Difference between revisions of "Team:XMU-China/Collaborations"

The 5^th CCiC , which full name is the Conference of China iGEMer Community Meetup, was held at ShanhaiTech University on the subject of “Among us, past, present and future meeting” from August 27^th to 31^th. Dozens of teams from all over the China as well as the Executive Vice President and Chief Operating Officer if the iGEM Foundation, Meagan Lizarazo took part in. During this conference, we fortunately got the chance to have deep communication with many iGEM teams including iGEM_BIT(Beijing Institute of Technology University), iGEM Tianjin (Tianjin Unniversity) and LZU_China (Lanzhou University), and here we really appreciated their advices on our project about the competitive experiments, Kai ABC systems and the OMVs systems. Luckily, we won the best presentation award. What's more, we were greatly benefited from Meagan’s lecture pointing out the importance of “After iGEM”. This strengthened our determination to contact the old members of XMU-China and luckily we got precious experiences and further understanding about this competition.

From July 30^th to August 3^rd, 2018, we participated in the 6th Asia-Pacific iGEM Conference hosted by National Chung Hsing University, Taichung. There was a total of 22 teams and 140 participants from Taiwan, China, and Japan, warming up for the final Jamboree in Boston at the end of October.

The conference invited wonderful speakers from the field of Synthetic Biology and Ambassador of the iGEM HQ to give a talk at the Opening Ceremony. Among them, Prof. Kenji Tsuge from Kobe University explained the emerging synthetic biology technology that can link quantities of large fragments of genes and perform these genes; Dr. Zhang Jui-Jen, an associate researcher at China Medical University Hospital, shared his experience in using synthetic biology entrepreneurship; iGEM Asian Ambassador Chen Hong explained some new systems and shared experience on behalf of iGEM. We gained tons of new ideas from these lectures, which had great influences on our next work.

In the five-day conference, we also had a 20-minute English presentation and a poster exhibition. It was the first time to present our project frankly to iGEMers from Asia, and a good opportunity to practice for the final Jamboree. At the end of the exhibition, professor Yang Wen-Ming from the field of molecular biology at National Chung Hsing University gave a comment on our presentation. Through the conference, we also made suggestions to other Asian teams, longing for more cooperation opportunities.

This conference has provided us tremendous new ideas to improve our project and final presentation.

SUSTech iGEM

This year, the SUSTech iGEM team used the microfluidic chip as the core carrier to build a complete hardware platform, which was very similar to the idea of XMU-China team in hardware design. On this basis, these two teams had an online communication on issues related to microfluidic chips.

SUSTech used high-precision and single-channel chip tubes to achieve cell sorting functions, with a peristaltic pump that provides driving force, and a flow meter that filters and encapsulates cell droplets. These devices greatly improve the precision of the entire device.

XMU-China also made a relevant introduction about the design of microfluidic chips. What's more, our team additionally answered questions about how to control liquid flow in the centrifugal force-driven microfluidic chip.

Figure 1：The design of microfluidic chips of SUSTech iGEM(left) and XMU-China(right).

In terms of the project, we believe SUSTech iGEM team's using chips to study the interaction between cells is very innovative. From our professional perspective, we gave some advice on cell signaling pathways and cell-cell interactions, and recommended several related articles to them, hoping to help them. Based on our project, they raised some questions about whether our cell-free system belongs to the field of synthetic biology. We put forward our views, and the two parties had a futher discussion. We believe that synthetic biology is not a simple use of biobrick to construct gene loops. Instead, it should be a broader definition. We think that standard components are like building blocks, but it is up to people to decide what items should be joint together, rather than building blocks themselves. Therefore, biobrick can be used to build systems outside the genetic loop.

In addition, both of us exchanged ideas on the Art&Design. We carried out visual design communications with SUStech on aspects involving poster, Wiki and PPT. We showed them our methods and ideas in visual designing, including drawing graphics of experimental process and other details.

At CCiC, we are very delighted to find that BIT projects have a lot of intersections with us. We have similar representations.Therefore, our team communicated with them in the following three aspects.

The first is the exchange of ideas on the subject. We have had a two-hour telephone conversation with them. On the phone, we exchanged the purpose of the project and some detailed designs, introduced our own project to them and proposed some questions for each other.

Secondly, we asked the BIT team about a difficulty in the experimental program. I am very happy that they are effective. We proved that our aptamers and complementary chains are combined. We gave the results back to them and gave them suggestions of improvement. In addition, we also exchanged some experimental methods and protocol.

Finally, in order to prove the feasibility of their respective experimental designs, we mailed some materials to each other and successfully verified the effectiveness of the other's combination, which is also a very effective part of our cooperation.

The experimental results are shown in the figure below. Well 1: Aptamers, Well 2: Complementary chains, Well 3: Aptamers + Complementary chains. As can be seen from the figure, the electrophoresis speed of the combined DNA is slower than that of the aptamer and the complementary strand, and it is indeed combined.

On July 31, 2018, at the 6^th Asia-Pacific iGEM Conference hosted by National Chung Hsing University, Taichung，we met with NAU-CHINA team and established a deep friendship. Since then, our two teams have exchanged and discussed "how to build a team."

The professor affirmed the feasibility of our project and gave us some invaluable advice. Under the suggestion of Professor Zhu Zhi, we chose EpCAM and aptamer SYL3C. In addition, we are very grateful to Professor Zhu for her support on many instruments and materials provided during our experiments.

First we discussed "what kind of team should we build?" The International Genetic Engineering Machine Competition is a creative synthetic biology event and an interdisciplinary competition involving cross-disciplinary fields in mathematics, computers, statistics and so on. So our team should be a creative, comprehensive synthetic biology team. Our team members should be creative and comprehensive students. Most students of our two teams have multiple roles in the team.

Second, we discussed "how to find new partners." After we know what kind of team we want to build, we could find the companions we need. First, we have presentations, exhibitions, lab activities, etc. to make students realize that, what kind of the team they will join in and what is the team building for? what role they will be in the team, and what should be done by themselves? In order to join this team and make this team better, how should them prepare and learn? Then we divide the interviewers into different groups according to different division of labor and their wishes. Different groups determine the way of assessment according to the division of labor. For example, the number module is tested by some models, and the art team performs preliminary selection through some art production tasks... We will give priority to students with multiple skills.

Third, we communicated on how to train the new team members in the early stages of team formation. First of all, we will introduce our team and International Genetic Engineering Machine Competition through presentations, posters, WeChat pushes, etc., and also convey our requests for new recruits. We will then train the interviewees in groups and we will select them during the training process. Our training is mainly to share the learning materials for students and let them learn by themselves.

Our two teams made recommendations on each other for training new members. They suggested us add a literature reading part to the training to teach students how to read literatures and how to extract important information from the literature. Then they shared with us some materials for teaching students to read the literature. Their advice has helped us a lot, and we plan to adopt their suggestions to improve this year's training. At the same time, we also suggest that they increase the opportunities for students to practice, let the students design their own topics, increase their free space, make them more creative and have more new ideas. In addition, we exchanged our training materials on modeling, hardware, software, art and web design with each other.

Finally, we communicated with the daily management of the team. At the beginning of each team, all the students will participate in the design of the project and conduct laboratory training. After the preliminary determination of the subject, the students were divided into different groups, responsible for different labors like experiments, modeling, human practice and so on. We hold group meetings every week, each group reports the progress of the project, and different groups communicate with each other. In addition, we will also hold regular entertainment activities such as picnics, parties, etc. to relax and enhance team friendship. Both of our teams have one thing in common. Most members are in multiple roles, which better strengthens the communication between groups. It shows that iGEM competition is a common combination. There are different groups in this team. Everyone is not working separately, but is always intimately connected.

Through the exchanges with the NAU-iGEM team, Our team has a better construction model, and we have more experience in the follow-up training this year. Thanks to the NAU team for their help.

This year XMU-china team and H14Z1_hangzhou team's cooperation can be divided into the following two parts:

First, XMU-China team helped and instructed H14Z1_hangzhou team to fill out the judging form, and to offer some advice about the relevant representations of one of a previous year biobricks to meet the bronze standard four. In addition, we also assisted H14Z1_hangzhou to complete the design of the first level menu and the second level menu in the navigation bar, so that their results can be better displayed in front of the judges.

Second, XMU-China and H14Z1_hangzhou assumed the task of the experimental representation each other. H14Z1_hangzhou helped XMU-China measure the fluorescence characterization data of BBa_K2623025. XMU-China helped H14Z1_hangzhou complete the experimental curve of the number of engineering bacteria in the process of fermenting yoghurt with the change of time.

The experimental steps and results are as following:

Experimental steps:

1. The first day, Lactobacillus NZ9000 and GMCA respectively were inoculated into 50ml GM17 medium, fermented at 30 ℃ overnight (about 12h). (Place them in a 30 ℃ incubator, no shaker shocks required).

2. Next day, fresh milk was heated to about 55-60 degrees Celsius, and then adding some white sugar, 3000rpm stirring for 10 minutes mixing. Divided them into 250ml shaker, and the volume of liquid in every shaker is 100ml.

3. Sterilize the above solution at 90 ℃ for 5min, then cool it to 30 degrees Celsius to prepare for inoculation and fermentation. Then collect Lactobacillus acidophilus in shaker and clean them 1 times with sterile water. Add Lactobacillus acidophilus to the sample making the initial OD is 0.1 (600nm). Then let them ferment statically in the 250ml shaker at 30 ℃ (Place them in the 30 ℃ incubator, without shaker vibration)

4. Measure the OD value every two hours and count the corresponding number of cells to draw the curve. Simultaneously, test the pH of the solution (Measure for 14 hours)

Experimental results:

Table 1 The comparison of biomass and product formation in two different yogurt

2018 is the first year for FJNU-China team to participate in the iGEM competition, yet the teams competing in the first year are often lack of the relevant experience and grasp of the subject scale.

Since XMU-China team and FJNU-China are the only two teams in Fujian province in China, it is incumbent upon XMU-China team to instruct FJNU-China team and communicate with them to make the team fell they are parts of iGEM family as soon as possible.

In August, we held the Conference of Fujian Province iGEMer Community in China，and at the meeting, the both teams presented their own topics. Based on the topic of ideas, gene circuit design, experimental programs and practical application level, XMU-China put forward their own ideas, which helped FJNU-China better prepare for the competition and explain the ideas of their subject. After the meeting, we introduced them to the hospital's dermatologist and led them to visit the Xiamen Environmental Protection Bureau.

At the end of the competition, XMU-China provided years of experience to help FJNU-China to complete the safety form and judging form.

In the brainstorming stage, in order to solve the problem of preservation of Cas12a protein in microfluidic chips in hardware design, our team retrieved a large number of topics related to protein preservation in previous years. Finally inspired by 2017 TU_Delft's TDPs project and improving the characterization method. But it costed a lot of our time and efforts. After communicating with the team SYSU_Software in September, we asked them to quickly and accurately search for the previous project. They upgraded the functions of their software to cater our needs. We compared the information obtained by the manual search and the information obtained through the software search, and found that the software can be well positioned to the part of the experimental plan we need, which is equivalent to the accuracy of the manual search, but the work efficiency is improved and the work efficiency is lowered. After obtaining the results, we made recommendations on the user-friendliness of the software's user interface operations and the search algorithms can be optimized later.

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This year, the Tianjin team in China worked on Clock Mechanisms, which would utilize some circadian clock proteins discovered in Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2).

We XMU-China also made efforts in Circadian clock “Kai”. Unfortunately, three kinds of protein which we used can not be produced in our lab, because the DNA ordered from IDT was disabled.

However, when we talked about circadian clock with members in Tianjin Team, we were lucky enough to be informed that they could provide us with the DNA we needed. Thanks to their donations, our study on rebuilding circadian clock “Kai” in E.coli can proceed.

More details about Tianjin’s work can be found in https://2018.igem.org/Team:Tianjin

This year we have newsletters with other iGEM teams from schools of all over the world, like Boston University (BU), Technische Universiteit Delft（TUDelft）,TUST, ECUST, JNU and so on. Those letters are precious and beneficial since they enable different teams to share projects and views with each other, especially on topics like team information, team introduction, project description, etc. There is a link that you can see the new version of the newsletters. Through this platform, more people could learn about our projects and we have more opportunities to communicate and cooperate with the external world.