Difference between revisions of "Team:HUST-China/Practices"

In our Human Practice this year, we majorly concentrated on promoting the concept of synthetic biology through interdisciplinary communication and field practice at fishery industry. During this process, we gained a better perception of the development of synthetic biology in China, and also learned valuable practical knowledge from experts, public and other iGEM teams.

Communication with experts in different disciplines

In the preparing stage of the project, after early investigation and brainstorming, our team chose applying synthetic biology in silt reinforcement as our project theme. To gain more information on this topic, we consulted Professor Zheng Junjie from Civil Engineering College of Huazhong University of Science and Technology. Prof. Zheng is an expert in civil processing who is also experienced in microbial silt reinforcement.

Our teammate, Shuyan Tang is talking with Prof. Zheng

Prof. Zheng explained the current role that Biology plays in the interdisciplinary study of silt reinforcement. Bacillus is widely applied in most microbial silt reinforcement studies for its high performance in biomineralization. It can release massive CO2 from respiration, immobilize surrounding Ca²⁺, and generate carbonate deposition, thus accomplishes the silt fixation. For now, scientists are still optimizing the experiment condition and questing for better strain. Silt reinforcement technology has a bright future in engineering science. It can not only be applied in ancient architecture repairing, sea filling and land accretion, but also help build artificial reefs and aquafarms. Currently, most artificial reefs are constructed through chemical methods. They are made by cement concrete, molded into certain shapes and put into the ocean to help accelerate the biodiversity evolution process and restore the ecological environment.

Prof. Zheng’s introduction on artificial reefs raised our interests, and the effect of ecological restoration brought by microbial artificial reefs was what we hope to achieve by applying synthetic biology. After team discussion, we set a new direction for our project and presented it to Prof. Zheng. We intend to use the marine yeast as our chassis, which has survival advantages in marine environment. We hope to improve its survivability in special marine environment and use surface display technology to attach the yeast to the sand, which can solve the inefficiency caused by stream. It will not only enlarge the application area of yeast, but also improve the solidification capacity. Moreover, as the growing resource consumption and pollution are causing more and more environmental problems, scientists are seeking solutions in the light of biological science to accomplish the task of energy conservation and environmental protection. Our project is going to make an attempt by using environmental friendly adhesives technology, which will bring much less pollution to the environment.

After listening to our presentation, Prof. Zheng praised our idea and creativity. He said that although it was the first time that he heard about synthetic biology, he believed that it would be exciting to turn the idea into reality. Interdisciplinary studies are more and more necessary for scientific progress now. Prof. Zheng told us that in the field of civil engineering, the existing chemical and physical technologies have grown quite mature and complete, but there are still bottlenecks in its development and further breakthroughs require inspiration and methods from the study of other disciplines, for which he is also seeking cooperation with professors from other disciplines. “Synthetic biology might be THE WAY to break through.” he said.

Prof. Zheng also told us that microbial silt reinforcement technology still requires further developement. So far, there are room for improvement in terms of some physicochemical properties of the product, such as its resistance to pressure. Therefore, it is necessary to prove that our product is superior to existing technologies by conducting soil property experiment. Prof. Zheng suggested that we can perform experiment with small particles sand material, because the biodegradable adhesive we are going to use is flocculation protein, and over huge particles may counteract its solidification effect.

Suggestions

In addition, Prof. Zheng expressed his concern on the safety issue. He pointed out that if our project is applied in an open environment, necessary measures, such as fencing the area, must be taken to make sure that the diffusion of the engineering strain is under control; otherwise the diffused strain may cause the solidification of seabed soil, which will affect the survival of marine plants and animals. The safety issues were always the topic that we attached great importance to, so we began to discuss how to regulate the expanding of the strain colony. During discussion, we came up with the idea of experimenting with auxotrophic marine yeasts, whose diffusion can be regulated by controlling the amount of nutrition. In the end of the discussion, Prof. Zheng gave credit to our creativity and said he was willing to offer us further help on this project.

After meeting with Prof. Zheng, we gained deeper understandings on microbial silt reinforcement. These new insights strengthened our resolve in employing clearer and healthier material to build the artificial reefs. After information exchanging and discussion in our team meeting, we decided to choose Yarrowia lipolytica as the chassis, which has a preferable survival rate in the marine environment. We will put the strain together with sandy soil into the ocean at fixed point to form artificial reefs. Another benefit of this material is that the carbonate deposition generated by the strain will cause natural death of the strain without introducing new toxic or chemical materials to the environment. It also mitigates the diffusion problem, which is the highlight of our project. After deciding the topic and main direction of our project, our next step is a field trip to artificial reefs.

Visit to Zhejiang Marine Fisheries Research Institute

Before our field practice, we visited Zhejiang Marine Fisheries Research Institute (MFRI) and met Professor Wang Wei Ding, an expert in aquafarm and artificial reefs. He is the scientific advisor for aquafarm construction in Zhejiang province and senior engineer at Zhejiang MFRI.
Zhejiang aquafarm has gained impressive achievement in the past half year and has achieved the goal of preliminary ecological restoration: the artificial fish reef released was full of moss and small amount of fish live in it. CCTV has filmed a documentary series based on Zhejiang aquafarm.

Photograph of Jiatong Liu, Guozhao Wu and Prof.Wang. (from left to right)

Prof. Wang introduced two sorts of artificial reefs to us. The first one is casted by reinforced concrete with certain shapes of molds. The structure of the molds is essential and studied by many scientists in China now. The second kind of reef is constructed by throwing waste tires and subway carriages in to the ocean. This method is widely applied in America and Japan. Prof. Wang found our idea of building artificial reefs in the way of synthetic biology very interesting. He told us that the effect of waste materials was not satisfactory and massive reinforced concrete consumption also brought lots of trouble in transportation and manufacture. Employing new materials will bring new dynamic to this study. Therefore, he believed that our idea of using microorganism to reinforce sandy soil in the ocean was very impressive and creative.

Our teammate was visiting the Zhejiang Marine Fisheries Research Institute.

Suggestions

Prof. Wang also offered us some professional advices. To help our product sinking in the ocean, he suggested us to employ some weighting device. To make it more convenient for fish to live and hide in the reef, we can make our product porous by using molds; the resistance to pressure of our product and its reinforcement effect also need to be tested and strengthened to adapt to the complex marine environment.

At last, Prof. Wang reminded us that the efforts of fishermen are also very important for the maintaining and managing of artificial reefs. Especially in our project, the microbial artificial reefs may take longer time to show the effect and require constant nurturing. Therefore, we need to arouse the enthusiasm and participation of fishermen and inform them the importance of artificial reefs in ecological restoration, thus, a field practice to a fishery is imperative.

Field trip to Zhoushan Fishery

When we arrived at Zhoushan Fishery, we were impressed by its scale and prosperity. However, further investigation also revealed its problems. Due to ecological damage, the total fishery output has dropped tremendously in past years, thus the restoration of ecology will be very important to the future development of fishery. Statistics has already showed the great ecological and economic benefits brought by artificial reefs. Therefore, in the premise of ensuring safety, our project of building artificial reefs with synthetic biology methods will bring factual benefits for the fishery and fishermen.

Zhoushan Fishery

To gain a full view of fishermen’s attitude and understanding to artificial reefs by biological method and ecological restoration, we issued questionnaires and conducted interviews among local fishermen and practitioners.

Field trip report and questionnaire analysis (Click to see details)

1. Research purpose

During our visit to Zhejiang Marine Fisheries Research Institute, Prof. Wang emphasized that the efforts of fishermen are vital to the maintaining and managing of artificial reefs. To ensure that our project can be actually put into use in fisheries, we need to arouse the enthusiasm and participation of fishermen and inform them the importance of artificial reefs contracture and ecological restoration. Therefore, we hope to get a clear view of fishermen's work environment and their actual attitude towards artificial reefs.

Fisherman is filling the questionnaire.

3. Results and Discussions

In general, both questionnaires and interviews showed that the condition at Zhoushan Fishery was not optimistic.

The overall answer distribution is showed in Figure 1.

Figure 1:The questionnaire results in general(“NULL” is also a choice taken into consideration)

Figure 2: The result after removing all null answers. The answer of some questions shows obvious unify.

Figure 3: Other result of those choosing negative choice in Q4. As you can see,“NULL” appears in many groups.

Figure 4: Other result of those choosing positive choice in Q4.Then, ”NULL” disappeared.

We also found that many respondents had little knowledge about ecological restoration measurements, thus gave ambiguous answers to certain questions, which caused incomplete and biased results for our analyzing (Figure 3). Therefore, we took out distracting feedbacks according to the answer of Q4, and got a relatively clear result (Figure 4).

Q1 and Q3 analysis
We can see from figure 1&2 that the answers towards Q1 and Q3 are convergent:
Q1. Do you feel that the output of Zhoushan Fishery is decreasing in recent years? Yes
Q3. Do you think that Zhoushan Fishery has overfishing problem? Yes, the problem is very serious.
Therefore, we can draw the conclusion that most fishermen agreed that the Fishery was under bad management.

Q6 analysis
Q6. What’s your opinion on government’s restrictions on fishing tools, methods and time? I understand the necessity. But it’s hard to comply with them in actual activity.
The result showed that 85% of respondents held supportive attitude to the policy, but the implementation of the policy came across many problems. Most fishermen said that they hoped to improve the fishing condition but were not willing to sacrifice their personal interests.

Q7 analysis
Q7. If you think the policies are not carried out very well, what do you think might be the reason? (You can select more than one answer.)
A. Lack of finical support.
B. Lack of technology support.
C. Government didn’t attach great importance to the problem.
D. The fishermen didn’t attach great importance to the problem.
E. The regulatory system is not complete.
F. Lack of legal publicity.
G. The fishermen’s interests are impacted.
H. Other_____________________________

Figure 1: X axis: question number, Y axis: number of chosen answer.

According to Figure 5, most respondents, especially fishermen, thought that "Government didn't attach great importance to the problem". However, we learnt that since 2009, the government had been making more and more effort on ecological restoration at Zhoushan Fishery. Especially in 2013, large scale of artificial reefs was sunk into the costal sea. On the other hand, during interview of local public, we found that local government would broadcast videos about artificial reefs on televisions and internet at regular intervals. However, due to lack of education, the fishermen couldn't see the long-term benefits of these technologies. Instead, they tended to blame the government for not acting efficiently to the problems.

In all, the environment at Zhoushan Fishery are under terrible condition. Fishermen’s ignorance to technologies and unwillingness to sacrifice a little interest for long-term benefits cause more difficulties to ecological restoration.

We drew the conclusion that in spite of the bright future of artificial reefs, lack of understanding and support from fishermen severely impaired its ecological restoration effect. This also coincided with professor Wang's worry.
After the discussion, we figure out that in order to enhance the construction of artificial reefs, the publicity of the technology among fishermen and the public is essential. Ensuring the transparency of government policy and regaining the public's trust are the foundation to carry out policies that benefit the public, and only then will the task of restoring ecology be eventually fulfilled.

Investigation

Interviewing a fishery retailer.

We also randomly interviewed some fishermen, practitioner and local residents.

What we found in our investigation is the determination of Chinese government in marine ecological restoration and the public’s wishes to improve the living environment. But due to economical pressure and lack of scientific knowledge, some fishermen and practitioners still have doubts about the new technologies. In our field trip, we introduced some basic knowledge and its potential ecological and economical effect to local people and fishermen. It reduced some fishermen’s doubts and they began to hold positive attitude to the application of new technologies.

Discussion

Coming back from the field practice, our team members had thought a lot about the development of synthetic biology. In China, synthetic biology is still a novel technology that is not familiar to people. The public knows little about its use in environment protection, medicine, and engineering. And even in interdisciplinary studies, scientists generally focus on filtering dominant species and improving the conditions of strains domestication and little of their research involves integrating favorable properties of different species by means of synthetic biology. Thus, it’s meaningful to spread the idea of synthetic biology to more researchers in the interdisciplinary field and offer them a new perspective in their study, which is also conducive to popularize synthetic biology.
In addition, there are also challenges in the development of new technologies. The safety issue and supervision system must be ensured in the applying of synthetic biology technologies. To achieve these goals, instead of concentrating on short- term economic benefits, we must have a long-term vision in the development. There is still a long way ahead for synthetic biology to go, and we hope to constantly make our effort on it.

Project-in-action: meeting with other iGEM teams

While promoting our project, we also attended several conferences and shared ideas with iGEM teams from different universities and countries.

Meetup in Wuhan

iGEM teams from WHU, HZAU and HUST held a seminar in Wuhan University, during which we exchanged ideas about the progress of our projects and discussed existing problems. We also reached the consensus to establish Wuhan iGEM Committee in the future and held conferences and Science Fair at regular intervals to spread the idea of synthetic biology.

Photograph with HUST-China, WHU-China and HZAU-China iGEM teams.

We are introducing our project

2015 iGEM conference held by NCTU

NCTU iGEM conference is the largest and the most experienced iGEM conference in Asia. During the conference, we were able to share our ideas with teams from different Asian countries, and they also gave us many valuable suggestions. The iGEM team leader from SYSU suggested us to enlarge the scale of our microbial silt reinforcement study, such as applying it at the Loess Plateau which is the upstream region of the 2nd longest river in China, the Yellow River. This region is facing severe problem of soil and water losses in long time. Those new ideas gave us a new inspiration for our future projects and we appreciated the help from all iGEMers!

Photograph with Asian iGEM teams at NCTU.

CCiC (Central China iGEM Consortium)

The Central China iGEM Consortium meeting was held in Peking University this year and 31 teams from all over the country attended it. In this meeting, we presented our project to all the participants. A professor from Lanzhou University gave us interesting suggestions on the selection of techniques and devices. According to his experience in studying Yarrowia lipolytica fermentation, he recommended us to use multi-copy to increase the strain’s expression quantity and to use culture devices with large radius and low height in Yarrowia lipolytica culture, which is more beneficial for strain cultivation.

We are introducing our project at CCiC.

Photograph with teams at CCiC.

Effort on the publicity of iGEM and synthetic biology

In the preliminary stage of our project, we found that the public knew little about synthesis biology. We hope to grasp every opportunity to introduce the concept of synthesis biology to well-educated people. Therefore, we signed up a scientific research innovation contest held by Huazhong University of Science and Technology.

During the contest, we introduced the idea of our project, knowledge about synthesis technology and iGEM competition by presentation and posters. Our project was widely appreciated by judges and other competitors and won the gold Prize.

We also spread the idea of iGEM and synthesis biology to students and teachers who were interested in scientific research. Most of them hadn’t heard about synthesis biology before. During the contest, we got the opportunity to introduce the basic ideas of synthesis biology to teachers and students, especially the concept of future biology engineering. This is our first step in the promotion of synthesis biology. We hope that in the future more and more people will be attracted by it and make further development to this promising discipline.

People are interested in iGEM, synthetic biology and our previous project.

Explaining to Professors.

Introducing to public.

Conclusion

In the preliminary stage of our project, we found that the public knew little about synthesis biology. We hope to grasp every opportunity to introduce the concept of synthesis biology to well-educated people. Therefore, we signed up a scientific research innovation contest held by Huazhong University of Science and Technology.