Team:SYSU-Software/Human Practices
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Team:SYSU-Software/Human Practices
Modeling
This year, in an attempt for a more inclusive and comprehensive project, we conducted human practices across many disciplines ranging from molecular biology, opto-genetics, biosafety, to computer science and jurisprudence. Human practices have shaped our project in a subtle yet profound manner.
Silver Medal
- Wet-lab Experiment
After we explained the specific idea of the whole project and the current progress to Professor Luo Guanzheng, Professor Luo expressed great interest in it and gave us some suggestions: The first is to emphasize that the iGEM competition is more about innovation than comprehensiveness and direct practice. We should focus on innovation and not let it be limited by our own skills; Then the teacher pointed out that we might have problems with the size of the database and the time it took for users to obtain information. At the same time, we hope that we can seriously consider in which specific applications of photocontrolled protein have higher cost performance or irreplaceability than other methods, not limited to the applications found in the current literature.
- Optogenetics Invest
With the goals of our software set, we went to visit Dr. Yuehui Tian, who is specialized in optogenetics and currently a researcher at Sun Yat-sen university, for advice. Dr.Tian approved the potential of our project to help researchers in relevant fields, proposing that we lay more emphasize on its application over metabolism rather than on neuron, and kindly responded our questions on methods of quantify the degree of protein aggregation by introducing us to the widely used technology of quenching. He also gave us many suggestions on equipment setting and experiments operation.
- Questionnair
After the prototype of the project was established, we designed a questionnaire for several key parts of our project in order to clarify whether the features needed to be deepened and expanded, and put it on the iGEMers' exchange group in China to collect feedback from fellow users for summarization.
SYSU_Software is an iGEM Software Track team focusing on opto-controllalbe proteins.If you could link a light-controllable protein to another functional protein, you would expect to accomplish which functions below?
If you obtain a fused light control protein, what cell would you apply it to?
In your own experiment which involves fusing two proteins ,where does the design of the linker come from?
To what extent do you think using the algorithm for fusion protein activity prediction will help in subsequent experiments?
Do you think it is feasible to link target enzymes by light oligomerization of photosensitive proteins so that they aggregate in the light to a controlled extent?
By what means do you prefer to choose to control the expression intensity of a transcription factor.
To what extent you think that by designing fusion proteins of light-controlled oligomerization proteins and transcription factors, it is possible to control the effective concentration of transcription factors by changing light?
- Mini Class
In order to make this field known to more people, SYSU-Software held a science popularization seminar on September 26 with the theme of "Synthetic Future". It introduced the SYSU-Software project to freshmen majored in biology and popularized the relevant knowledge of synthetic biology and bioinformatics to stimulate interest in synthetic biology in freshmen.
In this presentation, we unveiled the mystery of synthetic biology from concrete examples, explained the basic ideas and design principles of synthetic biology through one question, and introduced the related concepts of bioinformatics, showing the infinite prospect of intertwining the two disciplines.
As one of the teams participating in the 2021 igem competition, we took this presentation as an opportunity to show more about the stormy journey of our software team and the project we are going to participate in this competition: "Phoebus".
Phoebus is a optoi-controllable element designer as the core of the automation control platform, through the design of a light-controlled element, to help scientists to achieve a high spatial and temporal precision control of cellular activities through light control. Through the presentation of the project inspiration, basic principles and underlying algorithms, the participants had a deeper understanding of SYSU-software, what we are doing and what we aspire to do.
Integrated Human Practices
Biotech Company
Vland ™ is a multi-national company with a diversified and global reach committed to theinnovation of enzymes, probiotics, vaccines, bio-medicine and the discovery of biological solutions to other traditional industries. Vland actively promotes an innovative environment and supports the use of "ecomagination" and"healthymagination" in order to facilitate the discovery of solutions which deal with the most challenging ecological problems. Innovation comes from Vland ™ ‘s guiding philosophy of using biotechnology to restore the ecological world. Remaining committed to the development of bio-industry, we strive to build a comprehensive and diversified group of world-class high-tech biotechnology enterprises.
Q：Do you think there are many cases in production and research where the production rate of a substance has to be continuously and dynamically adjusted (including periodic oscillations, different production rates at different stages of growth and at different times of the day, etc.)?
A：From a production point of view, the plant is generally looking for a stable output. Especially from the fermentation engineering point of view, it is to control the simple growth of the strain in the early stage, whose medium and control conditions are determined in advance, rather than real-time regulation. So our project is difficult to apply in a dark environment like a fermenter is difficult to apply. But R&D and production are two different things, and our project ideas may have more room in the R&D process.
Q：Producing a substance generally requires a multi-step reaction. And the multi-step reaction can be used to verify exactly the enzyme aggregation part of our design? Do you know if this is convenient to build in E. coli
A：You can look for fungi or plants about some pathways that synthesize pigments, such as lycopene. All of these pathways are more fluidly constructed in E. coli which you can easily find some protocals.
- Biosafty
Biosafety has always been the first priority of scientific research, and the premise of all research is not to violate ethics and social safety. We specifically visited Zhumei He, a professor in the School of Life Sciences at Sun Yat-sen University. We consulted him about the bioethics and biosafety part of the software.
Q：What are the effects of fusion protein leakage from experimental bacteria?
A：Generally there are no safety and ethical issues, and the risks can be avoided under normal laboratory operations.
Q：The platform of the software is open for public, what if someone used to synthesize hazardous substances?
A：We can't control his use, but we can enable the appropriate user alerts.
Q：What are the ways in which gene fragments can leak from bacteria?
A：Horizontal transfer of genes can happen, but genetic engineering has a history of near 50 years, but there are still a few incidents in this area, and the requirement is that the experimental operation must be standardized.
Q：E. coli is a relatively safe strain, but does the addition of the new sequence require more stringent management?
A：It is still necessary to regulate the requirements because we are not in a position to assess whether such a new strain will be more viable in the field for the time being.
Q：As a design platform, how can we reduce risk for users and keep us away from risk?
A：The starting point should be security conscious; specific questions need to be advised and warned, and the platform should provide a user agreement.
- Intellectual Property
Q：In one part of our project, we integrated several databases from the web, some of which were obtained by direct download and some by web crawling. Is there any illegal use of databases in the above process? And please ask what we need to add and pay attention to in that process.
A：We need to develop a user agreement, which is legally required for the users who use the software. Our project involves more conventional terms. It is only necessary to prepare some basic terms and conditions, disclaimers, the user's results to be owned by themselves, and we only provide a platform for communication and optimization.
Q：In the part of structure, is there any infringement problem in the process of keeping part of an open source software and modifying another part of our software by ourselves?
A: Using an open-source software as an auxiliary function, we take little responsibility. We just need to indicate the citation as the original inventor required.
- Phoebus community
We consider "Phoebus community" as an indispensable component of human practice for our software. Through this platform, not only can we provide a convenient thought-exchanging platform for synthetic biologists with full respect for users'privacy, we will also be able to gather practical advices from our users, updating and improving Phoebus to make it more user-friendly and develop better functional plugins to fit in more real-time senarios that scientists may faced in the future.
- Synthetic Biology Concept Promotion
We will explain the theory of synthetic biology and introduce the iGEM competition to the students stimulate their interest in synthetic biology and biology in general. Posters will also be printed on site to introduce the projects of our teams.
To deepen the students' impression, two interactive mini-games were designed to let them understand synthetic biology in the game, and after completing the little games, they could get a customized souvenir from the team.
