Team:XJTU-China/Partnership
Partnership
NWU-CHINA-A
Based on the previous cooperation and the advantage of geographical location, we have always maintained a good relationship of cooperation and mutual assistance with NWU-China-A since before the project was established.
Here are several important events in working with NWU-China-A in chronological order.
June 23rd
At this point neither of our teams had decided on a project. Although we were all still isolated at home, through the online meeting, the team members were still able to speak freely, put forward their own ideas, and raise questions and suggestions on other people’s ideas. The captain of NWU-CHINA-A gave us a lot of advice and guidance related to project approval. In this discussion, we collected about 20 mature ideas from XJTU players, most of which were supplemented and improved by NUW-CHINA-A members.
July 25th
In the Shanxi Meetup hosted by NWU-CHINAa-A, the two teams of us are for the first time holding formal presentations and exchanges with their respective projects. And this was the first time we had meetup since we confirmed the soil reconstruction project. In the communication, we also asked NWU-CHINA-A lots of questions about project modeling, and listened to students from Northwestern University.
Liu, from Northwestern University, provided guidance on modeling symbiotic relationships, growth curves, and escape prevention systems for our project.
After the meetup, we have carried out in-depth cooperation with Team NWU-China-A of Northwest University in the field of mathematical modeling. During the implementation of the project, the modeling principals of the two teams helped each other to find the relevant parameters of our modeling, modified the model with each other, and exchanged modeling methods and experience in real time.
August 15th
In the communication between Jialu Li form XJTU-China and Yu Zhang from NWU-China-A, our two teams proposed to continue to complete the plan of Parts repository in Shaanxi province proposed last year. As there are very few iGEM teams in northwest China, it is very inconvenient to seek help from nearby teams. Based on this, at the Shaanxi Meetup in 2019, we decided to establish a northwest database of common genes or parts of iGEM teams in northwest China for the convenience of future teams. This year we will continue to complete the five-year Northwest Alliance plan that we introduced last year. iGEM officials will provide free 20 KB -DNA synthesis per team per year, which we plan to use to build our parts library. This year, we continued to synthesize gene fragments of interest to form a DNA database. That will make it easier for us to get some common genes or genes that we’re interested in real-time, for the project to go ahead and for the northwest team to use in the future. Besides, we will continue to enrich the database over the next few years to benefit teams in the northwest and across China.
September 3rd
We have in-depth cooperation with the A team of Northwestern University in China in the field of mathematical modeling. During the implementation of the project, the modeling leaders of the two teams helped each other, found the relevant parameters of our modeling, modified the models, and exchanged modeling methods and experiences in real-time.
In terms of modeling, we deeply exchanged views on modeling with team a, and observed the model of NWU-CHINA-A. The model items of NWU-CHINA-A fit well and the parameters were very comprehensive. We had reached a consensus on the application of some formulas and discussed CA model in depth. We have encountered many problems. It is difficult to find the parameters needed in the bottleneck period in the literature. After clarifying the relevant problems, NWU-CHINA-A pointed out that the parameter fitting should be carried out in combination with the experimental data. At the same time, we also solved some problems of each other. The growth model of the other party lacked some parameters. Our opinions were put forward around programming and Gan, and exchanged the measurement experience of pH and soil parameters. We are all aware of the importance of data query, and the direction of modeling is clearer.
September 21st
We also have extensive exchanges and cooperation in experimental methods, web page construction and submission. In terms of experimental methods, we exchange some things to pay attention to when cultivating bacteria, and summarize the experiences and reasons of their failures for further experiments. Sum up the experience and lessons, and improve the success rate of follow-up trials. On September 21st, we focused on the problems encountered in the experiment. We first proposed that the colony PCR negative control had bands. NWU told us to change to new water and primers, and to separate the new primers, taking out a new tube each time to avoid repeated freeze-thaw degradation of the primers. In view of the insufficient lysis of NWU, we have proposed an improved lysis solution formula as follows:Before:Bacterial lysis solution 1.0: 50mM/L tris-HCl 0.5mM /L EDTA 50mM/L NaCl pH=8.0
After: Bacterial lysis solution 2.0: 20mM/L tris-HCl 150mM/L NaCl
And after adding the lysis solution, let it stand for a while to fully lyse.
October 3rd
Members of our modeling team went to Northwestern University for on-site exchanges. Regarding the problem that our team could not find the parameters of the suicide switch activation mechanism in the modeling of our team, NWU-CHINA-A proposed to fit the corresponding parameters first, and then select the appropriate ones from the part library The promoter construction system is used to simulate and optimize the experimental design of the project, which facilitates modeling and increases the connection between modeling and experiment. We put forward some suggestions for the cell expression simulation process in the modeling of the NWU-CHINA-A team. For example, the dynamic modeling of related process principles can be added to the statistical method modeling to reduce the risk of overfitting.
October 10th
In terms of web production, on October 10th, we discussed web design methods with NWU-CHINA-A. We used GitHub and other methods to compile the Wiki, and established a complete Wiki, which inspired them a lot, so with the cooperation of the two groups, we successfully established their respective websites. We also discussed and researched the award criteria and reminded each other of the relevant materials that need to be submitted on the web page to ensure the integrity of the wiki.
October 26th
On October 26th, our two teams finally finalized the components that we want to add to our Northwest Part library this year and submitted the order. We will publish the part library data on the website, hoping to provide help for follow-up iGEM teams.
NWU-CHINA-B
In the experiment, we helped them detect the expression of UGT78D2 protein induced by IPTG at different concentrations.
In the process of the experiment, the students of NWU-CHINA-B were unable to measure the OD value in time and the laboratory data were covered, resulting in some experimental data errors and some data loss. So we can't complete the first part of our modeling. According to the actual situation, it is suggested that the conversion relationship between the number of E. coli and OD value can be obtained by directly checking the data without diluting the bacterial solution and smearing the plate. In addition, we should measure from the first hour to the 20th hour, so as to ensure that the maximum number of bacteria is included in the measured data and make the modeling more accurate. It is suggested that they should contact with the senior brothers and sisters in the laboratory to ensure the continuous use of the instrument without being disturbed, and the experimental data will not be covered by other people's data.
In addition, we provide our own suggestions on modeling. The modeling team members of NWU-CHINA-B do not know much about biology, but do it based on the growth model in statistics. After listening, we said that the explanation of the principle and mechanism was reasonable. For the problem of missing parameters, we suggested that we should refer to the literature and clarify the experimental direction, and use the experimental results to supplement the parameters, which played a role in promoting the establishment of model of group B.
In the experiment, we were also helped by NWU-CHINA-B. In the early stage, we provided three genes for linalool synthetase: LGF, DHJ, RXY and hoped that the other side could help us test the data of last year. In the process of activation, only one strain LGF survived. This strain contains two plasmids (GPP and linalool synthase), which can be directly cultured and induced to express protein. The synthetic linalool can be collected directly from the culture broth. So NWU-CHINA-B tested the bacteria and finally collected and tested the final product.