Difference between revisions of "Team:ShanghaiTech/Integrated HP"

Integrated
Human Practice

Institution visit

This year, we visit several companies and hospitals to collect practical experience and application possibilities for our project. On one hand, we obtained suggestions about the host and the part o-ribosome we used. On the other hand, we have found potential for our system to be used in intestinal administration and various other directions.

Shanghai Realbio Technology

Shanghai Realbio Technology (RBT) headquartered in Minhang District, Shanghai, is a government-approved company that specializes in gene technologies and health services. Presently, 16S rRNA sequencing is one of their main scientific research services. We have learned that there are difference in the sequence of 16sRNA in different microorganisms and each 16S rRNA would recognize different Shine-Dalgarno sequence on the target mRNA. Inspired by RBT, we thought it is necessary for us to improve the o-ribosome we designed with mutated 16s rRNA to confirm the accuracy and expand the range of application for our system.

Besides, RBT has designed various products in detection for the gut commensally microbiota. Their introduction enlightened us to apply our system to intestinal administration by redesigning certain gut microbiota. However, we further noticed that practical application use this method seldomly because of the complex procedure it covers. But it might be possible to produce helpful substances, for example, serotonin.

Shanghai Tongji Hospital

Shanghai Tongji Hospital is a comprehensive hospital integrating medical treatment, education, scientific research and prevention. With the initial envisage we generated in RBT, our team communicated with the relevant doctors in the hospital about the gut microbiota and drug administration. The detection and administration of intestinal flora requires high accuracy. Currently, related drugs and methods only play a supporting role. At the same time, many drugs have a narrow range of efficacy, and only when the drug concentration is in a narrow range, can they play an effective function.

After listening to the introduction of our project, the doctors suggested that we could focus more on how to maintain a consistent supply in medicine secretion, that is, maintain a regular quantitative output.

Bioclub

Bioclub is an innovation center for healthcare innovation companies focusing on accelerating the industrialization of scientific research products. From the dialogue with Manager Fan, we learned that the domestic human microbiology industry has just started. In order to realize the transformation of laboratory products into market products, industrial testing, simulation experiments and market research are required. During this process, the joint efforts of researchers and marketers are needed.

To reach a final industrial project, domestic human microbiology industry faces a huge challenge in building the links with patients. Presently the medical product market mainly concentrates in hospitals but not relevant companies. This is because public have barriers in understanding academic knowledge behind the project, but believe in the instruction of doctor and the reputation of hospital. Therefore the transition of laboratory product should focus more on the certification of safety and stability that public admits as well as effective publicity in both relevant knowledge and products.

What we learned is that to apply a lab-designed system to the human microbiology industry and achieve the final application outside the laboratory, it needs greater efforts testing safety and stability.

Communications with experts

Dongliang Wang

Dr.Wang is an expert in the field of clinical immunology, and also the chief doctor of affiliated cancer hospital of Harbin Medical University. We came up to him after we had an idea of using our project in medical field, and ideally tried to lower the secretion level of inflammatory factor, in order to prevent CRS from happening. Prof Wang highly affirmed the creativity of our project, but he also pointed out some misconceptions we had about CAR-T therapy. The true need of CAR-T development isn’t about restraining the power of T cells, but to intensify its ability of killing cancer cells, as well as the ability to pass through some barriers that surrounded solid tumors. His humorous words and metaphors about the theory of CRS vividly explained the cause of CRS and how our project may affect this disease. By amending the directions where we should consider, he really gave us a lightbulb on the way to the application of our project. To our great gratitude, he also generously recommended another professor specialized in immunology for us, named Wenjun Zhang, and he helped us arrange the meeting with Dr. Wenjun Zhang.

Wenjun Zhang

Grasping inspiration, we came further in utilizing our project to cure the CAR-T accompanied CRS. Through the kindly help of Dr. Dongliang Wang, whom we interviewed earlier, we managed to have a Skype interview with Dr. Wenjun Zhang, an expert in CAR-T therapy and the resultant CRS. The initiation and development of CRS were better introduced in detail during our talk, some of which effectively corrected our deviated understandings. The true cause of CRS, for instance, was identified as macrophage instead of CAR-T cells and the innate antibody-antigen interactions was also voiced as highly timely, with no requirement of a speedy switch-like control. Albeit insufficiencies, Dr. Zhang and Dr. Wang spoke highly of our idea and encouraged us to investigate other clinical possibilities with self-immune diseases proposed as an example. Their professional suggestions have been substantially helpful in the ensued exploration of application paths of our project, while their patience and approval have powered the process as well.

Haopeng Wang

To explore other possibilities of our project in immune diseases, we visited Haopeng Wang, affiliate professor of ShanghaiTech, whose research area focuses on the T cell activation in cancer therapy. After a brief introduction of our project, he expressed his appreciation of the repetitive-switch ability achieved through our circuit, yet meanwhile identified the range of our control targets - mere exogenous genes - as a core limitation. With his help, we narrowed the application direction of our project to proteins that are both indispensable yet disadvantageous toward its surroundings, especially human body. Special stress was put on the fundamentality of our circuit during the talk - we were motivated to change the input signal from molecules to heat, light or even ultrasound, which extended the probabilities of application.

Dong Wei

To figure out potential industrial and agricultural applications for our circuit system, we talked to Dr.Wei from Biological Refinery Lab of Sustainable Technology Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences. Dr Wei focuses on production of biofuels (cellulosic ethanol and bio-butanol) and utilization of agricultural residues. Dr.Wei considered our project to be quite novel as few people had come out with enhancing the sensitivity of system to input signals by constructing a circuit. However, he also pointed out that our circuit system would not be that necessary in industrial production. There are two reasons for that. First, the induction of industrial production is far rougher since the fermentation mainly pursues to gain higher yields. Second, due to the limitation of cost, for the protein may be toxic to cells, the researchers are more likely to produce the target products as many as possible in one time and sacrifice the cells in the fermenter. Indeed, he recommended us to apply our system into research or medical field which have higher requirements for precise control in yield and halflife.

Junsong Sun

Professor Junsong Sun is an expert in metabolic engineering and enzyme engineering. He has rich experience in bacteria experiment. As Prof. Sun taught us the BIO1206 Microbiology, he offered us a lot of help on bacterial expression experiment techniques. For example, he figured out that the 'laboratory contamination' under 400 magnified visual field was just unusual phenotypes E.coli growing under pressure.

Chaopo Lin

When we considered to make the circuit of negative feedback loop (NFBL) for our project for the first time, we wanted to make sure that our designed loop would work as predicted, not only for every single component but also for the combination.

Prof. Lin shows great interest in studying complex networks of biological systems by simplifying the network nodes. He indicated us that the function of the system is decided by the topological structure. Basically, our design is a network with three nodes which is the simplest form of system biology model. If it uses the feedback control, it must gain the basic character of adaptability. He aslo made us aware that our design can be described as an improvement of simple induction system. As we still show the doubts on the actual result of the loop, he recommended us to look for some real examples in organisms to give us deeper understanding of the function of the negative feedback loop.

Min Zhuang

To further improve our project and get full preparation for the final presentation in Boston, we invited Prof Zhuang, secondary PI of 2017 iGEM team Shanghaitech, to our regular meeting.

Prof Zhuang suggested that to create a new system, we should use exact example to show its advantages and disadvantages. Signal regulation has various form, including liner and non-liner. What we should consider thoroughly was how to satisfy different signal form with our system.

Besides, Prof Zhuang recommended us to clarify the relationship between our lab project, modeling and human practice. She emphasized that in order to combine all these three parts, our team should work out how to engineer our system for specific applications.

Haotian Guo

As the host of the 5th Conference of China iGEMer Community, we received attention from experienced iGEMer Haotian Guo. We had several deep conversations, which gave us lots of feedbacks.

Finding that the small subunit has a long half-life time, we used to have serious concern that would reduce the accuracy of our time-control-system, as the orthogonal ribosome is the most important part in our system. Guo explained that although the small subunit’s half-life time is long, what our system produces was a 16s rRNA, rather than a mature ribosomal small subunit, who will degrade much faster relatively. He pointed out that we must consider the situation in a more holistic way. In practical situation, the E.coli will multiply constantly and rapidly, which means the o-16s rRNA would be diluted in each E.coli. Moreover, we need to consider it in a more holistic way. In practical situation, the E.coli will multiply constantly and rapidly, which means the o-16s rRNA would be diluted in each E.coli.

Guo repeatedly asked us about the necessity of adding the orthogonal ribosome into our system. In Guo’s opinion, the three-node-model is effective enough to reach our goal of fast control. In this way, the orthogonal ribosome is not necessary, instead, it will increase a burden to the host. We argued that it was unavoidable that the system will affected by the host due to the complexity of our three-node-model. To expect our experiment’s result to follow our mathematical modeling better, our system had to be more orthogonal to the host system. That is why we must pull the orthogonal ribosome in it. He doubted that in this case, why don’t we use cell free system to insulate the ribosomes. We contended that we expect our system to have wider application prospects, such as environmental monitoring and mitigating cytokine release syndrome, all of which require biological vectors. The cell free system shows limitations in these fields.

However, we still make some changes follow Guo’s suggestions. A plasmid without o-ribosome is constructed, only retaining the three-node-model, which can be used for applications that do not need orthogonal ribosome. Meanwhile, we still pay more attention to our system with o-ribosome, as it shows more wide application prospects.