UD’s Wommack part of $25 million USDA food supply safety study

February 21, 2012 under CANR News

K. Eric Wommack, professor of environmental microbiology in the Department of Plant and Soil Sciences at the University of Delaware, is part of a five-year, $25 million U.S. Department of Agriculture (USDA) study aimed at preventing potentially fatal illnesses linked to Shiga toxin-producing E. coli bacteria (STEC) in the nation’s food supply.

STEC poses a serious threat to the food supply, resulting in more than 265,000 infections in the United States each year.

The coast-to-coast study includes a team of 48 investigators from multiple universities and government agencies, with the University of Nebraska and Kansas State University as the lead institutions.

Wommack became involved with the project after serving on a USDA grant review panel with Jim Keen, the lead project director from the University of Nebraska, who had been studying STEC for a number of years and was putting together the project proposal.  “It was really just good fortune on my part to be lucky enough to be involved with the group,” said Wommack, adding that he has not previously worked with STEC but can potentially bring a new angle to the research through his experience in microbial ecology.

As a microbial ecologist, Wommack said he is “interested in all the microbes that make up communities of microbes.” He equated this to an environmental ecologist, only instead of looking at “all the plant species within the make-up of the forest or the grassland, I look at all the microbes that comprise a microbial community.”

For this study, Wommack will examine the microbial communities that form around STEC to see if there is a pattern that scientists can pinpoint. This would allow the researchers to trace non-toxic levels of STEC by determining the kinds of microbial communities where it is most likely to occur.

“It is difficult to detect STEC when it is at the non-poisonous levels, but it is still there and so my work may show that there are other microbes that just happen to occur alongside STEC but are a whole lot easier to find. It is not like (STEC) is the only bacteria in a cow, so we are interested in looking at the larger communities that surround the pathogenic organisms.”

Wommack also will try to understand the ecology of STEC on a fundamental level.  “Although it is an organism that is an awful pathogen and kills people,” Wommack explained, “it is also a microbe that is out there and it has to live in whatever environment it is found in, and so most everything we know about STEC is when it is making people sick. We don’t really know much about it other than that — meaning its place in the ecology of microbial communities.”

Wommack said he is excited to get started on this research project, anticipating that he may begin work as soon as March. “It is hard to argue against knowing more,” he said. “Knowing and understanding more about the biology and the ecology of the organism will ultimately help us to control its incidence in the food supply.”

About Prof. Wommack

K. Eric Wommack is a professor in UD’s Department of Plant and Soil Sciences in the College of Agriculture and Natural Resources.

He also has appointments in the Department of Biological Sciences in the College of Arts and Sciences and in the marine biology and biochemistry program in the College of Earth, Ocean, and Environment. His laboratory is based in the Delaware Biotechnology Institute.

Wommack received a doctorate in marine estuarine environmental sciences from the University of Maryland, a master’s degree in physiology from the University of St. Andrews in Scotland and a bachelor’s degree in economics from Emory University in Atlanta.

He is a member of the American Society for Microbiology, the American Society of Limnology and Oceanography and the International Society for Microbial Ecology.

Article by Adam Thomas

Photo by Evan Krape

This article can also be viewed on UDaily

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UD researchers identify novel regulatory network within legumes

January 26, 2012 under CANR News

Three collaborating laboratories in the Department of Plant and Soil Sciences at the University of Delaware — those of professors Blake Meyers, Janine Sherrier and Pamela J. Green — recently identified a novel regulatory network within legumes, including in alfalfa and soybean plants.

The work was performed predominantly by Jixian Zhai, a doctoral student in the department and was published in the December issue of the prestigious journal Genes & Development, one of the top journals in molecular biology and genetics. The genomics project was funded by a grant from the U.S. Department of Agriculture.

Conducting their research at the Delaware Biotechnology Institute (DBI), the investigators set out to get a comprehensive view of how small RNAs function in legumes and how they might be important to these plant species. They focused their work on the chromosomal sequences (genome) of Medicago, a legume genus that includes both the crop plant alfalfa and the species that was recently sequenced, Medicago truncatula.

The researchers sequenced libraries containing millions of small RNAs, important gene regulatory molecules, as well as the genes targeted by these small RNAs. Using advanced computational techniques to categorize the RNA sequences, they identified a novel function for a handful of “microRNAs” — special small RNAs that direct the targeted destruction of specific protein-coding messenger RNAs.

Among these plant microRNAs, the team determined that many target genes encode NBS-LRRs, or “guard proteins” that function in defense against pathogenic microbe infiltration. These NBS-LRRs function as an immune system to battle pathogens but presumably must be suppressed to allow the interactions with beneficial microbes for which legumes are particularly well known. The result of this microRNA targeting is a complex network of co-regulated small RNAs that Zhai characterized using a set of computational and statistical algorithms and analyses.

“The NBS-LRRs keep pathogens out, but these plant cells are still allowing beneficial microbes to enter,” says Sherrier. “The regulation of genes encoding NBS-LRR proteins has been largely unknown until now.”

Over time, these mechanisms have evolved into a more elaborate system in legumes to take advantage of this defense-suppressing system and facilitate the development of nodules, the specialized root structures of legumes in which the beneficial plant-microbe interactions take place.

“We may have found the ‘switch’ that recognizes good versus bad microbes,” adds Meyers, Edward F. and Elizabeth Goodman Rosenberg Professor and chair of the Department of Plant and Soil Sciences. “These guard proteins usually trigger cell death when a pathogen is recognized, but the plant cell is triggering cell death when it encounters a ‘good’ microbe. The circuit we identified may play a role in preventing cell death when the microbe is a friend.”

This discovery could ultimately prove important to the improvement of plant-microbe interactions in other crop plants by allowing plants to become healthier by letting in the good microbes, but keeping the pathogens out.

“We didn’t expect to find something as exciting as this,” says Sherrier. “It’s exciting because no one knows about this kind of gene control and also because it is showing us the diverse interaction between plants and bacterium as well as plants and fungi that could help us develop better mechanisms in other plants, like Arabidopsis.”

“Beyond the applied significance, the finding that NBS-LRR genes are key targets opens up a new frontier for basic research,” says Green, Crawford H. Greenewalt Professor of Plant and Soil Sciences.

If this diverse regulation of beneficial microbes could be added to other crop plants, it could mean scientists could program the plants to grow stronger and taller with less water, and even fertilize themselves.

Article by Blake Meyers and Laura Crozier

Photos by Evan Krape and Kathy F. Atkinson

This article was originally published on UDaily

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University’s Kniel, Everts join study of produce safety

December 9, 2011 under CANR News, Cooperative Extension

Researchers at the University of Delaware are participating in a project that is focused on increasing produce safety and delivering more trustworthy salad fixings.

Total funding for the University of Maryland-led project amounts to $9 million, with $5.4 million in contributions coming from the U.S. Department of Agriculture’s National Institute of Food and Agriculture and substantial industry funds.

The three-year study promises to be one of the most comprehensive studies of fresh produce safety ever conducted.

Produce safety has been a hot topic ever since 2006, when a deadly batch of spinach killed three people and sickened hundreds of Americans. The project will involve extensive testing and data collection by industry, supplemented by field experiments involving eight other university and federal laboratories around the country.

Kali Kniel, associate professor in UD’s Department of Animal and Food Sciences, and Kathryne Everts, professor and Cooperative Extension specialist in plant pathology at Maryland with a joint appointment at UD, are part of the University of Delaware team.

“Since the large outbreak of E. coli in 2006 which was traced back to spinach grown in the Salinas Valley of California, produce commodities have been under great scrutiny,” Kniel said of the project. “As we all know fresh fruits and vegetables are grown outside, which puts them at great risk for coming in contact with biological hazards like pathogenic bacteria and viruses. There are some processes that growers and packers can do to reduce the risk but the science is still not there to completely understand what those are. This project will help to resolve that for very important and ‘high-risk’ products, including leafy greens and tomatoes.”

Kniel explained the role that she and Everts will play in the study, saying, “Dr. Everts and I will be working with the farmers and packers to both develop metrics and to disseminate the science-based results of the project.  I am particularly looking forward to working with regional growers and packers to help them deal with the food safety challenges including increased biological testing and best practices for safe compost and water use.”

Robert Buchanan, a University of Maryland professor and director of its Center for Food Safety and Security Systems, is heading the research initiative.

In addition to UD and Maryland, other universities involved include Ohio State University, Rutgers University, the University of California Davis, the University of Florida and the University of Maryland Eastern Shore. The USDA and the Food and Drug Administration (FDA) will be involved in the research as well.

The initiative’s industry partners — representing more than 90 percent of the leafy greens and tomato production in the United States — will conduct about 200,000 separate tests during the project to measure the presence of pathogens.

“This project is very unique in that it has the support of the industry on a significant scale. We have a great team of scientists and great industry support,” Kniel said.

The research aims to create the scientific basis for detailed safe, hygienic practices in farming, packing, transporting and storing fresh produce.

The idea is to prevent water, air or ground sources of pathogen contamination by setting standards or benchmarks that can be applied in a variety of growing regions and countries.

The study will examine questions such as how far apart do you need to keep a lettuce patch from pigs or other farm animals to prevent bacterial contamination and what kinds of barriers are needed to prevent contaminated water from reaching crops?

Members of the research team said they believe the project will give regulators, farmers, packers and others along the supply chain the scientific and technological knowledge needed to develop and defend produce safety protocols, or “metrics” as the industry calls them.

At the production stage, the research will focus on air, water and other environmental factors related to potential contamination by pathogens; risks during harvesting, packing, and processing; as well as temperature and other handling concerns as produce moves to market.

Photos by Ambre Alexander

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UD’s Wisser receives USDA grant to study genetic barriers in corn

November 15, 2011 under CANR News

When it comes to crops in the U.S., corn is king. Just because it is king, however, does not mean that breeders and in turn growers are using corn to its fullest potential.

With this in mind, the University of Delaware’s Randall Wisser and a group of six fellow researchers have received a five-year $4.2 million grant from the U.S. Department of Agriculture’s National Institute of Food and Agriculture (USDA-NIFA) to study the genetics of adaptation and crop improvement.

Wisser, assistant professor in the Department of Plant and Soil Sciences, said that “there is a great deal of diversity in corn, or maize, particularly in the tropics, which has generally been underutilized in the U.S.” This is because tropical sources of maize are unadapted to North American environments.

Wisser added, “It is virtually impossible to realize the potential breeding value of maladapted materials; finding ways to efficiently adapt crops to new environments is a frontier of agricultural genetics research.”

Populations that lack genetic diversity can fall prey to climate change or other stressors by not having an array of genes on which to draw from. Breeding-based solutions to addressing abiotic and biotic challenges require access to genetic diversity. “If you’re drawing from a limited sample of diversity, the likelihood that you’ve got the necessary genes is less,” Wisser said.

Through its research, the team aims to help plant breeders increase breeding efficiency and access more genetic diversity, increasing their capability of responding to current and future challenges in food production.

Wide-ranging study

The research team is conducting a range of studies that combine field and controlled environment testing with genome sequence analysis and analytics.

In one avenue of research, they are working to better understand the genetics underlying how environment variables such as temperature and day lengths influence plant maturity, a primary barrier to adaptation.

When tropical maize is grown in a North American environment, like Delaware, where summer day lengths can reach up to 15 hours (compared to 10-12 hour days in the tropics), the plants are not receiving the appropriate signals that tell them to flower. They just keep growing, getting very tall and producing lots of leaves, flowering very late or not at all. The plants are out of synch with the growing season and get damaged by frosts or produce no seeds.

Maize that now grows in the U.S. has been adapted over hundreds of years with increasing selection intensities. Through many generations of breeding, an elite pool of maize plants have been developed for North American farmers that are insensitive to long days and flourish in these climates.

“In the process of intense selection, there’s been a big loss in potentially valuable genetic diversity,” Wisser said. “We are thinking about ways to recoup some of what has been lost to help deal with the complex problems of the future”

In another study of the project, the team will test if there are common regions in which the corn genome is associated with broad environmental adaptation or in which genetic barriers are created.

The group will track the flow of genes across generations of selection in the same tropical population adapted to a broad range of environments from Wisconsin to Puerto Rico.

“If adaptation is achieved through one or a few genetic tracks, then existing methods can be used to more quickly adapt tropical maize to different environments,” Wisser said. “If, on the other hand, there are multiple independent genetic tracks to adaptation then a different set of solutions will be needed.”

Wisser said he is hopeful that by studying the adaptation process researchers can pinpoint the barriers that limit use of tropical genetic diversity for North American maize improvement and “open the flood gates” for accessing maize diversity.

The research team

Other investigators in the study are Sherry Flint-Garcia from the USDA-Agricultural Research Services (ARS) and University of Missouri; James B. Holland from the USDA-ARS and North Carolina State University; Nick Lauter from the USDA-ARS and Iowa State University; Natalia deLeon from the University of Wisconsin-Madison; and Seth Murray and Wenwei Xu from Texas A&M University.

Further information about the Maize ATLAS (Adaptation Through Latitudinal Artificial Selection) project can be found at this website.

The study is funded by the USDA Climate Change Mitigation and Adaptation in Agriculture program, which also funded research by Carl Schmidt, associate professor of animal and food sciences and biological sciences at the University of Delaware, concerning heat stress in poultry. For more on that story, see the earlier UDaily article.

Article by Adam Thomas

Photo by Danielle Quigley

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Stink Bug Season

October 3, 2011 under CANR News, Cooperative Extension

Pull up the welcome mat; they’re back. It’s early fall in Delaware, which means pumpkins on the vine, apples on the trees and stink bugs in the house.

“Last year, I got a flood of calls about stink bugs during the last week of September,” said Brian Kunkel, an entomologist with the University of Delaware’s Cooperative Extension. “Sure enough, this past week, Extension has been hearing from homeowners trying to get rid of stink bugs.”

“As the days grow shorter and the evening temperatures cooler, Delawareans are discovering these uninvited houseguests in their garages, porches and decks, as well as inside the house,” Kunkel said. “The brown marmorated stink bug becomes a nuisance pest when it heads inside to find overwintering sites.”

While merely an annoyance to most homeowners, the brown marmorated stink bug (BMSB) poses an economic threat to Delaware agriculture. Fruit crops seem to be at greatest risk, especially peaches and apples. About 18 percent of the mid-Atlantic apple crop had stink bug damage last year, according to the U.S. Apple Association.

“West Virginia apple orchards experienced significant crop loss last season because of the BMSB,” Kunkel said. “Here at UD, we’re doing everything we can to make sure that we don’t see the kind of crop loss that West Virginia had.”

Several of Kunkel’s colleagues in Extension and UD’s College of Agriculture and Nature Resources are researching BSMBs in soybean, lima bean, sweet corn, field corn and sweet pepper fields.

Two of the most active researchers are Joanne Whalen, the Extension’s integrated pest management specialist, and Bill Cissel, an Extension associate who is investigating stink bugs as part of his graduate studies.

Cissel and Whalen, assisted by two interns, are examining stink bugs in conditions similar to home yards and gardens, too. In UD’s Garden for the Community, a one-third-acre plot on the Newark campus, the duo surveyed stink bug nymphs, adults and egg masses on plants commonly grown in home gardens — tomatoes, zucchini, yellow squash, cucumbers, eggplant, sunflowers and bell peppers. Plus, they’re studying a plot of ornamental plants to see which plants stink bugs use as hosts.

Rutgers University, Virginia Tech, the University of Maryland and the Delaware Soybean Board are some of the partners on one or more of these projects.

Although Delaware has several native stink bugs, BMSBs originates in Asia and were accidentally introduced to the United States. First collected in Allentown, Pa., in 1998, BMSBs have been spreading across the eastern half of the U.S. ever since.

Kunkel said spiders and birds have been known to eat BMSBs (he’s heard reports of house cats eating them, too) but the pest has no recognized natural predator here.

The USDA Beneficial Insects Introduction Research Lab, housed on UD’s campus, is investigating biocontrol measures. Biocontrol introduces natural predators into an environment to control, if not eradicate, the pest problem. But the rigorous research process and government approvals needed for biocontrol measures can take years, even decades.

Delaware’s farmers are asking for help now. So the focus of Whalen and Cissel’s research is on monitoring to determine when to control stink bugs, as well as which insecticides provide the best control.

Field observations in 2010 indicated that stink bug infestations usually start on the perimeters of fields, Cissel noted. “We’re studying whether perimeter applications of insecticides will prevent stink bugs from penetrating the interior parts of soybean fields,” he said.

“In our corn research, we are trying to determine how much damage stink bugs are causing and when the plant is most sensitive to damage — is it when it’s silking, during grain fill or closer to harvest?”

Insect research projects typically run for two to three seasons, and most of the UD studies are in their first year. So it’s too early to discuss preliminary results, Cissel said, especially since the BMSBs weren’t as active this summer as previously.

“We had a really large outbreak last year,” Kunkel said, “but we’re not seeing those kinds of numbers this year.”

Tell that to Kathy Fichter, a resident of Chadds Ford, Pa.

“It’s just as bad as last year and it’s only the beginning of stink bug season here,” said Fichter, who always has a tissue at hand, ready to scoop up stink bugs. “My two sons won’t go near them, and these are boys who like bugs,” she said.

“Our neighborhood seems to be a ‘vacation destination’ for stink bugs. They come here by the hundreds, maybe even thousands,” she added. “My neighbors are in the same predicament. Yet, a few miles away, they aren’t such a nuisance.”

Kunkel isn’t surprised by Fichter’s stink bug woes, even though regional conditions are generally better. “Stink bug outbreaks — and insect outbreaks in general — tend to be localized,” he said. “We often hear of one neighborhood getting slammed while another neighborhood a half-mile away will have very few bugs.”

If the BMSB already has arrived at your house — or you want to make sure it doesn’t — take control measures now. The best thing you can do, Kunkel said, is to seal all cracks around windows, doors, siding, utility pipes and chimneys. Often overlooked, he said, are the cracks that can appear around dryer vents and gaps around window air-conditioning units.

“Try to look on the bright side,” Kunkel said. “Stink bugs that get inside are helping you to winterize your house. Wherever they got in today is where the cold winter winds will, later this year.”

Article by Margo McDonough

This post also appears on UDaily.

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Mexico delegation visits UD Extension

September 21, 2011 under CANR News, Cooperative Extension

A delegation representing the Mexican Ministry of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA) recently visited the University of Delaware to get a firsthand look at how agriculture extension works in the First State and how that might be useful in establishing similar programs in Mexico.

The daylong sojourn included meeting with Robin Morgan, dean of the College of Agriculture and Natural Resources, and UD Cooperative Extension program leaders and county extension directors. A tour of the UD farm hosted by Scott Hopkins, farm superintendent, and a flavorful visit to the UDairy Creamy complemented morning and afternoon information sharing sessions held in Townsend Hall.

“We are delighted to have you here,” Morgan told members of the delegation. “We are always trying to promote Cooperative Extension.”

Morgan noted UD’s status as a land-grant university with a three-part mission that includes teaching, research and outreach.

“Celebrating that outreach component is very important to us,” Morgan said. “Cooperative Extension has really changed agriculture in America, and if we have anything to do with it, that will continue as we go forward.”

Jose de Jesus Alaya Padilla, director general of Mexico’s National Institute for the development of Capacities of Rural sector (INCA Rural), said that convincing faculty members that is to their benefit to participate in university-based extension programs represents a significant challenge.

“We find that some researchers in the universities say they don’t have enough incentives to go out there and do extension services,” Padilla said. “We worry about that.”

Morgan noted that a similar situation exists at American universities, where faculty members are promoted based on their publications and the grants they receive.

“What we have done here is to give people very clear appointments, and to let those people do scholarship in extension and document that,” Morgan said. “We have had really good success because individuals have done stellar work. We then document this with outside peer reviews.”

The remainder of the story can be viewed online on UDaily by clicking here.

Article by Jerry Rhodes

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Register for Jan. 15 Friends of Ag Breakfast

January 4, 2010 under CANR News, Cooperative Extension, Events

Register now for the January 15th Friends of Agriculture breakfast with Michael Scuse, USDA Deputy Under Secretary for Farm and Foreign Agricultural Services.  Click here for more information or to register.

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