Team:BIT-China/Attributions
Attributions
As the leader of group T7, I usually arrange and supervise the experimental progress.In the early stage of iGEM, I will organize our group to hold a group meeting before each meeting, and we will discuss and study the recent literature and share our experience.This not only avoids the repeated report in the group meeting, but also urges everyone to consult the literature frequently.When it came to the experimental stage of iGEM, as the group leader, I reasonably arranged the members of our group and adopted the form of graduate students helping undergraduates to carry out the experiment in an orderly manner.
In terms of experiment, as a team member, I actively participated in every meeting and discussed building the circuit with everyone.In practical operation, lead younger students familiar with the learning experimental process, practical operation.
Our T7 group is a big family with unity, love and mutual help. Under such an atmosphere, our group's experiment is also going on methodically.
The team is a group that loves each other and makes progress together. I have not only gained knowledge but also gained friendship in this team. In the team, I mainly play two roles, one is a member of the T7 group, and the second is the leader of the sponsorship group. I will describe the contribution of the team mainly from these two aspects:
1. T7
In the T7 group, the preliminary work was mainly carried out in the literature research. In the literature research, I have a good cooperation with the members and finally the design of the line was completed. In the later stage, the experimental part was mainly responsible, and the younger brothers and sisters learned the plasmid extraction, colony PCR and so on.
2. Sponsorship group
As the group leader of the sponsoring group, I mainly completed the acquisition of the contact information of the previous sponsoring company, prepared the sponsoring materials, and actively contacted the company. Although the final result was not satisfactory, it also improved myself in the process.
The ability to communicate with people enhances the ability to coordinate and work with team members.
During this period of time in the team, I have learned a lot.It feels that it is not easy for any team to grow. Every member of the team has devoted their efforts, so that our team can thrive. Of course, many problems have also been encountered in the process of team growth. However, in the process, everyone gradually recognizes their own shortcomings and problems in the team, and can overcome difficulties. Although I have many shortcomings and shortcomings in the team, I have contributed to the overall improvement of the team, so I think I am eligible for the iGEM International Genetic Engineering Machinery Competition award.
March
In the brainstorming stage, the idea of “gene antidote” was put forward. Literature on gene editing technology, biosafety, ethics and law was consulted.Coordinating with the BIT team, and completed the registration fee declaration of $4,500 and saved the school $1,000. Summarize the process and materials of applying for funds and it was written as textual material.Conduct the summary of group session.
April
In terms of service teams: Provide service of booking conference room for team In terms of self-improvement:Stick to report at group meetings to hone the expressive and comprehensive abilities.In terms of projects: The basic idea and framework of transcriptional resource allocation project were discussed.Organize the team members to consult the literature while writing the summary.
May
Several new members from the School of Chemistry and Chemical Engineering and the School of Computer Science & Technology were recruited. Assist in streamlining personnel and rationalizing organizational structure. Participated in the design of basic gene circuit of σ group. Organize the activity getting sponsorship
June
Apply for $7450 registration fees for Giant Jamboree. Report the experimental design to verify orthogonality of σ factors. According to the experience of last year's competition, write the handbook of embassy appointment and the handbook of DS-160. Assisted in the preparation of laboratory consumables.
July
Organize team members to participate in 7.7 Beijing meet up. Lead the team members to COFCO on July 26 for survey and communication. Put forward the idea of combining iGEM with the summer social practice required by our shcool, that is, continuously developing the practice resources that can be cooperated for a long time inside and outside the school. The history of team was connected, and a new team concept is put forward, that is to create a real intelligent cell factory. In terms of experiments: The plasmids were constructed four times, though all failed. In terms of team building: Many documents have been written to clarify, write and systematize some vague team discipline and team experience in the past. Found the BIT-China Heritage Cloud. Constantly sort out the resources and materials that can be obtained in this year and previous years, and summarize them by category, so as to form an orderly inheritance of iGEM
August
Participated in the redesign of gene circuit of σ group. Help to hold the 8.6 Beijing regional meet up. Gradually aware of some shortcomings in the team management and experimental cooperation mode, put forward some reform plans, and wrote the standardization of Wiki text and notebook. Book the flights and hotels to Boston Lead the team members to the sixth CCiC.
September
Reflect on the problems of team management more deeply, try to summarize the problems encountered in this year's project into text materials, and pass them on to the BIT-China 2020.
October
Writing on Wiki.
The work in September and October is still the connection route. Our team has completed most of the construction of PT7, P sigma B and P sigma F routes. Due to the plenty of school curriculumt，my main work is to write the wiki text. I was responsible for the significance of resource allocation in the background part. I spent most of my time looking up literatures to find appropriate research to prove the feasibility of our project and its impact.
In writing, I made some mistakes, such as language disorders, improper wording in some places, unclear explanation of some concepts, and irregular writing of proper nouns. In particular, the overall expression may be unclear, which may easily confuse the readers. These are the questions that I usually do not pay much attention to when writing articles, and I also realize how difficult it is for the teacher to read the papers I have handed in. I need more practice in writing articles.
This year I have moved from junior to senior, becoming an older undergraduate in this team. In this igem competition, I am in charge of the mathematical modeling. By considering the process of the whole experiment, I divided the whole experiment into two parts, cell growth part and cell production part. In these parts, according to the needs of the project, I have established four models: the relationship model between p_luxRpromoter intensity and p_luxIpromoter intensity in the growth process, the cell growth simulation model, the maximum model to optimize the arrangement of promoters in production, and the optimization model of the balance between production and growth. These models can be briefly described as follows:
The relationship model between PluxR promoter intensity and p_luxI promoter intensity in the growth process. The model considers how the intensity of p_luxR promoter affects the production of LuxI during the growth process. We use the fitting method to get the relationship curve of the intensity of the two, and then decide which promoter should be used in the actual production. Cell growth simulation model. In this model, we mainly consider the relationship between cell density and signal factor concentration during cell growth. In this model, we consider the LuxR-AHL system. And because the system are related to the number of cells, we add the Logistics growth model of cells, and finally describe the relationship between the components in the growth process.
The maximum model to optimize the arrangement of promoters in production. The purpose of this model is to adjust the sequencing of the three promoters to maximize the final yield. In this model, because of too many parameters, we simplify the model to a certain extent. By considering the solution of the whole process in the equilibrium state, the recurrence relation of each component is obtained, and the optimal solution is achieved by enumerating.
The optimization model of the balance between production and growth. The model is used to consider the transformation of cells in growth and production condition by periodic regulation. The aim is to explore whether it is necessary to regulate in this case and decide the regulation time.
I have also completed the wiki of the modeling part. The modeling mechanism is described in detail. The solution results are calculated by various software, and some principle pictures are made by myself. These four parts of modeling have been able to describe the whole project process completely, and have a prospect for the future. This modeling has basically completed the task successfully, and probably enough to meet the gold medal standard of igem.
In this project, I deeply feel the strength that the team can achieve anything. The team projects I've participated before are just small teams of two or three or four people like mathematical modeling competitions or college students' innovation and entrepreneurship projects. This is the first time a dozen people have participated in a large project. Team members coordinate their work or enable everyone to achieve the highest efficiency, which has brought me valuable experience. Although I am not a biology or chemistry major, but this experience makes me more confident in dealing with things in the future, so that I can complete other similar things more skillfully. After graduation, I may not go to the igem competition again, but I sincerely wish these brothers and sisters to go further and achieve better results in the future competition.
In the early stage of the project, I actively conducted literature research to find meaningful and suitable subjects for iGEM. During the brainstorming, I actively put forward my idea and discussed its significance and feasibility with my teammates to provide a kind of thinking for the team.
In terms of experiments, I was mainly involved in the work of the cell growth control and response team, designing experiments from scratch and carrying out experiments together with my teammates. In this process, I encountered many unexpected problems, and gradually solved them by consulting literature, teachers and classmates. Never thought of restructuring the carrier construction would become a big problem, from the beginning did not confirm the line began to experiment, the accuracy of the plasmid later replaced, encountered among a variety of unexpected problems, in the process of the construction of a recombinant plasmid, we tried all sorts of different ways, but the effect has not been very ideal, everyone in access to relevant information, consult the teacher elder sister, and the surrounding classmates, also to communicate and communication, and surrounding the iGEM team after the iGEM team communication and Peking University, from the two plasmids, they get in order to make full use of the two plasmids, After me and the players discuss decide to make a small change to our line, after a search information and ask the teacher our group decided to change a smaller molecular weight plasmid, god helps those who help, finally we build is successful, then in order to validate the promoter strength influence on subsequent expression, we in the iGEM's website to find the different strength of the promoter (strong, the strong and weak) to experiment, the results were surprising, promoter strength weak fluorescence intensity stronger instead, through discussion, we think LuxR may express too much hurt pLux open.
I think the iGEM contest answers the central question in synthetic biology - whether simple biological systems can be built and manipulated in living cells using interchangeable standardized components. Each team attempts to use a standardized library of biological module components to assemble artificial biological systems for specific purposes, and to manipulate and measure them using standardized genetic engineering methods. We used our spare time to cooperate to complete the corresponding experimental work, which fully exercised our independent academic ability and teamwork ability. The competition provided an international stage for students from different countries and different majors to communicate with each other. In the process of participation, I have improved my teamwork ability, logical thinking ability, English literature reading ability and other aspects. In the last period of time, I will work together with team members to contribute to the final perfect presentation.
My main contribution is in two aspects, experiment and speech.
In terms of participating in the experiment, I added "quorum sensing" to the overall idea of the project at the beginning of the group discussion. I completed the design and experiment of QS system with the team members.
In terms of attending speeches and exhibitions,when I went to CCIC and COFCO, I mainly presented the experimental design part.In July 7th, I hosted a IGEM meeting in Beijing.
From the very beginning, the team searched for materials, self-learning related background knowledge, and gradually cultivated their own research interests and experimental techniques.
As a member of the σ factor group, I actively participated in the construction of the experimental circuit. Enjoy the frustrations encountered during the experiment.
Throughout the project, I learned how to participate in teamwork. How to communicate and cooperate with each other can make the team most efficient. iGEM makes my research life rich and colorful!
Through the brain storm, the current project ATM is determined.
In the early stage, the whole project was divided into four major directions. I was fortunate enough to join the T7 squad. After a lot of literature research and many discussions of the team members, the route we designed continued to sublimate and finally determined the ideal route.
Based on the principle of appropriateness according to the local conditions, combined with the existing resources of the laboratory, we determined the feasibility of using the red fluorescent protein (mcherry), the chassis cell BL21 to verify our route and whether there is leakage expression in the mcherry.
Linking the cell growth team, the team members worked together to re-plan the ideal route 1 and determine the ideal route 2. I participated in the construction of the ideal route 2, and said that the teachers and sisters completed the relevant experimental operations.
Later, I re-planned the experimental route. I was responsible for the construction of plasmid 2. The ultimate goal of plasmid 2 was to identify the promoters of the three lycopene genes and to interface with plasmid 1 to maximize production. First, we need to verify the strength of the three promoters (PT7, PσB, PσF). In order to simplify the experiment, we chose red fluorescent protein (Mcherry) to characterize the three promoters and red fluorescent protein to plasmid pACYCDuet-1. And successfully introduced into the bottom plate cells, fermentation, and finally determined the strength of the three promoters by measuring the fluorescence expression of the three strains.
According to the strength of the promoter, the promoter sequence in front of the three lycopene genes in plasmid 2 was determined, and finally the plasmid 1 was ligated to achieve the purpose of maximizing lycopene production.
As a graduate student, I am mainly responsible for the design and implementation of the experiment in the BIT-China team. For the experiment, a brief description is to construct a population density sensing gene line and characterize it with a reporter gene. This is a long process of finding and building. Thanks to the help of the younger brothers and sisters in the lower grades, we were able to successfully find the components needed to build the genetic line. We had a tug-of-war with the difficulties, and the Gibson assembly failed many times, so I will come back. I tried OE, made an enzyme cut, designed the Golden Gate, and finally, after many failures, we succeeded. The construction of the gene line was only the beginning of the experiment, and in the following days, we characterized it from optimizing the conditions of shake flask fermentation to increasing the strain type. This way, the results have witnessed the growth of our group. Learn to use the iGEM website for Part Search. Design of the experimental scheme. Learning related software to design genetic lines.
From September to October, for me, for our T7 team, it was not a good time, the early construction of the line, the construction of the T7-Mcherry line, the construction of three plasmids later, the effect is not very good, Everyone is paying time and energy for the experiment, but Gibson's assembly, OE, and enzyme-cutting connections have all been tried. It is still not very successful. What makes us feel unreasonable is the problem of sending tests. When sending PaB-Mcherry, when we first sent the test, it was the sequencing failure. We called the customer service staff. The other party gave us the answer, the bacteria could not be raised, and then we extracted the plasmid ourselves and sent the test. As a result, the other party said that there is no signal, and it is like this before and after. We tried to design short primers and tried to change the method. The result is not correct. We can only start from scratch. iGEM is a comprehensive competency competition. The competition not only cultivated my research ability and experimental technology, but also improved me in teamwork, art design and even front-end programming. I believe that iGEM provides students with a wealth of academic knowledge, comprehensive skills, opportunities and experiences to develop international horizons, and students to build an international arena that communicates and competes with the world's best professors and students. Academic and career planning is a great help. Participate in IGEM to enhance creativity (through the subject inquiry process, give full play to students' imagination and creativity); logical thinking ability (designing the subject, checking the data, implementing the method is a great test of the students' logical thinking ability); English reading and expression skills (the whole process is the original English text, students use PPT and presentation in English); improve leadership and teamwork skills (the activities use group form, need to work together to complete various learning tasks); University laboratory study certificate; those who perform well can obtain the recommendation letter from well-known professors; those who participate in the international competition remote answer can obtain the certificate of the International Genetic Engineering Machine Competition. I think iGEM is a very high-quality synthetic biology competition and an interdisciplinary, all-round competition. In 2016, 42 countries and more than 5,000 players from all over the world participated in the iGEM competition. The entire competition lasted for one year and the process began with the formation of the team. After that, our team will learn a variety of theoretical knowledge of synthetic biology, and then open up the brain, trying to solve various environmental, material, and medical problems in a synthetic biology. The process of solving the problem includes predicting experimental results and conducting experiments through mathematical modeling. We can better play the role of the project by designing hardware and software and working with the community.
Liu ziyu, sophomore in Beijing Institute of Technology, majoring in BME. Not expert in experimenting but always dreaming of becoming an expert. Interested in new media and postor designing. Feels lucky to meet all the teammates and take prat in this great competition. Has faith in our ability to succeed.
background:
May background finishing
Summary of research published from September to October
σ factor:
April~June Work finishing + group will show
8.19~22 Assisting in the compilation of Shenzhen CCIC information
September~October wiki version σ part of the text
sponsor:
Team's past achievements
Speech:
7.7 Speech at the Beijing Exchange Conference
experiment:
July~September Plasmid extraction, PCR amplification, glue running, large intestine transformation, etc.
At the end of August, write the sigma factor experiment outline In early October, σ part finishing
Human practice:
7.8 Human Practice Research
8.6 Early communication and organization of university exchanges
Lycopene:
7.21 Overview + Method Comparison + Engineering Bacteria Selection + MEP Path + Picture Design Group will show
September to October lycopene background and experimental line
Brainstorming from proposing your own ideas to presenting at each group meeting, constantly advancing your own projects.
In the final documentary research, the basic circuit of the T7 system was proposed and continuously improved and improved on this basis. At the beginning of the experiment, the design of the circuit was verified, and the experimental circuit was later changed to determine a theoretically and practically feasible circuit.
Research on the literature on transcription resources, on the one hand, statistics on traditional methods of resource allocation, and the formation of written materials; on the other hand, from the constraints of traditional concepts, propose a different concept of transcription resources.
Join the σ group to assist the younger brother to carry out some experimental operations and focus on doing some research and improvement on the line.
Join the sponsoring group and try to get some sponsorship.
Check out some of the literature related to resource allocation to enrich your knowledge and present your ideas in discussions with everyone. Help the modeling team find relevant models and make constructive suggestions, such as Hill model, RNA polymerase distribution model, etc.
Following the experiment of the σ group, the most successful one was to pick the correct colony with mcherry.
The second is Gibson. After the transformation of the large intestine, colonies were found to have risen.
Team optimization of the route, through the literature, to see the previous year iGEM project designed 10 a negative feedback dynamic balance line based on antisense σ factor and antisense-antisense-σ factor.
Design the T7 negative feedback line. Complete the construction of the σ line with everyone. Help the growth team measure the fluorescence value of the fermentation broth
People in today’s society are under increasing pressure，so in the brainstorming, I want to design a pressure sensor to let people feel their pressure in time, through the review of the literature and the discussion of the group meetings, I feel that there are still many shortcomings in the implementation of my own ideas, but in the process, I have learned a lot.After discussion at the group meeting, we finally decided to do resource transcription distribution,I joined the sigma factor group.Because of this lack of knowledge, I started a lot of literature reading. After a lot of knowledge accumulation, I learned some knowledge that can be used on our route, finally, together with everyone, we will form the route of our group.As the leader of the sigma factor group, work with everyone to complete the experiment carefully, reasonably arrange the task division of the team members, and analyze the problems in the experiment in time.Our group successfully constructed a preliminary route and found a fluorescent leak,we tried to do some verification experiments. During the verification process, we found that our pσB and pσF are orthogonal and do not crosstalk with the internal σ factor of E. coli. We initially think that pLUX is leaking.Actively cooperate with other teams and team leaders to complete various tasks,and present my own ideas at each group meeting and seriously discuss with my partners.Participated in the part standardization work of our group.
Search for papers, participate in brainstorming, and propose quorum sensing system. Join the quorum sensing system team and finish many experiments, like plasmid extraction, PCR amplification, glue running, etc, from June to October. Collaborate with BIT team and verify each other’s group result. Organize and participate in Beijing iGEM Exchange Symposium. Complete the text of the industrial application and project meaning of the background section, the text of Beijing iGEM Exchange Symposium and collaboration with BIT team in the human practice section and the text of notebook of quorum sensing system.
In my team, I’m responsible basically for: information/academic search, such as negative feedback loop, how to control production from the perspective of individual cell growth; experiment conduction, including T7 experimental group and leakage-prohibition system building; human practice program conduction— I was one of the speakers in Jul. 7th Beijing Meet-up, organizer and video maker of the video info session in RDFZ (High School Affiliated to Renmin University of China), the main contact in our collaboration with team Tsinghua; the edition of words on wiki concerning the parts I have been working on. What’s more, I was one of the two writers of team advocating video and organized the filming of it.
In April, I was involved in brainstorming possible projects for the team. In may, I conducted a literature survey, searched some materials about t7, and predicted some possible situations. From June to August I participated in the early experiments of t7. From September to October, I was mainly responsible for the supply of notebook, part of HP and some t7 related materials. And on July 11th, I returned to my Alma mater to give a speech about iGem. At the end of August, I attended CCiC and communicated with China iGemer.In April, I was involved in brainstorming possible projects for the team. In may, I conducted a literature survey, searched some materials about t7, and predicted some possible situations. From June to August I participated in the early experiments of t7. From September to October, I was mainly responsible for the supply of notebook, part of HP and some t7 related materials. And on July 11th, I returned to my Alma mater to give a speech about iGem. At the end of August, I attended CCiC and communicated with China iGemer.
I joined the team midway. When I tried to understand the iGEM competition, I was deeply attracted to it. I am also very honored to use my art design skills to help the team. Start with the team's logo design. I am responsible for the entire team's uniforms, exhibiting posters, power points for presentations, website design, photographs of team members, etc. At the same time, I also participated in the early experiments to achieve some results.
I was mainly responsible for the art design, including the design, sizing and customization of summer and winter team uniforms, as well as the team's human practice and the production and artistic processing of the final contest PPT. I joined the iGEM team midway.So when I tried to understand the team project and the current progress, I entered the T7 group to conduct some experiments in the summer vacation. While mastering more basic experimental skills, I also deepened my understanding of the team project itself. Although hard but harvest a lot. Finally, I would like to thank everyone in the team for their efforts. What's more, I would like to thank my boyfriend who, as a member of the team, could complete the task so excellently and make my idea come true.
I am mainly responsible for the construction of the WiKi, including the docking design with the art team, the docking text scheme with the text group, the realization of some website special effects, and the construction of the overall framework of the website.
As a student of Computer Science, I am mainly in charge of the team's WiKi. I designed structure and implemented the visual effects of the website. What's more, I also participated in polishing media files.