying in the intestine since not ingesting food for a long time can also result in a low uric acid content in human’s intestine. To this question they answered well, saying that they will add a temperature switch on the suicidal system. The temperature inside the intestine is roughly 37 degrees celsius, and the temperature outside human body is, of course, lower. This way, the suicidal system can start successfully.

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