Team:NAU-CHINA/HP/Gold Integrated
------“If I have been able to see further, it was only be
-cause I stood on the shoulders of giants.
- Reaction:
-
A termed coined by physicists, it refers to one object exerts
a force on another object, then the second object exerts
an equal and opposite reaction force on the first.
Likewise, in order to better understand the
effectiveness of our project, we discussed
the dangers of FHB with many experts
and compared the different approaches
to control FHB. They are also insightful
on providing us with advice on how to
ameliorate the system to become more
robust and accurate.
Overview
Human practices is a highlight of our project in this year’s iGEM. As a researcher, we need to focus primarily on scientific research and laboratory work. But we cannot decide the direction of our research by soaking up in experiment time. We will always keep the code in mind: whether projects are safe ? will it benefit the folk？
We put great elbow grease into connecting human practice with laboratory work. We tried to make our human practice progress along with experiments. To achieve this goal, we first analyze the demands for our project. We went to the farm of our university and went to a farm in the city center to get rigorous information of morbidity and current remedy . Secondly, we would like to know the effectiveness and the safety of our project, thus we discussed the dangers of FHB with many experts and compared the different approaches to control FHB. They are also insightful on providing us with advice on how to ameliorate the system to become more robust and accurate. One of the professors— Huaigu Chen made us form an significant adjustment: degradation of toxins . Wegu Chen made us form an significant adjustment: degradation of toxins . We these stakeholders very much.
Moreover, letting scientific project exert real impact on the society, we would like to spread our project and iGEM culture. In publicity and education, we have made presentations to introduce synthetic biology, iGEM competitions and the project carried out by our team to students in high school and our university. We sincerely hope that increasing people will know us and join us. Let us see what we have done about human practices.
We put great elbow grease into connecting human practice with laboratory work. We tried to make our human practice progress along with experiments. In order to analyze the demands of our project. We went to the farmland of our university and a farm in the city center to get rigorous information of morbidity and current remedy.
farm of our university
a farm in the city center
We interviewed a farmer in our city who has had five years experience with wheat planting on his land. He commented that he has suffered a great loss from FHB. In 2015, 40%~50% wheat in his field was affected with FHB. He uses chemical pesticide every year, but it doesn’t always work. It is necessary for him to purchase a new kind of chemical pesticide because plant pathogens were resistant to the original one.
This experience gave us the opportunity to explore the impact our project might have on society. They also assisted us in thinking about responsibility in science.
“safety is important”，it inspired us that “Got to talk more in depth with people who were interested”.
You can read about our interview script HERE!(Liu HE)
What did we discuss?
1.Could you please tell us the incidence of wheat scab in recent years?
——last year (2016) continued raining and drizzling, as a result wheat scab is particularly serious, the incidence rate of infection is approximately 50% to 60%.
This year ( 2017 ) wheat grew particularly well, almost no wheat scab, the morbidity was less than one percent. You know, infected musty wheat contains vomitoxin. Taking the Huaihe River as the boundary, in the south of the Huaihe River, due to Huainan climate mostly wet and humid, higher the morbidity is, vomitoxin content is almost in 1500~1600ppm. Last year the situation is relatively more serious, the wheat vomitoxin content is about 7500ppm. While the EU criteria on the vomitoxin stipulate the vomitoxin should be less than 1000ppm.
2. What is the cause of wheat scab disease?
——the incidence of wheat scab has a great relationship with weather,the growth of winter wheat cultivated in Jiangsu province depends on the next year April’s weather. Although China has an old poverb "Man will conquer nature", but people engaged in farming industry will substantiate that people will never conquer the nature . The yield and morbidity of wheat are sheer dependent on the weather . Once the wheat scab occurs , there is no other way back.
3.What are the dominant ways to control wheat scab?
——Spraying pesticides in the blossoming stage of wheat. When wheats are about to blossom, we will spray pesticide on every single wheat we see. Another massive scale spray will be expected to need at the 10% to 15% of blossoming stage. During the entire growth cycle, we will have to control the times of pesticide utilization, generally it is no more than three times. However wheat scab can only be prevented, it can not be cured. Once it happens in the field, there is no other way back. Like the human skin, once the skin is damaged, the bacteria will arrive and reproduce immediately.
4.Will wheat scab be resistant to the usage of pesticides?
——Unfortunately yes, thus every year pesticide will be renovated and replaced, pesticide researchers will also introduce new pesticides every year. A pesticide will be replaced and disappear for up to two years. Actually, pesticide used in field crop will be expected to need a renovation every year, even it is for killing weeds and Aphidoidea.
5.How to deal with the infected wheat?
——Wheat with serious infection, the vomitoxin content is way higher than the criteria, it can not be made as food for human. However, they are more prone to be made into feed. The two toxins produced by the scab can be accumulated in the food chain . As a farmer who cultivate wheat , I am also very concerned about the problem of mycotoxins in food. It now appears that there is a great potential that excessive mycotoxins may be in the food, these food flows into the market circulation, the crippling hazard to the human body accumulate gradually. If you do not pay attention, the adverse consequence may occur in the near future.
As a part of the project, we reached out to experts on the matter of Fusarium head blight, farmer, government officials. We asked them on a range of aspects, from the purely technical to the environmental. Here the summaries of the interviews are shown.
Visiting professor Zhou mingguo
When the idea of wheat scab occured to us, we found that there were only few professors’ researches were on that track in Nanjing Agricultural University. After scouring a immense amount of the literature we construct a rough scheme, however we decided to consult professor Mingguo Zhou who has been researching the precaution and remedy on Fusarium head blight of Wheat for many years about it. It is also noteworthy that professor Zhou have gained a great achievement in the chemical control of Fusarium head blight of Wheat. Professor Zhou illustrated the features of this disease by contrasting different wheat diseases such as smut.When we asked about the current treatment of Fusarium head blight of Wheat, professor Zhou told us the most prevalent approach is to use chemical products. He exhibited his up to date research for us, and there is, admittedly, a great advantage of chemical products which is its persistent feature. This is also insightful for us, if we hope to make our final products predominant in the field, we also should make it persistent.
Visiting professor Chen huaigu
Chen huaigu is a professor who specializes in Fusarium head blight. He mostly focuses on the chemical control , and he acknowledged the biology control is a promising treatment for FHB . He gave us the professional suggestions on the mechanism of our project.
Visiting professor Zhou
We introduced our project to professor Zhou, getting many useful feedback. His suggestions helped us view our project in a different way, find the existing problem in our project, and lead us to think more about application and the practical problems. We used his advice and constantly kept in touch with him. In addition, we also gathered information and data on the Fusarium head blight to assist us with modeling from professor Zhou.
Visiting professor Wang yanzhang Tang weihua
Institute of Plant Physiology & Ecology ，SIBS, CAS
Tang and Wang are professors who work on the “The Interaction of Fusarium and host plants”. We had made a strong impression and a solid case for continued suggestions from these experts in this area.
Professors help us better understand how this pathogen proliferates within the host plant.
More knowledgeable after the visit : the strategy of infection; the synthesis of toxins; the mechanism of host plant ’s defense response; the mechanism of fungicide resistance……
“First and foremost, You need to know the production of proteins from the yeast ,then you should think about how to spray drugs , just like the easiest way that you can spray biological pesticide , but you have to purify the proteins first. Besides, you had better know when to spray the biological pesticide and where to spray.”
Email and phone communication with
Communications with Dr. Zhang Haoqian
As we brainstormed and planned our new research, we had phone meetings and email communications with Dr. Zhang Haoqian.
Technical Communications with Dr. Lee, Nanjing Genscript
Technical Communications with Dr. Lee for Project Design, and Testing. We consulted experts in biology marketing. This experience might come in handy especially if we want to carry out a product to all farmers.
A Visit to Nanjing Government-Food Lab
To understand the criteria of two toxins’ (DON, ZEN) content and design a detecting method , we went to Nanjing government where we visited two officers and a technician. We consulted about the content of the two toxins circulating in the food chain which involved wheat grain, wheat derived flour gislated on the criteria of two toxins.(GB 5009.111 for DON, GB 5009.209 for ZEN). Unfortunately, it is undeniable that, in the context of unfavorable climate condition, the bottom will fall out of the quality as the content of toxins will be definitely above the stipulated value.
We also visited the quality-control laboratory of the government in which we found that it was such a both labor-consuming and time-consuming process to detect the two toxins. Basically, the government will need 3-4 days to finish a set of detection. Besides, the devices they utilize are expensive and inconvenient. All these issues have inspired us a brand new idea—a device serve the function of detecting!
You can read about our interview script HERE!
1.Could you describe the tension arising from FHB, and its adverse consequences for farmers and our country?
——In China, although as a whole there is no significant decrease in the gross production of wheat, it still could be a cataclysm for some agriculture-oriented provinces’ wheat production. It does trigger a serious economy descending not only for big companies but also for individual farmers, so I believe FHB to be a tough and tricky disease for agricultural.
2.What do you think the public and the farmers would react to our genetically-modified yeast as a measure for precaution in the soil? Would they accept it?
——Well, in China it could arouse unrest. Because the public haven’t been exposed to this kind of genetically modified method before. Also, you know, the people may conjure up the fear of a former issue, a heatedly debated legislation through the last decade, whether we should allow genetically modified food circulating in the market. So, I guess it wouldn’t be very sought-after.
3.Is there any foreseeable problems that may come along with the utilization of genetically modified yeasts?
——Well, you should be very aware that perhaps this method which inoculate genetically modified yeasts into the soil may not work out… I know quite a few researches carried out by professors with great prestige. It took them years to isolate microorganisms that could to some extent control diseases of wheat, however when they inoculated them back in the soil the problem showed up—some plants got sick and then recovered, others didn’t… It’s complicated.
4.What are the common ways to detect the two toxins, DON and ZEN? Is it time- consuming ?
——It usually takes us 3-4 days to get the final results. Basically, as soon as we got the samples. We would firstly process the samples, and then we sent these samples to be tested by HPLC(High performance liquid chromatography). This device is complex and expensive. Few institute can afford that.
4.Could you tell us the rough content of two toxins that circulate in the food chain?
——It’s hard to say. The content of toxins is climate dependent. For example, in 2015, the content was way higher than the standard. According to the law, the content of DON in wheat should lower than 1000ug/kg, and ZEN should lower than 60 ug/kg.
we created a handbook to introduce our project to almost all farmlands in Nanjing and students in our university and a high school in Nanjing.
This allowed us to reach out to those we cannot educate face-to-face.
We also appreciate the effort and hope that this postcard distribution will make people more familiar to our project.
We also appreciate the effort and hope that this postcard distribution will make people more familiar to our project
Pocture provided by government official
In order to best understand background of our project (The situation of wheat scab in china ) and the requirements of our hardware, we contacted plant protective station to inform them about our project and find out the features they wanted to see in our designs.
After visiting, We knew that FHB caused by F. graminearum has been a serious disease in Jiangyan district for over a decade. Losses are estimated to be in the millions of RMB annually.
We also gathered information and data on the Fusarium head blight to assist us with achine learning and software.
Visual Analysis Based on Information
Retrieval and Natural Language Processing
For those who don't major in Biology, how can they be informed of Wheat Scab? We proposed a method to do this based on information retrieval and natural language processing
Pocture provided by government official
In order to best understand background of our project (The situation of wheat scab in china ) and the requirements of our hardware, we contacted plant protective station to inform them about our project and find out the features they wanted to see in our designs.
After visiting, We knew that FHB caused by F. graminearum has been a serious disease in Jiangyan district for over a decade. Losses are estimated to be in the millions of RMB annually.
We also gathered information and data on the Fusarium head blight to assist us with machine learning and software.
Workflow of our method
In this method, we first choose ＇小麦赤霉病＇(＇Wheat Scab＇in Chinese) as the key word which will be put into the biggest Chinses search engine -- Baidu. Then we use web spider to get what the search engine returns. And we process the above text, by using natural language processing techniques including but not limited to Chinese word segmentation, word embedding and so on, We will get ＇Relevant Word List＇ and a picture which is called ＇Word Cloud＇ based on ＇Relevant Word List＇.
Word Cloud
iolarge the font is, the higher the word frequency is. From this picture, we can acquire some useful information, For example, ＇长江流域＇(＇Yangtze River Basin＇in chinese ) may imply us that most of the wheat scabs occur in the Yangtze River Basin. Ahd,＇甲基硫霉灵＇(＇Methyl Thiophanate ＇in Chinese) may represent a chemical that can treat wheat scab. All in all, we can acquire some useful information, even we didn't major in Biology before. At the same time, we do another basic work to find ‘Similar Word List’ and build a knowledge graph.
We acquire alomost 20,000 entities from one of the biggest Chinese input meth ods -- Sogou, and then we put them into the biggest Chinese encyclopedia --BaiduBaike which is similar with Wikipedia . In this way, we can get large volume text and then process it by using natural language processing techniques as well. we use word2vec which was developed by Google in 2012 and word segmentation to train a model. We finally get ＇Similar Word List＇, and top 10 words in ＇Similar Word List＇,which are similar with scab and relevant to wheat, are put into BaiduBaike to acquire information we want.
Top 10 words ＇Similar Word List＇(＇Wheat Stripe Rust＇,＇Sheath Blight＇,＇Virus＇,＇Disease＇,＇Wheat Leaf Rust＇,＇Rust＇,＇Wheat Hemiptera＇,＇Head Smut＇,＇Total Disease＇,＇Powdery Mildew＇,＇Wheat Aphids＇in English)
A knowledge graph is finally built using the information we get from BaiduBaike.
Knowledge Graph
Questionaire
FHB is caused by a range of Fusarium fungi, which infects the heads of the crops when they are growing in the field. The disease is often associated with contamination by mycotoxins produced by the fungi which can cause severe economic losses .
According to literature review, we know that FHB is responsible for significant grain yield reduction world-wide. In China, wheat scabs affected areas are about 7.5 million hectares, accounting for the 1/4 of the total area of wheat. The annual loss of damage caused by scabs is about 2 million to 3 million Ton.In the U.S and Canada, Fusarium ear blight emerged in the 1990s as a widespread and powerful threat to cereal production.[1] From 1998-2000 the Midwestern United States suffered $2.7 billion in losses following a FEB epidemic.
Fusarium toxins have negative effects on the immune, gastrointestinal and reproductive systems of animals.[2]DON is a protein synthesis inhibitor, which also called vomitoxin, due to its negative effects on feed intake in pigs. Pigs are the most sensitive to DON, while ruminant animals such as cattle have higher tolerance.[3]Many countries monitor Fusarium mycotoxins in grain to limit negative health effects. In the U.S there are advisory levels for DON in human food and livestock feed.[4]The European Unionhas legislative limits for several Fusarium mycotoxins in grain aimed for human consumption[5]and recommended limits for animal feed.[6]Extensive research has been put into the development of control measures of Fusarium ear blight. Scientists, growers and food processors aim to develop effective control measures, including the reduction of mycotoxins.
Based on the above literature review, a questionnaire is designed to survey consumer groups’ opinions on FHB.
First, we would like to know whether the consumer group is concerned about wheat safety. Second, we try to give a simple test on the knowledge of the damage of FHB. By the way, we send the correct answer after people finishing the questionnaire. So they can get a feedback as soon as possible. Third, we want to introduce the biological control to the public.
This is our questionnaire
We have analyzed the data we have collected. The analysis results are as follows:
We have collected 411 valid questionnaires (all completed) at the end of the survey.
The participators come from 30 different provinces in China. Most of them are between 18-35 years old and have a bachelor degree.Here are results:
1.The concern about FHB
The survey shows that Only a few( 14.84%) respondents pay attention to the safety of the wheat in daily life. And some consumers(63.99%) have no idea about the situation of FHB. Some reasons for t having no appropriate approach to the information. Besides,Most consumers(74.94%) express their need to learn about the FHB and its damage,inculding36.25% o have a strong need.
2.The knowledge about FHB
The similar 4 questions shows people do not know the basic knowledge of FHB.There is a knowledge gap in wheat food safety. Over a half of the respondents express they know few about wheat scab.We set an interference option about aflatoxin. But we find people have a more clear recognition of it for 38.44% of the respondents can choose the right answer about the toxin FHB brings. Besides we set a feedback to all respondents after the respondents finishing the questionnaire. We hope they can know a little more from the questionnaire.
3.Summary
To summarize, though the results of the survey may be a bit partial and incomplete to some extent due to the small sample size, it is undeniable that people's knowledge about wheat scb is insufficient. Especially after we have learned consumers have a high request on the quality of food, we consider it is important to know the wheat scab and toxins involved.
Our NAU iGEM team aims to know exactly the public recognition of FHB, and popularize the basics of FHB, its hazardous effects to people’s health, measures to take after poisoning, etc.
We are careful about not arousing unnecessary public panic. This is also our social responsibility.
1.McMullen, Marcia; Bergstrom, Gary; De Wolf, Erick; Dill-Macky, Ruth; Hershman, Don; Shaner, Greg; Van Sanford, Dave (2012-07-11). " "A Unified Effort to Fight an Enemy of Wheat and Barley: Fusarium Head Blight"Plant Disease. 96 (12): 1712–1728. ISSN 0191-2917. doi:10.1094/PDIS-03-12-0291-FE.
2. D’Mello, J.P.F.; Placinta, C.M.; Macdonald, A.M.C. "Fusarium mycotoxins: a review of global implications for animal health, welfare and productivity". Animal Feed Science and Technology. 80 (3-4): 183–205. doi:10.1016/s0377-8401(99)00059-0.
3.Miller, J. David (2008-02-01). 2008-02-01). "Mycotoxins in small grains and maize: Old problems, new challenges". Food Additives & Contaminants: Part A. 25 (2): 219–230 ISSN 1944-0049. doi:10.1080/02652030701744520.
4. Nutrition, Center for Food Safety and Applied. "Chemical Contaminants, Metals, Natural Toxins & Pesticides - Guidance for Industry and FDA: Advisory Levels for Deoxynivalenol (DON) in Finished Wheat Products for Human Consumption and Grains and Grain By-Products used for Animal Feed".www.fda.gov. Retrieved 2017-03-13.
5."EUR-Lex - 32006R1881 - EN - EUR-Lex"eur-lex.europa.eu. Retrieved 2017-03-13.
6."EUR-Lex - 32006H0576 - EN - EUR-Lex" eur-lex.europa.eu. Retrieved 2017-03-13.
- Farmland Investigation
- Interview
- Handbook
- Postcard distribution
- Visiting plant protective station
- Visual Analysis
- Questionaire
