Team:WPI Worcester/Human Practices

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Dr. Robert Wick, PhD, UMASS Amherst Professor of Plant Pathology and Nematology

We decided to speak with Robert Wick, who has extensive research and knowledge regarding plant pathology. Our hope was to gain more insight into the mechanisms that cause bacteria to gather on plants, along with some commonly used preventative techniques.

  1. What are some of the common bacteria involved in contamination of field crops? What are some of the common sources of these pathogens?

    Dr. Wick said that bacteria such as E. coli and salmonella are harmful to humans but not to plants. Bacteria harmful to plants tend to cause diseases such as black rot, while human pathogenic bacteria such as E. coli have no visible effect. These human pathogenic bacteria end up on plants from various sources, including animal manure, fecal matter from wild animals, and contaminated irrigation/wash water.

    When we described the use of antifreeze proteins in our project, he suspects their mechanism of action is a disruption of lipid membrane composition, leading to an antimicrobial effect. He also advised us to be wary of the level of expression of antifreeze proteins. Although plants control protein expression and energy consumption robustly, a constituently expressed protein would prove deleterious for the host plant. Dr. Wick also expressed interest in whether the plants we are working with have similar DNA sequences to the genes that encode antifreeze proteins. If so, this may enable better precision of expression. Additionally, he was curious into the typical inducers of these proteins (e.g., photons, temperature drop, etc).

  2. Do you see bacterial contamination of field crops as a prominent issue in agriculture?

    Dr. Wick said that bacterial contamination issues vary more from crop to crop rather than farm to farm. For bacterial diseases in plants, issues tend to be seedborne, with only 1 in 10,000 contaminated seeds potent enough to infect an entire crop field. All seeds are contaminated from the parent plant. If we are able to keep the host plant from getting contaminated, one can protect the seeds as well.

  3. Which types of farms are most usually affected (i.e. small farms, large farms, organic farms, non-organic farms), or does it depend on the farm and situation (i.e. any patterns)?

    He described two common modes for plant infection: buying seeds that are already contaminated or growing a crop in a site that had a bacterial disease the previous season. Many contamination issues are governed by weather patterns, with rainy conditions encouraging greater bacteria proliferation than in drier conditions. Water is a breeding ground for bacteria and wind can carry bacteria across a field. When asked which types of farms are most at risk for contamination, Rob reiterated that contamination is plant-specific and highly dependent on weather. Dr. Wick also mentioned that rotating crops every season helps forestall the spread of contamination, as most bacterial infections arise based on the host infected. For example, black rot of the cabbage family occurs in members of the cabbage family but not in unrelated crops.

  4. What is being done to control bacterial contamination of field crops? What are some of those proposed solutions? Is there any progress yet?

    He mentioned while sophisticated tests for human pathogens exist, tests for plant pathogens are less commonly used and not as accurate. When buying a batch of seeds, any bacterial growth proves too minuscule to detect. You cannot assume that a batch of seeds is completely disease-free. In addition to bacteria spreading by a rainstorm, farmers can spread contamination by hand when handling fresh crops.

    Regarding conventional ways to prevent contamination, antibiotics are utilized but not as often. Copper can be used to kill bacteria, but it is often ineffective and is washed off by rain rather quickly. Methods of protecting plants are few and but farmers exercise caution in practice: they attempt to limit bacterial spread by not picking crops right after a rainfall.

  5. What are some the of the biggest challenges facing our proposed solution? Would it be viable economically and obtain regulatory approval? Do you think farmers would mostly express approval or disapproval of our solution, or would they be indifferent? What is your personal opinion on our project?

    Dr. Wick said that both he and other farmers would be behind the idea. Some of our project ideas are troubling to him, however. He is concerned that expressing antifreeze proteins all of the time could be too energetically taxing to the plants and disrupt their normal metabolism, but then again it might not hurt them. He recommends looking into how these proteins are induced and how they affect the plant's growth overall.

Dr. Patricia Stapleton, PhD, WPI

  1. You asked, for regulatory purposes domestically, whether a GM/ “new” crop is “substantially equivalent” to the existing, unaltered crop. Can you elaborate on this distinction? For example which are considered transgenic, genetically modified, or natural?:
    • In the case of taking a gene from a tick (or any other insect or mammal) and subcloning it into a crop
    • In the case of taking a gene from another plant and inserting it into a crop
    • In the case of spraying a protein derived from an insect, mammal, or another plant onto a crop
    • Does the criteria vary from crop to crop and from situation to situation?
    Prof. Stapleton said that regulations vary from country to country, and sometimes from crop to crop. U.S. regulators look at the item to be modified and the potential modifier. If both the modified item and the modifier are well-known, any new crop is considered “substantially equivalent.” For example, carrots and tomatoes are both regulated and well-known, so a transgenic plant comprised of both carrots and tomatoes is allowed. She also said a transgenic, or GM, organism is created from any procedure involving the placement of genes from one species into another. Breeding is not considered genetic engineering, only laboratory procedures. Any plant deemed transgenic is not considered organic. Surprisingly, there is a list of pesticides and herbicides that can be used on organic plants, but under heavy regulation.

  2. What are some the of the biggest challenges facing our proposed solution? Would it be viable economically and obtain regulatory approval? What are some regulations we would have to consider?
    3. We spoke about two methods of implementing antifreeze proteins: using an antifreeze protein spray or genetic modification of plant genes. Trying to pass a spray would be more difficult because it is considered an application and falls under a different set of regulations. This will entail a battery of tests (e.g. soil tests for environmental impact). We would have to work closely with the EPA and FDA with this type of solution because the environmental and public health risks are higher. In contrast, we would face fewer regulatory hurdles with the transgenic option. The government has been working with transgenic plants for a long time, and with this experience comes leniency towards solutions in this category. If we do consider employing either solution, Prof. Stapleton recommended that we work with a large agricultural company, as they have the framework, experience, and equipment available to accelerate the approval process.

  3. What is the difference between cisgenic and transgenic?
    4. Cisgenic plants have been created for thousands of years through selective breeding. Cisgenic refers to the breeding of two of the same species of plants, and is not referred to as genetic modification by regulatory bodies. Transgenic describes laboratory genetic modification between species of plants.

  4. What is the overall view of farmers and consumers of GMOs and transgenic plants? Are they mostly supportive, disapproving, or indifferent? Are there misconceptions? Does it matter to the larger public?
    5. Farmers may be opposed to a spray solution because it could be toxic to their crops. A transgenic solution could be more likely to garner farmer support, especially using the carrot antifreeze protein (as opposed to the tick). Regarding consumers, they often only change their behavior when something has gone catastrophically wrong. In general, consumers don't seek out in-depth information about where their food comes from or what they are eating until a negative event draws their attention to it. People who have had food poisoning might be more likely to try our solution and weigh the options.

  5. What is being done to control bacterial contamination of field crops? What are some of those proposed solutions? Is there any progress yet?
    6. There are many challenges facing farmers with regard to foodborne illnesses. Some common sources of contamination include exposure to water runoff, wild animals, fertilizer, manure, applications, and handling by farmers. Once contamination is found however, it is difficult to determine where in the supply chain it occurred (i.e. field, point of harvest, during processing, packaging, transport, supermarket, at home or restaurant). Although it is difficult to prevent contamination, it is easier to prevent exposure, by having fewer people involved and limiting the transportation time of produce. She said that contamination will most often occur in the field.

  6. You mention that about 80% of all GM crops are modified to make them resistant to herbicides, and are likely transgenic from bacteria. What do you mean by this? Do you mean that bacteria are used to make these plants transgenic? Is this common practice?
    7. Professor Stapleton said she was referring to using genes from bacteria in transgenic plants. Bacterial genes have been used for a long time and are highly-regulated.

Dr. Susan Roberts, PhD, WPI Chemical Engineering Dept. and Michelle McKee, Graduate Student, WPI Biology and Biotechnology Dept.

We spoke with Prof. Susan Roberts, PhD, WPI Chemical Engineering Dept. and Michelle McKee, Graduate Student, WPI Biology and Biotechnology Dept. to gain insight into the field of transgenic plants and some considerations for our gene gun. Both Prof. Roberts and Michelle have performed extensive research in transgenic plants. Michelle has also extensively used a particle bombarder in her laboratory.

  1. Which plant cell species do you typically work with when using a gene gun? Beck told me that you typically work with plant tissue cultures, correct? What is the reasoning for working with a plant tissue rather than an entire plant itself?
    2. Susan Roberts: We work with Taxus plant cell cultures that produce the anticancer agent Taxol. We aim to engineering the cell cultures for various objectives, including increased Taxol production. We use cell cultures because that is the system used commercially to synthesize Taxol.

  2. Most of our project work has been with bacteria and using bacterial promoters. What are some of the typical plant promoters that you use in this line of work? What are some of the requirements / conditions for these promoters? Which promoters would you recommend us using?
    3. Susan Roberts: There are a range of promoters that you can choose for use in plants. I have attached an article that we wrote a while ago regarding development of a particle bombardment method for transient gene expression in Taxus that describes some of the promoters that work in our system. Michelle McKee, a PhD student in my lab, has perfected the gene gun technique and I’m sure she has suggestions for you.

  3. Do you find that a certain number of base pairs works better than others? Is there a sweet spot or a desirable number of base pairs for getting plant cells to express a certain gene?
    4. Michelle McKee: I think the smaller the plasmid is, the better, but obviously you need to have all the important sequences in there. I have heard that if the plasmid is too large, efficiency will go down. As for promoters, we just went with the most basic/common sequence, but the stronger the promoter, the more GFP or marker protein there will be to detect. I don’t know about bacteria, but I have found that bombarding from the correct height/distance has played a huge role in efficiency. Lots of people use particle bombardment for stable transformation – it is just easier if you have a faster growing cell line (Taxus is a bit slow).

  4. How many generations would you expect a typical gene to carry on for in your experience?
    5. Susan Roberts: It can really vary. Generally, the gene gun technique results in transient expression, which may last for months. Although sometimes you can get stable expression. For plants, we typically use agrobacterium-mediated transformation to get stable expression.

  5. What are some of the factors we need to take into account when testing our gene gun (ie. pressure, height, etc.)?
    6. Michelle McKee: It is important to consider both the height and pressure of the particle bombarder. The height and pressure vary from protocol to protocol and can take many attempts to perfect.

Glenn Stillman, Stillman's Farm, Worcester, MA

Conscientiously GrownTM
On Wednesday, July 18th, we visited Stillman’s Farm, located in New Braintree, Massachusetts. We met with the owner Glenn Stillman for about an hour and a half. Glenn had bought the New Braintree farm in 1990 and later adopted a slogan for the farm that encapsulates his responsible growing and environmental practices. He adopted the Conscientiously GrownTM slogan because he was dissatisfied with “conventional” and “organic” produce labels. Conscientiously GrownTM serves as an umbrella term for many different growing practices. Stillman’s farm does not offer GM (genetically modified) crops for marketing reasons. Glenn, personally, has nothing against GM crops but does not believe that the benefits of growing GM crops outweigh the negative publicity they may garner. Regarding sprays, Stillman’s farm only uses select herbicides and synthetics on their produce. Not all crops require the use of chemical sprays, however. Glenn told us that he does not list his crops as organic, but mentioned that organic crops have a list of pre-approved chemicals, many of which he does not use on the farm. With his methods, Glenn said he is able to achieve 6-10% organic matter in his soil, an amount higher than typical. The final component of the farm’s Conscientiously Grown practices includes an awareness of local wildlife and the environment by refraining from using toxic organic and traditional sprays.

Sources of Contamination and Washing
Glenn listed two sources of bacterial contamination on his farm: manure and wash water. Glenn stopped using manure after he read a story about contaminated spinach. Briefly, some consumers got sick from bacteria taken up by spinach roots from surrounding manure. This type of situation is particularly bad because bacteria that is present inside the spinach cannot be washed off or easily detected. As a result of this, Glenn opts to not use manure on the farm. For washing produce, Glenn uses water that is treated with bleach. By law, Stillman’s farm is required to have their wash water tested once a year, which has never tested positive for bacteria. Regarding the washing process, produce is picked daily, rinsed and dipped once in water, and is sold. Glenn said that washing not only on the farm but at home, is extremely important to preventing contamination. Bacterial formation is highly dependent on location and transport. For example, crops sold by Stillman’s farm go directly to the consumer, so there is less time in between for the bacteria to grow. Meanwhile, produce that is shipped by large distributors across many states provides bacteria ample time to proliferate. While it is unlikely that a small amount of bacteria will make an otherwise healthy individual ill, individuals with compromised immune systems, young children, and the elderly are at a higher risk of contracting an infection. For shelflife, Glenn said that produce can sit for up to ten days before it is sold!

Farming Practices for Lettuce
Glenn first germinates lettuce seed in a greenhouse under controlled precipitation/moisture and heat. The seed is germinated under controlled conditions to help it survive and manipulate its growth. Usually, they are germinated in synthetic soil with a high organic composition because traditional field soil would harden up. After germination, the lettuce is transplanted and transferred outside where it hardens up in plastic-lined raised rows before it is picked and sold.

Opinion on Our Proposed Solution
Glenn said he wholeheartedly supports our proposed solution. He said that many farmers would likely be in support as well. Farmers would appreciate the peace of mind our solution would provide, knowing that their crops would not be contaminated and make anybody sick. Knowing the success of the farm is totally dependent on the success of the harvest is a constant stress for many farmers. If a harvest is poor or somebody gets sick, it could spell disaster for a farm for years to come. Our solution not only would help prevent illness, but protect farmers’ livelihood.

Human Practices

At iGEM we believe societal considerations should be upfront and integrated throughout the design and execution of synthetic biology projects. “Human Practices” refers to iGEM teams’ efforts to actively consider how the world affects their work and the work affects the world. Through your Human Practices activities, your team should demonstrate how you have thought carefully and creatively about whether your project is responsible and good for the world. We invite you to explore issues relating (but not limited) to the ethics, safety, security, and sustainability of your project, and to show how this exploration feeds back into your project purpose, design and execution.

For more information, please see the Human Practices Hub. There you will find:

  • an introduction to Human Practices at iGEM
  • tips on how to succeed including explanations of judging criteria and advice about how to conduct and document your Human Practices work
  • descriptions of exemplary work to inspire you
  • links to helpful resources
  • And more!

On this page, your team should document all of your Human Practices work and activities. You should write about the Human Practices topics you considered in your project, document any activities you conducted to explore these topics (such as engaging with experts and stakeholders), describe why you took a particular approach (including referencing any work you built upon), and explain if and how you integrated takeaways from your Human Practices work back into your project purpose, design and/or execution.

If your team has gone above and beyond in work related to safety, then you should document this work on your Safety wiki page and provide a description and link on this page. If your team has developed education and public engagement efforts that go beyond a focus on your particular project, and for which would like to nominate your team for the Best Education and Public Engagement Special Prize, you should document this work on your Education and Education wiki page and provide a description and link here.

The iGEM judges will review this page to assess whether you have met the Silver and/or Gold medal requirements based on the Integrated Human Practices criteria listed below. If you nominate your team for the Best Integrated Human Practices Special Prize by filling out the corresponding field in the judging form, the judges will also review this page to consider your team for that prize.

Silver Medal Criterion #3

Convince the judges you have thought carefully and creatively about whether your work is responsible and good for the world. Document how you have investigated these issues and engaged with your relevant communities, why you chose this approach, and what you have learned. Please note that surveys will not fulfill this criteria unless you follow scientifically valid methods.

Gold Medal Criterion #1

Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the purpose, design and/or execution of your project. Document how your project has changed based upon your human practices work.

Best Integrated Human Practices Special Prize

To compete for the Best Integrated Human Practices prize, please describe your work on this page and also fill out the description on the judging form.

How does your project affect society and how does society influence the direction of your project? How might ethical considerations and stakeholder input guide your project purpose and design and the experiments you conduct in the lab? How does this feedback enter into the process of your work all through the iGEM competition? Document a thoughtful and creative approach to exploring these questions and how your project evolved in the process to compete for this award!

You must also delete the message box on the top of this page to be eligible for this prize.