Integrated Human Practices

Overview

From the beginning, we wanted to build a project which is responsible and good for the world. This has been carried out through two main axis:

  1. 1. Integrated Human Practices

  2. 2. Education and Communication.

1-1 Build a diverse team and Assist in brainstorming

We get multidisciplinary: consider bringing Biology students; Medical students; Students majoring in artificial intelligence; industrial designers onto your team.

During the brainstorming, we assisted team members to determine that our project is a useful application of synthetic biology and our project goal through a wide range of background research. Finally, we roughly determined the direction of the project: synthesis of biological fertilizer with composite functions. Finally, we counted and compared the advantages and disadvantages of existing herbicides, which further confirmed the practical significance of our project.

This work is presented in our Project background/description pages.

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Reference:

[1] Yan Yan, Qikun Liu, Xin Zang, et al. Resistance-gene-directed discovery of a natural product herbicide with a new mode of action[R].the US:Macmillan Publishers Limited,2018:1-22.

1-2 Herbicides have a huge problem right now

Our team members considered that we have not been exposed to agricultural research, we chose and engaged in a project we were not experts in, simply students with the will to create a feasible and coherent project. To do so, we contacted s stakeholders, pecialists and potential users at each step of our project in order to get constructive feedback and crucial advice, which helped to enhance our confidence in progress and formed a closed loop to optimize the project. Integration of all these informations and implementation was the indubious key of our project success.

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1-2-1 Considering the direct stakeholders, we have selected two herb planting bases with different uses: ornamental herbs and edible fruits herbs. Through the information integration after the survey, we found that our project is of great significance and application value, which can greatly reduce the labor cost and protect crops and other plants through intelligent release herbicides.

1. Ornamental herbs:

We visited the Jiangshan Scenic Area in Shangluo City, Shaanxi Province, which is located in the depths of the Qinling Mountains in China. There is a large-scale planting of Qumai. Qumai is commonly known as "Ten Scenes", which has high ornamental value. In addition, the whole grass is used as medicine, which has the effects of clearing heat, diuresis, breaking blood and dredging channels.

During the field investigation, we personally experienced the process of manual weeding. Due to the hot weather and huge workload, we deeply felt the difficulty and hardship of manual weeding. Later, we had an in-depth interview with Uncle Ren Xiaofeng, a professional who planted Qumai, about why he chose manual weeding, his evaluation of commonly used herbicides and his acceptance of our project.

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For the reason of choosing manual weeding,because Qumai are herbs, spraying the herbicide may cause the persecution of the seedlings of Qumai, so we only choose artificial weeding, and it's not reasonable to use the machine to cut grass, because weeds that just come up is too small, and similar to seedlings. We can only manually use sickle to pull grass and cut grass, causing us a lot of trouble.

He indicated that there were some disadvantages in common herbicides. At present, glyphosate is commonly used, but the effect may be slow after spraying, and it will be inhaled, so it is necessary to plow before planting to prevent glyphosate from destroying the growth of the Qumai.

Accept and expect our results. Weeds grow too fast, there may be weeds after the next rain. Recently, Shangluo has a lot of rain, and weeds grow one after another, which will lead to the waste of a lot of manpower and material resources for weeding, and the growth of the Qumai is also slow. It would be great if there were such a herbicide!

2. Edible fruit herbs:

1) We visited Wangqu Village, which is located around Xi'an City, Shaanxi Province, China. The corn planted there is in the fruit ripening period. We went to interview about 4 families. One farmer led us to his corn field, where we learned about the details of corn planting and the high labor cost of weeding.

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For the details of corn planting,the "impurity removal" in the corn field is not only for large-scale weed removal in the corn field before sowing, but also for some redundant corn seedlings in the field during the corn growing period. It is necessary to ensure the consistency of the corn seedlings. Of course, the redundant corn seedlings can be removed directly, which is not laborious. It is mainly for early weeding.

As for the cost of weeding , the farmer estimates that the cost includes the herbicide and corn seeds purchased from the seedling station, and hired labor, among which the cost of weeding accounts for about one-third. The manual spraying of herbicide can spray nearly one mu of land in half an hour. If the time can be reduced, the labor cost can be greatly reduced, thereby reducing the cost of weeding.

2) Due to the incertain sanitary situation, we can only carry out practical activities around the school. Therefore, we received the help of SZU-China(Click here to learn more about this partnership with SZU-China.), a cooperative school, who replaced us to conduct a face-to-face interview with a rice company and the Shenzhen Institute of Agricultural Sciences. The main contents include the use of herbicides and the attitude towards biosynthetic herbicides.

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For the use of herbicide,it is generally applied for three times: for the first time, glyphosate is applied before tillage. Because glyphosate has the effect of inactivation, early application will lead to the death of rice, so it cannot be used when rice is available; Use butachlor or closed herbicide for the second time; Use Daoxi for the third time.

With regard to the attitude towards biosynthetic herbicides , biopesticides or chemical pesticides are now used in agriculture. Farmers or technicians pay more attention to whether herbicides are low-cost and effective. If the cost performance ratio is similar, they prefer environmentally friendly biosynthetic herbicides.

1-2-2 From the initial idea to the complete design, because our ideas are limited, in order to better present a perfect work to the farmers, many key points must be considered carefully; And with the gradual development of experiments and modeling, there are many challenges. Fortunately, we received guidance and advice from experts in the field of agriculture and synthetic biology, and formed a closed loop to optimize our design.

1. Chen Kunming, Northwest A&F University

Professor Chen Kunming is a doctor of science in botany and a doctor of development and cell biology. He is very interested in our project and has given us many suggestions and help. We mainly discussed the reasons why glyphosate has been gradually replaced and the suggestions for improvement of our project. The interview details are as follows.

Among them, he talked about whether the production of glufosinate-ammonium analogues reached the lethal dose, which made up the design loopholes of our project. In the subsequent modeling test, we paid special attention to this, and we newly designed EPS synthetic circuit to ensure the effective concentration of herbicide in the soil. In addition, for the evaluation of production cost and application potential

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In view of the reason why glyphosate has been gradually replaced,he pointed out that the safety of the use of glyphosate pesticides. A large number of authoritative studies have proved that normal use of glyphosate is very safe, and it is the most important pesticide at present. Most herbicide resistant transgenic crops use glyphosate resistant genes. Therefore, the safety of glyphosate may not be the main safety concern in the pesticide field. We should pay more attention to the problem of herbicide resistance. For example, resistance rather than safety is the main reason that restricts the application of glyphosate;

It is necessary to produce high yield and low cost as much as possible. He said that I think it is meaningful to research and develop the engineering strain of glufosinate-ammonium analogues. However, whether the engineering strain can produce high yield glufosinate-ammonium analogues to achieve the purpose of weeding is the main concern; Second, whether the production cost of the bacterial agent has application potential also needs to be carefully evaluated.

2. Hu Zhaonong, Northwest University of Agriculture and Forestry

Professor Hu Zhaonong is a professor of the College of Plant Protection, mainly engaged in the research of botanical pesticides. The interview content includes the relativity of weeds, main hazards and comprehensive control measures, which provide new ideas and new content for our education lectures.

(Click here to get more content of the education lectures. )

Similarly, the professor also pointed out that we need to pay attention to the yield of herbicides, but from different perspectives, due to insufficient concentration, weeds may be in a sublethal state and prone to resistance; In addition, he pointed out that we should try our best to ensure that the synthetic herbicide is L-type. For the above, we will repeatedly test in the hardware later, and this part of work will be shown in the hardware.However, due to limited time, we will optimize the circuit design in the future to ensure that the synthetic herbicide is L-type as much as possible.

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Avoid sub lethal state. ,If the release amount of glufosinate-ammonium analogues analog is not reached, it will not kill weeds, but will make it exist in the environment. Instead, it will be in a sub lethal dose. Increasing environmental selectivity will often lead to the generation of drug resistance. Therefore, it is necessary to note the release amount and conduct actual tests before release.

Improve the synthesis rate of L-form as much as possible. The herbicides we synthesized belong to amino acid derivatives. Research shows that only L-form has this herbicidal effect, and D-form has almost no activity. Therefore, it is significant to improve the synthesis rate of L-form as much as possible in production. The cost can be significantly reduced.

Experimental suggestions. You wanted to be scalable. And I know that the iGEM team from Singapore, two years ago, they made a similar system, also, maybe a blue light induction system for bioproduction, because then you can have a bio reactor full of bacteria, and then whatever you want to induce, you can very easily induce the whole tank, rather than adding a chemical. So this will allow you to grow a lot of cells with a very low amount of glufosinate-ammoniumand and then induce the expression when you needed. And otherwise you're talking about lysis system. And that seems to be a good way to open the cell and get it to leak out. So the only thing I could consider to get to kick things started would be a phage infection, because many phage, they shut down the whole cell, right? So if you want whole cell to start focusing on your glufosinate-ammonium production, then I don't know if there's something that could be done there where you use elements from a phage that is turning off everything else, but I don't know how much you want that either, because you need, you probably need in multiple metabolites and enzymes from the cell to support the production. It's something you could consider, right? Some phages, like T seven, it has 11 minutes in the cell, right? So has 11 minutes completely changed the time metabolism, destroy the cell and then get out. So it's, it's very efficient at that. So it could be something you could look at a little bit like your lysis.

3. Julius Fredens, National University of Singapore

We have always had some confusion in the experiment, so we contacted assistant professor, Julius Fredens, at National University of Singapore on October 3. He is an expert in synthetic biology. Previously, we learned that he published an article entitled “Total synthesis of Escherichia coli with a recoded genome” in Nature as the first author, which we were very interested in. We have exchanged a lot with professors. In addition to professional knowledge and project related issues, there are also reasons for professors to choose synthetic biology and their expectations for the future of synthetic biology. After the exchange, we will feed back the results to the experimental group, and be more determined to do a good job in biological fertilizer and spread the dividends of synthetic biology.

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Discuss uncertainty about bacterial release, It depends on where in the world you go. So in certain parts of the world, you will not be allowed to spread GMO like that, not yet , but other areas you could. I don't know how how nature reacts to huge amounts of Ecoli. You could say we're using animal and and also human fertilizer. Have used that in agriculture for many years, and that is a lot of that is Ecoli, right? So I don't think it has to be a problem. After words, it's a bacterium, but it's a pretty clean bacteria from your spreading here. If you talk resistance, so you should probably get all antibiotic resistance markers out of the bacterium before you spread it so it can outspread antibiotic resistance, right? I think that will be necessary to do. And you may also have to do something so it can't do conjugation, can't do horizontal gene transfer. It should be possible to do something there to protect it a bit, but you can never be sure if your bacteria miss alive on the field, even briefly. Then you could also have bacterial phages that can go in, grab DNA and move on, right? So try to avoid problematic elements. And then you're talking resistance to the growth of weeds. We don't really know the mechanism, but I assume that there will be resistant at some point. But that was case, so I don't think you can avoid that. It would be a test and see how long can it last, and how much those is there. So we know from other treatments, antibiotics, e.g., that if you give a very low dose for very long time, then you give the the pathogenic bacterium quite a good window to become resistant, right? Where if you give a higher dose, and you just give it once, then you can kill them. So the same could be true for your field here, that if you give too little of your compound, then the weeds have a better chance of becoming resistance. If you want to use it, you should really use it. But it's difficult to convince the farmer to use a lot, I guess.

a cell-free system . I think that's a really good consideration to take in. You can see the spirit of iGEM is very much to pack everything into machine. But cell free is definitely not a bad idea to think about. Or simply just say, you're producing this in a bio reactor, and then you harvest your herbicide, and then you, and then you spread the herbicide specifically, right? And you don't have to purify it very finely. You just have to treat it in a way where you think, now there's no live bacteria and almost no genetic material, so you're not really exposing nature to that. And I think that is a very viable, may be a little academically, a little less exciting, but a very viable solution. So it's actually a matter of bio production rather than a superbuck that can kill the weeds and hang out on the field. So I think both are really good to have in mind.

The aspects we need to pay more attention. I think it can have very great significance if it's acceptable to use, if it's safe to use, and it actually has a beneficial effect. And we are spending a lot of energy on making artificial fertilizers. if your bacteria can be used as fertilizers, then you can really help, especially small farming, but maybe big farm as well, if it is safe. The safety is, of course, the big issue right here, and that's probably where you, in your previous question, had the answer with the cell free. And I think you may be able to get around some of it, but surely some of the bacteria will get around it and start growing, right? But that's not necessary a problem either.

Your expectations for the future development of synthetic biology Synthetic biology of bio economy is predicted to be one of the big pillars in the 4th Industrial Revolution. I think the more exciting bit is probably the the self therapy that is increasing. I would characterize that as synthetic biology as well, where you can reprogram cells to do something practical. And we're not just talking fixing genetic diseases. Car-T therapy is probably the most famous, or most useful examples so far, but I think we're gonna see a lot of that. When we take cells, we reprogram them to do something functional with a logical circuit, and then we sent them into the body. We have to be careful. They are dangerous. There's a lot of considerations. But it's a very appealing and promising area.

1-3 Later application

Through a series of social practice activities, we were recognized by direct stakeholders and experts, but a good project should pay more attention to its practical application potential in the future. Therefore, on October 2, 2022, we went to Shaanxi Zhangyuruina Castle Winery, a famous raw material (grape) planting base of red wine brands, located in Xianyang City, Shaanxi Province, China.

Through our introduction, we learned that they still lack a suitable herbicide product. Finally, we reached a consensus with the person in charge that they should provide a test field for product testing in the later stage. Before that, they provided us with grape seedlings, the soil and the data of grape growth conditions in the industrial park: including growth temperature, ventilation, air humidity, light intensity, etc. We will conduct small-scale simulation in the hardware. to test the effect of the engineering bacterial powder.

The highlights of our integrated human practice are described more briefly on the following page, which can be used as a reference for the silver award criteria.

Silver human practice:

https://2022.igem.wiki/xjtu-china/silver-human-practice

Education:

https://2022.igem.wiki/xjtu-china/education