01. Interview with synthetic biology experts
We attended 2018 CCIC meeting, interviewed with our consultants Dr. Yunzi Luo and Dr. Fei Huang, through which activities, we got a lot of profound and useful advice to optimize my project.
Dr. Yunzi Luo is an expert in synthetic biology and also a consultant for SCU-WestChina in 2017 iGEM. Her suggestions are as follow:
- It is plausible to regulate gene expression by changing the extent of mismatch between sgRNA and target DNA, but up to now, there is no related model to measure this process.
- Owing to the genome differences between E.coli DH5α and BL21 strains, we need to pay attention to sgRNA expression level in those two strains.
- In order to make different plasmids compatible in one bacterium, we had better use the special strain with pRSF DUET and use plasmids with the different origin of replication (ORI)
- Using antibiotic resistance genes would be more convenient than using GFP and RFP genes to verify our logic circuit. Because it is easy to measure the survival rates when using antibiotic resistance genes to measure the CRISPRi efficiency, while it is hard to measure GFP and RFP relative expression ratio to demonstrate the efficiency.
- Softwares, such as Chopchop, can be used to predict the 3D structure of sgRNA.
Dr. Fei Huangis a biologist in a biological company and has been our team’s consultant for a longtime. He showed great interest in our project and gave useful advice, as follows:
- chemical synthesis of indigo in the industry currently has caused great environmental pollution, while biological synthesis of indigo is pretty much more environmentally friendly and is promising to be used in the industry for mass production.
- At present, regulation of multiple genes’ expression in industry is hard to fulfill. However, CRISPRProgrammer provide a insightful and innovative strategy to solve this problem because the regulation of multiple genes’ expression can be achieved by only transforming a small plasmid.
- It is easy for bacteria to lose plasmids because of the unsynchronized rate of plasmid replication, in other words, big plasmids are replicated more slowly that that of small plasmids, as a result, smalls plasmids have more copies and thus more likely to be maintained in one bacterium. Therefore, we had better insert big genes into E.coli genome in order to balance the plasmids length and give those plasmids comparative replication rates.
Figure 1. interview with Dr. Fei Huang (in the middle)
02. 2018 Conference of China iGEMer Community (CCiC)
We participated in the 5th Conference of China iGEMer Community (CCiC) held by ShanghaiTech University, ShanghaiTech-iGEM. Through discussions with other iGEM teams from top universities across the country and communications with excellent iGEM seniors, we have gained a lot of suggestions about our project and innovative ideas about Human Practice. Furthermore, we also gave other teams feedback after listening to their presentations.
CCiC is an excellent platform for iGEMers to learn from each other. Every year, iGEMers from many colleges gather to introduce their projects, discuss their problems, ask questions and make suggestions to other teams, aiming to improve their project. Moreover, we acquired more information about After iGEM and the frontier of synthetic biology.
Figure 2. CCiC
We showed the audience and judges our project, CRISProgrammer, and then several teams expressed their interests in our design. During the questioning session and poster session, they also communicated with us. In the panel session, Dr. Xuan Wang asked us more detailed questions on the progress of our experiment and encouraged us.
In the poster session, we introduced our ideas to other teams. Other teams also shared their experience related to us.
We also invited Dr. Haotian Guo to give some advice. We introduced our subject and designing philosophy to him and hoped that he would comment and guide our topic. Dr. Haotian Guo put forward questions about the relationship between the amount of gRNA and the efficiency of dCas9 protein, which made us think deeply. In the communication with Dr. Xuan Wang, he expressed appreciation for our subject and suggested that we should focus on the achievement of the logic, pointing out that our ideas may solve "the key issue in the biological laboratory", and encourage us to continue to do this.
Figure 3. CCiC
Students from Peking University and Tsinghua University came to our poster area to learn more about our topics, during which they provided us with valuable suggestions. We also asked them some questions in their poster areas and gave our opinion. Meanwhile we introduced our "Competition Guide about How to Hold a Synthetic Biology Competition in College" to some of them, which won unanimous praise from everyone. We believed that Human Practice could integrate more elements, attract more teams and create more innovative forms in the future.
03. China iGEM Southwest Union (iSWU)
On the basis of iGEM teams in southwestern China, the China iGEM Southwest Union（iSWU）, which was
founded in 2015, devoted itself to exchanging the knowledge and optimizing the methods of synthetic
biology, aiming at accelerating the popularization and development of iGEM competition. In 2018, for
the further cooperation and optimization of projects, the China iGEM Southwest Union meet-up was hosted
in June by the team “SiCAU-China” in Ya'an Campus of Sichuan Agricultural University, Ya’an, Sichuan.
This year, the union was composed of iGEMers from University of Sichuan Agricultural University（SiCAU-China）,
University of Sichuan (SCU-China ) and University of Electronic Science and Technology (UEST-China & UEST-software).
Figure 4. iSWU
iSWU meet-up was held ahead of experiments this year which aimed at enhancing allied communication
and cooperation to achieve the optimization of an experimental project. In the iSWU meet-up, each iGEM
team gave a presentation of the project. After each presentation, there would be a Q&A session, where
audiences could raise questions or offer advice about steps interested in. Via these communications,
we knew the process and dilemma of other projects while discovered the shortage of our project.
In summarization, we not only optimize our project but also reach a win-win result.
Figure 5
In this meet-up, team “UEST-China” showed the project “Decomposing straw and producing clean energy
with E.coil”. They wanted to degrade straws through E.coil and produce the hydrogen and butanol
in two pathways separately. However, the metabolic pathway was too long to ensure the efficiency.
we showed our query and suggested they simplify the pathway which decreases the stress of E.coil and
the difficulty of plasmid structure. After their comprehensive consideration, they adopted our suggestions.
Nevertheless, when team “SiCAU-China” showed that they would remold tomatoes to meet the need for
engineering production of breviscapine. We suggested that they could consult Zhang Yang, a professor
in SCU who had tried the expression of breviscapine. In our perspectives, the professor's experience
may benefit theirs for optimizing the project and improving the efficiency. What's more, we intended
to transfer the code sequence in E.coil and regulate it through “Minimid”. Fortunately, “UEST-China”
and “SiCAU-China” reminded us of the difficulty to transfer code sequence in a genome. So we amended
the experimental project that could avoid repetitively useless work in a further experiment. Furthermore,
communication and cooperation were existing as well as in the meet-up.
Figure 6
Shishi middle school and Huayang middle school couldn’t attend the meet-up because of the time arrangement.
After this meeting, we also explained the lab safety to them. They also sought support on the experimental instrument.
Figure 7. iSWU
The iSWU created a communication platform and cooperative opportunity for iGEMers in Southwest.
It also gave diversified improvements to every project from various perspectives. We really enjoyed
the communication with so many other iGEMers. We enlightened about some fresh ideas about the project.
At the same time, the union was propitious to the development of iGEM in southwest China. We are looking
forward to the coming of new friends and bringing iGEM in southwestern China to a new stage.
