UD professor seeks holistic understanding of disease resistance in maize

February 25, 2014 under CANR News

UD professor seeks holistic understanding of disease resistance in maizeThe University of Delaware is leading an interdisciplinary project aimed at unraveling the biology of a durable form of disease resistance in maize.

A grant from the National Science Foundation Plant Genome Research Program (NSF-PGRP) has brought together a team of experts in breeding, genetics, pathology, bioimaging and computer science to generate new knowledge that can be leveraged in the staple crop when breeding for disease resistance.

Randall Wisser, assistant professor in UD’s Department of Plant and Soil Sciences is leading the five-year, $3.9 million project.

Working with seven other investigators at Iowa State University (ISU), Cornell University, North Carolina State University (NCSU), and the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Wisser explained that the group is trying to gain a holistic understanding of disease resistance.

“To date, we’ve focused on dissecting the genetics, trying to figure out what the genes are,” said Wisser. “In some cases we’ve been successful, but there are many more genes we have not yet identified; we still don’t understand how the genes work or how they act together to cause resistance.”

How cells react

A significant component of the project at UD consists of the researchers adapting bioimaging technologies to study natural genetic variation in disease resistance. For this, three of the labs are collaborating.

In controlled environments, Rebecca Nelson, professor at Cornell University, and Peter Balint-Kurti, research geneticist with USDA-ARS at NCSU, perform genetic experiments from which infected tissue is sampled and shipped off to UD.

Wisser and Jeff Caplan, director of the BioImaging Center at the Delaware Biotechnology Institute (DBI), work together to analyze microscopic images of the samples.

Studying hundreds of tissue samplesthe team captures numerous snapshots across each sample in microscopic detail and in 3D. Then, from more than 1,000 separate images taken on each sample, the researchers use computational techniques to reconstruct the images into their original form.

With these large format images, the team initiated a collaboration with Chandra Kambhamettu, professor in UD’s Department of Computer and Information Sciences and director of the Video/Image Modeling and Synthesis (VIMS) Laboratory, to adapt methods from computer vision research that allow features within the images — such as the number of cells the pathogen has infected — to be characterized.

In the end, the team is able to gain an understanding of how a specific resistance gene or a group of resistance genes act to cause resistance.

Wisser summarized the technique’s important effect, saying, “We’re not just taking a picture of the surface, we’re actually taking pictures as though we are peeling layers off the tissue one at a time. Also, because of the relatively large area of the leaf we can now image, we can observe plant-pathogen interactions at an unprecedented scale and gain a better understanding of variation in the interactions between pathogens and plants.

“Essentially, what we’ve been able to achieve is the development of an imaging and analysis platform that allows us to quantitatively examine the effects of different genes at the tissue and cellular level. It’s eye-opening, and we’ve only begun scratching the surface.”

Gene identification

The team is simultaneously trying to shine light on the specific genes that underlie disease resistance.

Jim Holland, research geneticist with USDA-ARS at NCSU, leads a component of the project on genetic mapping. Holland, Balint-Kurti, Nelson and Wisser collaborate on sequencing and comparing the genomes of over 250 maize varieties using advanced techniques in genetic mapping, when researchers try to determine the specific genes that control a characteristic like plant disease resistance.

There is typically uncertainty in the process. Therefore, Balint-Kurti and Nick Lauter, assistant professor from ISU, are validating the effects of these genes by searching for extreme mutations and deregulating the gene. If disruptions of the gene cause a change in the plants’ resistance to disease, then they know they are onto something.

Lauter and Alicia Carriquiry, professor from ISU, are also working with Cornell and NCSU to study how the genes are regulated when the pathogens infect. A gene may be turned on or off in response to infection, which further clues the researchers in to the genes that underlie resistance.

Looking at all of these results together allows the researchers to understand the genes associated with resistance, how they function in terms of their internal wiring, how they connect to each other to form a network, and how that network gives rise to disease resistance or susceptibility.

An applied impact

The work on this project addresses issues that relate to the global sustainability of agriculture. Pathogens often evolve quickly to overcome the resistance genes in the cultivars breeders produce, resulting in a constant tug-of-war between the breeder and the pathogen.

This basic research project intersects with applied efforts to have greater durability in disease resistance. The knowledge, methods and resources from the project can be leveraged in the breeding of varieties that have longer lasting resistance, resulting in better food security.

Wisser said that while the group is using maize for its study, the results could have positive effects on many plants. “The things we find are not just applicable to maize and diseases we’re working on here, but there are also some general rules that are likely to surface. So we think that our project has more to offer than helping to solve the issues associated with these specific diseases and the crop that’s the focus of the project.”

Article by Adam Thomas

Photos by Danielle Quigley

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UD’s Ernest receives USDA grant for research on lima beans

December 11, 2013 under CANR News

Emmalea Ernest Research Assistant for Vegetable crops. Plant and Soil Science, Cooperative ExtensionEmmalea Ernest, extension agent in the University of Delaware’s Department of Plant and Soil Sciences (PLSC), has received federal funding from the U.S. Department of Agriculture’s Specialty Crop Block Grant (SCBG) Program for a project aimed at developing heat-tolerant lima bean varieties.

“Lima beans are Delaware’s largest acreage vegetable crop and anchor the state’s processing vegetable industry,” said Ernest. “The varieties that are currently available to growers suffer yield loss or delayed yield when they are exposed to high temperatures during flowering.”

In order to be eligible for funding from the program, grant money had to be used toward specialty crops as opposed to field crops, such as corn and soybeans, or animal agriculture. Specialty crops are a wide-ranging category that includes fruits, vegetables, dried fruits, tree nuts, horticulture, and nursery crops.

With her funding, Ernest aims to develop procedures for heat tolerance screening in the existing lima bean breeding program, examine the physiological mechanisms for heat stress tolerance or susceptibility in lima beans, and investigate the underlying genetic basis for heat stress tolerance in lima beans. Her findings could greatly impact Delaware vegetable farmers’ yields.

Ernest said she has collaborated on multiple USDA Specialty Crop Block Grants in the past six years and acknowledged that the program has been a vital source of funding to the Extension Vegetable and Fruit Research Program. The money has allowed Ernest to help address production problems many Delaware fruit and vegetable growers have experienced, as well as explore new crop prospects.

The SCBG program seeks out projects like Ernest’s in order to promote and enhance the local agricultural economy.

“My past and current grant projects through this program have included work on lima beans but also on a variety of other crops, including processing sweet corn, blueberries, snap beans, cucumbers and cantaloupes,” said Ernest.

Her research with lima beans will be over the course of the next three years and take place on UD’s research farm in Georgetown.

Ernest said that in the genetics portion of the project, which will be built off of work funded by the Building a Better Bean SCRI Grant awarded to UD researchers last year, she will be working closely with colleague Randy Wisser, assistant professor of plant and soil sciences, and Gordon Johnson, extension vegetable and fruit specialist.

Article by Angela Carcione

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UD awarded $1.5 million USDA grant to study lima beans

January 11, 2013 under CANR News, Cooperative Extension

Researchers from UD study lima beansDelaware is currently the number two producer of lima beans in the United States, second only to California and with the possibility of becoming number one in the future.

Because of this, it is imperative to study the many aspects of various diseases affecting the crop in Delaware and throughout the mid-Atlantic region.

Such work requires a collaborative effort and a team has been assembled thanks to a five-year, $1.5 million U.S. Department of Agriculture (USDA) Specialty Crop Research Initiative grant.

The grant awarded to the University of Delaware includes researchers from UD, Delaware State University, the University of Maryland, Ohio State University, Cornell University and the University of California Davis (UC Davis) who will begin studying the various effects of plant disease on lima beans in the First State.

The many aspects of this grant will include studies that are being conducted for the first time in history.

There are six components to the grant, each with various researchers studying different parts of the problem. They are conducting research on downy mildew, pod blight, white mold, root knot nematodes and germplasm resources and developing an economic analysis.

Downy mildew

Downy mildew is a fungal-like disease of the lima bean caused by Phytophthora phaseoliand the goal of the research team is to improve disease forecasting and look at genetic diversity of the population of the pathogen. In this way, researchers will be able to inform farmers of their risk of occurrence of the disease and have a better understanding of the genetics of the pathogen.

Tom Evans and Nicole Donofrio, professors of plant pathology in the Department of Plant and Soil Sciences in UD’s College of Agriculture and Natural Resources, and Nancy Gregory, plant diagnostician for UD, will work together on this part of the project.

Pod blight

Pod blight is caused by the pathogen known as P. capsici and Gordon Johnson, assistant professor of plant and soil sciences at UD, will work on this part of the study with Evans and Gregory.

Unlike downy mildew, which is a disease that generally affects only lima beans, P. capsicihas a very wide host range. Once it strikes a particular crop, it is very difficult to get rid of, with pathogen’s spores lasting up to 10 years in the soil. Because of this, pod blight is an increasing problem for growers. The disease occurs in low-lying areas of fields and is more frequent in wet years. Therefore, this part of the project has three goals: to look for a fungicide to deal with the disease, to monitor the disease, and to look for alternative or organic non-pesticide driven strategies for control.

The study is also looking at risk management strategies, including information for growers in the state about the best time to spray for disease control and consideration of alternate control strategies.

Gregory, who diagnoses field samples collected by the research team and growers, maintains cultures of the pathogens and produces  the inoculum for the studies, said that the researchers are eager to “learn more about the epidemiology and the spread of pod blight and downy mildew, that will enable us to do a little bit better job on forecasting.”

She also noted how great is to have so many expert researchers involved, noting that she is looking forward to making significant progress on problems that have plagued the region for years. “To pull together a strong team of researchers like this and many new graduate students is really going to pull a lot of this research together and we’ll really come up with some great results.”

White mold

Kate Everts, an adjunct associate professor of plant and soil sciences at UD and a Cooperative Extension specialist with both UD and the University of Maryland, is leading research on alternative ways to control white mold, another disease that is very difficult to eliminate.

With an even broader host range than P. capsici, and an even longer life — persisting in soils for 20-30 years — finding out as much about the disease as possible, as well as possible ways to control it, is imperative.

Everts will look not just at lima beans but other crops, as well, as she tests biological control strategies and alternative control strategies for dealing with the white mold.

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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

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Wisser and Meyers establish connections with African Institutions

August 16, 2011 under CANR News

Researchers from the University of Delaware College of Agriculture and Natural Resources (CANR) visited Ghana earlier this summer to meet with plant breeders and discuss the development of a software package they are calling “The Breeders’ Toolbox.” Since 2009, a team of researchers have been fleshing out ideas, assessing demand, and identifying partners for the production of an integrated suite of software tools tailored to the meet the needs of plant breeders in developing countries.

Randy Wisser, assistant professor in the Department of Plant and Soil Sciences, who serves as the group’s principal investigator, and Blake Meyers, Edward and Elizabeth Goodman Rosenberg Professor and chair of the Department of Plant and Soil Sciences, traveled to Ghana in June. They were joined by co-investigator Stefan Einarson, Director of Transnational Learning from Cornell University.

Other UD group members include Lori Pollock, professor in the Department of Computer and Information Sciences, and Jong-Soo Lee, assistant professor in the Department of Food and Resource Economics.

During their visits to Ghana in October 2010 and June 2011, team members established important connections with representatives of plant breeding educational and research institutes and got feedback on the proposed software, which would help improve yields of a wide range of crops. “Plant breeders are key players in the fight for food security. Breeders produce the varities grown by practically all farmers; empowering breeders with efficient tools can have a widespread impact,” explained Wisser.

The team established collaborative relations with the West African Center for Crop Improvement (WACCI) located in Accra, Ghana. WACCI trains many students, offering doctoral degrees in plant breeding, and Wisser added, “We’re partnering with them because the students going there are the future plant breeders of Africa. They are the end-users of the tools we develop.”

Wisser also noted that the students attending WACCI are from all over Africa, so they represent different cultures and have had different experiences in their home countries. This gives the team the opportunity to develop tools with greater awareness of the various needs across Africa so that they are more likely to be widely adopted.

Another key partnership is with breeders at Crops Research Institute (CRI), located in Kumasi, Ghana, which is the epicenter of plant breeding in Ghana. Wisser noted that making the connection with CRI-Kumasi is important because “many of the countries breeders who specialize on different crops are stationed at one location, and that’s important for us because we are trying to develop a tool that can work for any crop.”

Wisser explained that current software at the disposal of plant breeders is not designed for plant breeding. The Breeders Toolbox the research team is seeking support to develop will be open-source and very flexible. It would simplify the design and analysis of field experiments in a more user-friendly platform for plant breeders of various skill levels.

Travel to Africa was made possible through funding from UD’s International Research Office, CANR, and the departments of Food and Resource Economics, Plant and Soil Sciences, and the College of Engineering’s Department of Computer and Information Sciences.

Article by Adam Thomas

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CANR researchers team up to combat lima bean disease

February 3, 2011 under CANR News, Cooperative Extension

When battling downy mildew, a potentially devastating disease that strikes lima beans (Phaseolus lunatus), one of Delaware’s most important vegetable crops, assembling a team of experts to attack the problem from all angles is a must. That’s why a diverse group of plant scientists in the University of Delaware’s College of Agriculture and Natural Resources has joined together to battle this important plant disease.

Tom Evans, professor of plant pathology in the Department of Plant and Soil Sciences, and many graduate students have studied downy mildew over the past 15 years.

Evans said lima beans are vital to agriculture in Delaware and are “the cornerstone of the state’s processing vegetable industry.” Approximately 6,000 hectares of baby lima beans are grown annually, with a farm value of over $6 million. If lima bean cannot be grown profitably in the state, then many other processing vegetables would not be grown due to the economics of processing.

Downy mildew, caused by the fungus-like organism Phytophthora phaseoli, is prevalent in Delaware because it thrives in humid conditions, and lima beans are grown on small, dense acreage. Evans said that most lima bean growers are concentrated in close proximity from Dover to Georgetown and from the Delaware Bay west into Maryland, so wind-driven rain makes it easier for the pathogen’s sporangia to move from one lima bean field to another.

That was the case in 2000, when downy mildew caused $3 million damage in what Evans called “the largest downy mildew of lima bean epidemic ever recorded.” Two factors contributing to this epidemic were the emergence of a new race of the pathogen, Race F, which overcame the genetic resistance of lima cultivars being grown, and frequent wind-driven rain that spread the pathogen’s sporangia.

With the emergence of Race F, growers could no longer rely on downy mildew resistant lima bean cultivars to prevent the disease, as they had in the past. New cultivars with resistance to Race F need to be developed and in the meantime growers have relied upon fungicides to manage the disease.

Bob Mulrooney, extension specialist in plant pathology, has tested fungicides for effectiveness against downy mildew for a number of years and has identified new more environmentally-friendly chemicals which offer good control. Mulrooney’s research results are the basis for growers’ current downy mildew management practices.

Evans and his group have been responsible for studying the biology of the pathogen, monitoring the evolution of new races of the pathogen and the epidemiology of the disease.

Extension associate Nancy Gregory diagnoses the disease on samples sent in by growers, maintains the pathogen in culture for field and greenhouse experiments, and determines their races.

Emmalea Ernest, an extension associate at the Carvel Research and Education Center in Georgetown, Del., breeds lima bean for desirable traits, such as disease and drought resistance, and is developing cultivars for Delaware farmers. Ernest and Evans work together screening lima bean germplasm from around the world for resistance to races E and F of P. phaseoli. Ernest has conducted experiments to determine how the resistance genes are inherited. After making crosses between resistant parents followed by several years of field screening, Evans and Ernest are testing lima bean lines with resistance to both races this summer.

Nicole Donofrio, assistant professor of plant and soil sciences, is responsible for the pathogen side of the study, trying to understand the pathogen’s virulence mechanisms, and how it evolves to attack certain aspects of the plant. Donofrio said, “In order to fight the disease, you have to know your enemy, and the more you know your enemy, the more equipped you are to tackle it when things like a new race emerge.”

Knowing exactly how to fight against the disease from a pathogen standpoint is difficult. Donofrio points out that P. phaseoli has over 500 effector genes, molecules that bind to a protein altering its activity and enabling infection. To study effectors, Donofrio and doctoral student Sridhara Kunjeti took a two-pronged approach. First, they took what they knew about P. infestans, the pathogen responsible for the Irish potato famine and a close relative of P. phaseoli, and searched for similar genes in P. phaseoli to determine if it used similar mechanisms in its attack on lima bean.

Next, they looked at lima beans that had been infected for three and six days to see which effectors were active during those time-points of infection. Donofrio said this could lead to a breakthrough because if they are able to characterize the effector genes, they can look for traits that could be a countermeasure to pathogen attack and thereby block pathogenesis.

Randy Wisser, assistant professor of plant and soil sciences, works on aspects of quantitative genetics and plant breeding and Blake Meyers, Edward F. and Elizabeth Goodman Rosenberg Professor and chair of the Department of Plant and Soil Sciences, works on genomics of lima bean-downy mildew interactions.

In various combinations, the research team has received over $200,000 from various CANR seed grants and Delaware state grants to more fully explore P. phaseoli and downy mildew.

Article by Adam Thomas

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CANR Summer Institute offers glimpse of graduate student life

July 20, 2010 under CANR News

This summer five undergraduate students are conducting research with faculty mentors in the University of Delaware College of Agriculture and Natural Resources (CANR), experiencing the challenges and rewards of what a graduate education at UD might be like.

As participants in the Summer Institute in the Agricultural and Natural Resources Sciences, hosted by the college, these students are taking part in ongoing research projects guided by personal faculty mentors, networking with current graduate students and other staff within CANR, and interacting with industry professionals.

“The Summer Institute is a team effort by faculty from all departments in our college,” said Tom Sims, deputy dean of the college. “It provides these five outstanding undergraduate students the opportunity to conduct hands-on research and learn about the range of graduate education opportunities available in the agricultural and natural resources sciences.”

Now in its second year, the 10-week program — funded by the college and a Graduate Innovation and Improvement Grant from UD’s Office of Graduate and Professional Education – draws students from under-represented populations who are interested in a graduate degree in agriculture and natural resource sciences.

Maria Pautler, the program’s coordinator, said the Summer Institute was expanded from 4 to 10 weeks after last year’s participants suggested a longer program. The extended program allows students to become more involved with their research projects and present their findings at a campus-wide symposium at the end of the summer, she said.

“This, coupled with opportunities to attend seminars, workshops, and panelist luncheons, is exposing the students to facts and opinions on preparation for, and life in and beyond, graduate school,” Paulter said.

The 2010 CANR Summer Institute participants are:

Kamedra McNeil, of Forestville, Md., is a molecular biology major at Winston-Salem State University in North Carolina. McNeil is involved in the Winston-Salem Student Government Association, Tri-Beta Biological Honors Society, NSCS Scholars and Pre-Marc Scholars. She is interested in a career in forensic biology. During her time at the Summer Institute, McNeil is studying different genes associated with photoperiod in plants. Her faculty mentor is Randall Wisser, assistant professor of plant and soil sciences.

Shurnevia Strickland, of Philadelphia, is a senior applied animal science major at UD. Strickland is secretary and webmaster for Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS). She is interested in future research with genetics. At the Summer Institute, Strickland is studying the endothelin 3 gene in the silkie chicken. Her faculty mentor is Carl Schmidt, associate professor of animal and food sciences.

Rochelle Day, of Laurel, Del., is a senior pre-veterinary medicine and animal biosciences major at UD. Day is a member of Puppy Raisers of UD (PROUD) and MANRRS, and is looking toward a career in animal pathology. At the Summer Institute, Day is mapping the genome of the Infectious Laryngotracheitis Virus (ILTV), an upper respiratory disease in birds that causes economic losses for the poultry industry. Her faculty mentor is Calvin Keeler, professor of animal and food sciences.

Rothman Reyes, of Long Island, N.Y., is a sophomore pre-veterinary medicine and animal biosciences major at UD with minors in sexuality and gender studies, and women’s studies. Reyes raises puppies for Guiding Eyes for the Blind and is a member of the LEARN mentor program. He also serves as co-president of the PROUD special interest community. Reyes hopes to practice veterinary medicine at a zoo. At the Summer Institute, Reyes is creating a fosmid library, where he will induce a mutation onto the Infectious Laryngotracheitis Virus (ILTV) to create a vaccine. His faculty mentor is also Calvin Keeler.

Kristina Barr, of Kingstree, SC., is a senior biology major at Benedict College in Columbia, S.C. She is a member of the Environmental Awareness Club at her school and plans to pursue a career as an ecologist. Her research at the Summer Institute involves the effects of rose bushes on birds’ ability to forage for food. Her faculty mentors are Jacob Bowman, associate professor, and Greg Shriver, assistant professor, both of entomology and wildlife ecology.

Article by Chelsea Caltuna

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