UD Cooperative Extension aids UD researcher at Delaware Ag Week

February 10, 2014 under CANR News, Cooperative Extension

Professor Kent Messer and his team of researchers poll farmers at Ag WeekSometimes, an offer can seem too good to be true. The University of Delaware’s Kent Messer was worried that would be the case with his latest research project — one that promised land owners in the state who owned more than 10 acres of land $50 simply for completing a 30-minute survey and offered up to $40,000 worth of funding to support cost share and landowner incentives to help implement nutrient management practices on private property.

Luckily for Messer and his research team, University of Delaware Cooperative Extension — in conjunction with Delaware State University Cooperative Extension and the Delaware Department of Agriculture — was holding Delaware Ag Week in Harrington at the Delaware State Fairgrounds and welcoming around 1,900 visitors, many of them land owners.

“We were able to piggyback on Extension’s work and trust with the farmers,” said Messer, Unidel Howard Cosgrove Chair for the Environment in the Department of Applied Economics and Statistics (APEC). “Our research was more believable because we were at Ag Day.”

“This is an excellent example of outreach and engagement within UD,” said Michelle Rodgers, associate dean for Cooperative Extension in the University’s College of Agriculture and Natural Resources. “Cooperative Extension is a key partner in the Ag Week event which provided over 97 educational sessions with over 1900 attendees. Students involved in the survey were introduced to Cooperative Extension programming and through the event were able to meet face to face with their desired survey participants. This is was a win-win for the researchers and the research participants.”

Messer’s project is sponsored by the U.S. Department of Agriculture (USDA) Economics Research Service and at Ag Week, his team conducted a field experiment on nutrient management practices and landowners’ attitudes toward and adoption of those practices.

The USDA project had funding to support cost share and landowner incentives to help implement nutrient management practices on the ground. Messer’s team asked landowners about conservation buffers, areas that are vegetated along streams and ditches either by grass or forest, and asked the landowners how much they would be willing to share the costs of those practices.

Messer singled out Jennifer Volk, extension specialist in the Department of Plant and Soil Sciences, for helping to identify practices relevant to Delaware for the survey that are not currently available for cost share. “We didn’t want to fund practices that were already supported by state or federal programs; we want to learn about landowners’ attitudes and behavior related to new practices,” said Messer.

Messer said he combined this project with another one of his National Science Foundation (NSF) projects that focuses on the Murderkill Watershed, which has issues surrounding nutrients. If participants had property in the watershed, they were eligible for an extra $25 for taking the survey.

Survey team members included Walker Jones, a master’s degree student in the College of Agriculture and Natural Resources (CANR), Maik Kacinski, a postdoctoral researcher in APEC, Linda Grand and Seth Olson, both seniors in the Department of Applied Economics and Statistics, and Michael Griner, a student from Delaware Technical Community College.

The research team set up shop in Harrington for four days during Ag Week. With four and sometimes six tablet computers available for survey participants, the team members set up through each day of Ag Week and was able to attract 80 people to participate in the survey, which Messer called a “home run.”

“One of the reasons I love Ag week is that it helped ensure our validity. Our booth had a bright blue University of Delaware sign on it. We were in a UD event. Because, in many cases, you could say that this was a too good to be true offer — $50 for a 30-minute survey. We’ll pay up to $40,000 for you to do nutrient management on your land. Most people will see that survey and throw it in the trash because they think there must be a catch.”

Messer said that he was very happy to be able to conduct his research survey at a Cooperative Extension event.

“I’m fundamentally committed to good research that has Extension components. I think that’s a wonderful pillar of the land grant and these are exciting opportunities to collaborate. This is a time when the Extension efforts helped the research project,” said Messer. “We wouldn’t have been successful without having Extension do what it does and having this program that is servicing the landowners. And we were really just able to take advantage of it and participate in it.”

The next steps for Messer and his team include collecting data via mail from participants who were not at Ag Week and finalizing the results of the study.

Article by Adam Thomas

This article can also be viewed on UDaily.

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Sarah Weiskopf places third at the National Wildlife Society Meeting

October 28, 2013 under CANR News

Sarah Weiskopf and Shannon Kachel present their posterSarah Weiskopf, an honors student in the Department of Entomology and Wildlife Ecology (ENWC), presented her poster earlier this month at the National Wildlife Society Meeting in Milwaukee, WI.

The poster, titled, “What do snow leopards really eat? Using genetics to reduce bias in food habit studies,” placed third place at the conference amongst undergraduate presenters.

Weiskopf is completing her senior thesis in Kyle McCarthy’s Rare and Elusive Species Lab, where she works closely with Shannon Kachel, graduate student in ENWC, on snow leopard ecology.

As for the specifics of her research, Weiskopf explained that knowing what snow leopards—an endangered species that live high in the mountain areas of central Asia–eat is critical to their survival. “One of the reasons they’re endangered is lack of natural prey species so it’s really important to have accurate information on what they’re eating for management plans and conservation initiatives.”

Weiskopf, who is supported by the National Science Foundation (NSF) EPSCoR program, and the ENWC department and works with data from Panthera– a global wild cat conservation group–and samples collected by Kachel, said that their research found that snow leopards’ diet consists mainly of large mammals. “When we looked at all the samples that we collected, we found that small mammals like hares and Pikas were not as important in snow leopard diet as we previously thought, and they were actually eating a lot more large mammals like Ibex and Argali.”

The problem with the snow leopards’ diet consisting mainly of these two species is that they are both in danger as well, with both being targets of hunting and poaching and Argali being classified as an endangered species.

“They’re competing with domestic livestock for the food resources in the area and so when you have less natural Ibex and Argali populations, the snow leopards will turn more to eating domestic livestock which creates problems with humans in the area,” said Weiskopf.

Weiskopf said that she is very thankful that she gets to work with Kachel and McCarthy, assistant professor in ENWC, on the project, saying that they both have been very supportive and helpful, even allowing her to work in the lab on her own which she said was a great learning experience.

She also said that the conference was a great experience because she got to listen to a lot of wildlife biologists talk about their respective projects and had the opportunity to present her own work.

As for her work with snow leopards, Weiskopf said that if she continues to study the species, she would love the opportunity to travel to central Asia to study them in the wild, something she might not have known about herself had she not gotten this opportunity.

“It wasn’t something that I thought about before. I didn’t think, ‘Oh, I really want to study snow leopards’ but it was definitely a really cool project to get involved in.”

Article by Adam Thomas

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Researchers reveal the ‘dark side’ of beneficial soil bacteria

September 21, 2012 under CANR News

It’s a battleground down there — in the soil where plants and bacteria dwell.

Even though beneficial root bacteria come to the rescue when a plant is being attacked by pathogens, there’s a dark side to the relationship between the plant and its white knight.

According to research reported by a University of Delaware scientific team in the September online edition of Plant Physiology, the most highly cited plant journal, a power struggle ensues as the plant and the “good” bacteria vie over who will control the plant’s immune system.

“For the brief period when the beneficial soil bacterium Bacillus subtilis is associated with the plant, the bacterium hijacks the plant’s immune system,” says Harsh Bais, assistant professor of plant and soil sciences, whose laboratory group led the research at the Delaware Biotechnology Institute.

In studies of microbe-associated molecular patterns (MAMPs), a hot area of plant research, the UD team found that B. subtilis produces a small antimicrobial protein that suppresses the root defense response momentarily in the lab plant Arabidopsis.

“It’s the first time we’ve shown classically how suppression by a benign bacteria works,” Bais says. “There are shades of gray — the bacteria that we view as beneficial don’t always work toward helping plants.”

In the past, Bais’ lab has shown that plants under aerial attack send an SOS message, through secretions of the chemical compound malate, to recruit the beneficial B. subtilis to come help.

In more recent work, Bais and his collaborators showed that MAMP perception of pathogens at the leaf level could trigger a similar response in plants. Through an intraplant, long-distance signaling, from root to shoot, beneficial bacteria are recruited to forge a system-wide defense, boosting the plant’s immune system, the team demonstrated. In that study, the Bais team also questioned the overall tradeoffs involved in plants that are associated with so-called beneficial microbes.

In the latest work, involving the testing of more than 1,000 plants, the researchers shed more light on the relationship. They show that B. subtilis uses a secreted peptide to suppress the immune response in plants. It is known that plants synthesize several antimicrobial compounds to ward off bacteria, Bais says.

The team also shows that when plant leaves were treated with a foliar MAMP — flagellin, a structural protein in the flagellum, the tail-like appendage that bacteria use like a propeller — it triggered the recruitment of beneficial bacteria to the plant roots.

“The ability of beneficial bacteria to suppress plant immunity may facilitate efficient colonization of rhizobacteria on the roots,” Bais says. Rhizobacteria form an important symbiotic relationship with the plant, fostering its growth by converting nitrogen in the air into a nutrient form the plant can use.

“We don’t know how long beneficial bacteria could suppress the plant immune response, but we do know there is a very strong warfare under way underground,” Bais says, noting that his lab is continuing to explore these interesting questions. “We are just beginning to understand this interaction between plants and beneficial soil bacteria.”

The lead author of the research article was Venkatachalam Lakshmanan, a postdoctoral researcher in the Department of Plant and Soil Sciences; Sherry Kitto, professor of plant and soil sciences; Jeffrey Caplan, associate director of UD’s Bio-Imaging Center; Yu-Sung Wu, director of the Protein Production Facility; Daniel B. Kearns, associate professor in the Department of Biology at Indiana University; and Yi-Huang Hsueh , of the Graduate School of Biotechnology and Bioengineering at Yuan Ze University, Taiwan.

The research was supported by grants from the National Science Foundation.

Article by Tracey Bryant

Animation and images courtesy of Harsh Bais

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UD researchers show how beneficial soil bacteria can boost plant immunity

August 29, 2012 under CANR News

With the help of beneficial bacteria, plants can slam the door when disease pathogens come knocking, University of Delaware researchers have discovered.

A scientific team under the leadership of Harsh Bais, assistant professor of plant and soil sciences in UD’s College of Agriculture and Natural Resources, found that when pathogens attempt to invade a plant through the tiny open pores in its leaves, a surprising ally comes to the rescue. Soil bacteria at the plant’s roots signal the leaf pores to close, thwarting infection.

The fascinating defense response is documented in video and micrographs of live plants taken by confocal and scanning electron microscopes at UD’s Bio-Imaging Center at the Delaware Biotechnology Institute.

The research, which explored the interaction between the soil bacterium Bacillus subtilis and the laboratory plant Arabidopsis thaliana, is published in the August issue of The Plant Journal. The findings underscore both the importance of root-based processes in plant defense and the potential for bolstering plant immunity naturally through the emerging field of probiotics.

Postdoctoral researcher Amutha Sampath Kumar is the lead author of the journal article. In addition to Bais, the co-authors include postdoctoral researcher Venkatachalam Lakshmanan, researchers Jeffrey L. Caplan, Deborah Powell and Kirk J. Czymmek of UD’s Bio-Imaging Center, and Delphis F. Levia, associate professor of geography. The National Science Foundation, University of Delaware Research Foundation and Delaware Experimental Program to Stimulate Competitive Research (EPSCoR) provided funding for the study.

Millions of stomata, consisting of microscopic pores surrounded by guard cells, cover the above-ground parts of plants, from the stems to the flower petals. The pores resemble tiny mouths, or doors, which the guard cells open and close to allow carbon dioxide, oxygen, water and minerals in and out of the plant.

Pathogens also can slip through these stomata and begin infecting the plant. However, as Bais’s team confirmed, this invasion is halted when the beneficial bacterium Bacillus subtilis is present in the soil where the plant is rooted. The finding was based on tests of approximately 3,000 Arabidopsis plants inoculated with the foliar pathogenPseudomonas syringae pathovar tomato DC3000 (PstDC3000) during a year-long period.

When a foliar pathogen attacks, as shown in previous research by Bais and his group, the plant recruits Bacillus subtilis to help and facilitates its multiplication. The Bacillus subtilisbacteria bind to the plant’s roots and invoke abscisic acid and salicylic acid signaling pathways to close the stomata.

Abscisic acid and salicylic acid are both important hormones involved in plant defense. When a plant encounters adverse environmental conditions, such as drought, for example, abscisic acid triggers the stomata to shut tightly to prevent the plant from dehydrating.

In addition to ramping up plant disease resistance, the use of this rhizobacteria to promote drought tolerance in plants could be a very promising avenue, Bais notes.

“Many bacterial pathogens invade plants primarily through stomata on the leaf surface,” Bais says. “But how do plants fight off infection? In our studies of the whole plant, we see this active enlistment by Bacillus subtilis, from root to shoot.”

Strikingly, the research team’s data revealed that of different root-associated soil bacteria tested, only Bacillus species were effective in closing the stomata and for a prolonged period.

“We know only 1 to 5 percent of what this bug Bacillus subtilis can do, but the potential is exciting,” Bais notes, pointing out that there is increasing commercial interest in inoculating crop seeds with beneficial bacteria to reduce pathogen infection. “Just as you can boost your immune system, plants also could be supercharged for immunity.”

Article by Tracey Bryant

Photo by Ambre Alexander

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University of Delaware holds inaugural One World, One Health symposium

August 23, 2012 under CANR News

The University of Delaware held its inaugural One World, One Health animal, human and environmental health symposium, titled “Global Thinking for the Greater Good: Interdisciplinary Health Discourse and Research,” in the Townsend Hall Commons on Wednesday, Aug. 22.

The event was sponsored by the UD College of Agriculture and Natural Resources (CANR), the College of Health Sciences (CHS) and the Delaware Environmental Institute (DENIN) in collaboration with the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS).

The day started off with two concurrent morning sessions running from 9-11:30 a.m. The first, titled “Plugging In,” dealt with regional interdisciplinary health efforts and outlined ways in which University departments and individual researchers can “plug in” to ongoing and future projects.

Speakers included Karl Steiner, senior provost of research development for the Research Office; Kathy Matt, dean of the College of Health Sciences; and Bob MacDonald, coordinator for partnerships and grants at USDA-ARS.

Steiner spoke about the importance of having multiple principal investigators on research projects, noting that National Science Foundation (NSF) funding for multi-principal investigator projects has gone up 29 percent in recent years, while funding for single principal investigator projects has gone up only 7 percent. He noted that the NSF mirrors a national trend toward awarding multiple-principal investigator projects.

Steiner said that pilot funding is available for researchers through the University and statewide, with programs such as the Delaware Experimental Program to Stimulate Competitive Research (EPSCoR), supported by NSF, and the Delaware IDeA Networks of Biomedical Research Excellence (INBRE), supported by the National Institutes of Health.

He said that with more than 60 academic departments and schools and numerous institutes spread across the University, there is a need for collaboration between researchers.

Steiner also stressed that in the jungle of securing competitive grants, it is important for researchers to “use all the help you can get” and to “work with colleagues to do something innovative, because if you’re doing the same thing that somebody else is doing,” you won’t succeed.

Interdisciplinary work

Matt discussed the interdisciplinary opportunities available at UD specifically through the Delaware Health Sciences Alliance (DHSA) and the future opportunities that will be available at the Science, Technology and Advanced Research (STAR) Campus. Matt said it is important to not limit partnerships but to expand them, and spoke to researchers about the importance of pilot funding to help show initial results with their work.

“The challenge is when you have a new idea and you have to partner with other people, you don’t have a track record,” said Matt. “That’s why in every situation I’ve been in, seed funds, angel funds — these pilot funds — are greatly important so you can get together, get the data, get your publications, get an abstract, get your presentations and you can show that, ‘This isn’t fictitious, I didn’t just write this on the proposal, we’re already working together and we have some data and we know that we can do this.’”

Matt also talked about successful collaboration projects at CHS, such as the “babies driving robots” program that is a collaboration between the Department of Physical Therapy and the Department of Mechanical Engineering, as well as the possibility for future collaborations between UD departments and the community in general as afforded by the new STAR Campus.

Matt said it is hoped the campus will demonstrate “healthy living by design,” and said that will come about through a cooperative effort with the College of Agriculture and Natural Resources.

In the other concurrent morning session, “From Here to There: UD Graduate Student Resources and Career Planning,” speakers presented information on UD resources available to graduate students, career planning and the transition from graduate school to the workforce.

Next came lunch, which gave participants a chance to network with fellow researchers and look at research presentations on display.

Tips for researchers

From 1-3 p.m., there was a panel discussion titled “From Good to Grant,” which explored real world experiences and the logistics of developing and administering interdisciplinary research projects and grants.

The session was moderated by Leigh Botner, research development director for the Research Office, and panelists included:

  • Kali Kniel, associate professor in the Department of Animal and Food Sciences;
  • Manan Sharma, research microbiologist in the Environmental, Microbial, and Food Safety Laboratory (USDA ARS);
  • Steven Stanhope, professor in the Department of Kinesiology and Applied Physiology and lead scientist in the Bridging Advanced Development for Exceptional Rehabilitation (BADER) Consortium (CHS);
  • Carl Schmidt, professor in the Department of Animal and Food Sciences; and
  • Dan Flynn, associate dean of research (CHS).

Kniel said that it is important to know one’s personal strengths when working in a collaborative setting and that “patience is very important when dealing with different personalities.”

Schmidt stressed that talking to fellow researchers and going to meetings is very important, and said research should aim to have a broad impact. He also noted that it is important to establish a laboratory and get papers published as well as find people in the research field who complement you.

“My area of expertise is sequencing and bioinformatics and I knew that we had to use some quantitative genetics in my research and so I actively pursued one of the leading quantitative geneticists at Iowa State as part of this project,” said Schmidt, referencing a $4.7 million research grant he received through the Climate Change Initiative of the United States Department of Agriculture’s National Institute of Food and Agriculture (USDA-NIFA) to study heat stress in poultry.

Flynn spoke about programmatic grants, saying that the three most important aspects of securing a programmatic grant are to have:

• A grant leader who has very strong credentials;

• A compelling vision, something that addresses an important issue that scientists and the people of the society are looking at and talking about, allowing regional assets to guide the growth of the research program, and;

• Strong credentials among the faculty who participate on the program and high quality of their ideas.

“That’s what’s going to drive this and get that grant funded,” he said.

Flynn also said that it is important to remember that as the leader of a research group, you need to help to advance the careers of everybody on that team. “At the end of the day, the real lasting legacy of leadership is the careers of the people that you advanced behind you and then that’s a culture of leadership that you pass on.”

The symposium closed with a poster session and refreshments from 3-5 p.m., with tours of the CANR farm and gardens also available at that time.

Article by Adam Thomas

Photos by Danielle Quigley

This article can also be viewed on UDaily.

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Experimental watershed provides new insights, rich educational experience

June 25, 2012 under CANR News

Six years and about 4,000 water samples later, an outdoor experimental watershed laboratory established by University of Delaware faculty members Shreeram Inamdar and Delphis Levia at Fair Hill, Md., is now producing valuable data and novel insights into how water and chemicals move through the forest canopy, soils and watersheds, and how future climate change may impact or alter such responses.

Inamdar, associate professor in the Department of Plant and Soil Sciences, has investigated the role of soils, streams, and watersheds in leaching water and nutrients, while Levia, professor in the Department of Geography, has studied the interactions of atmosphere and the forest canopy in leaching water and nutrients. Together, they have provided a complete picture of watershed hydrology and biogeochemistry.

The two were awarded a National Science Foundation (NSF) grant in 2008 to study the mechanisms behind the leaching and exports of carbon and nitrogen from watersheds and how these chemicals evolve as they change in space — traveling through the forest canopy, soils, and stream drainage network — and as they change in time through the different seasons.

Both carbon and nitrogen are important elements of natural ecosystems but in excess can cause problems. Excess dissolved organic carbon in runoff and drinking water supplies can result in the production of cancer-causing byproducts when the water is chlorinated for disinfection. Elevated nitrogen concentrations, such as nitrate, ammonium and the organic forms, can result in degradation of water quality and the production of algal blooms in stream, ponds, and lakes and large water bodies like the Chesapeake Bay, making them unfit for swimming, fishing and other recreational activities.

Network data collection

To characterize the movement of water and chemicals in the watershed, Inamdar and Levia implemented an intensive network of multiple, state-of-the-art, automated instruments, sensors and sampling devices that record rainfall and weather data, streamflow runoff, groundwater elevations, soil moisture and water quality. These sensors have been recording data at a frequency of 5 to 30 minutes for the past six years.

Automated water samplers trigger whenever needed, even in the middle of the night, in response to rain events or extremely large events such as hurricanes Irene in 2011 and Nicole in 2010. Such intensive, high-frequency data, combined with laboratory analyses, have provided invaluable insights into watershed functioning and response.

For example, 30-minute groundwater level and stream runoff data has captured the daily fluctuations of water in summer in response to the evaporation from trees and soils, peaking during mid-day and reaching a minimum just before dawn.

Similarly, water samples collected during Hurricane Nicole, which occurred after an extended dry summer period, revealed very unusual patterns in carbon concentrations and quality in stream runoff, trends that were not seen during regular storms.

“What we found was a larger amount of bioavailable carbon coming out during extreme storms,” said Inamdar. “When I say bioavailable, that means the carbon can be easily consumed by aquatic organisms, so the more bioavailable carbon or nitrogen in your streams or water bodies, the greater the chances for algal growth.”

Inamdar went on to explain that the big storms, especially the ones that come after droughts, “flush out a lot of this material into the creeks and rivers which could eventually end up in the Chesapeake Bay or larger water bodies and cause potential problems.”

Climate change scenarios suggest that storms will become more intense with dry intervening periods similar to the conditions associated with the Hurricane Nicole event, and thus studying such extreme events provides a critical window into the future.

Sampling for multiple years has provided insights into how water chemistry changes with seasons. These measurements have allowed for the researchers to investigate how unique seasonal events – such as autumn leaf fall or spring emergence — alter water quality in the stream. These episodic events are also referred to as “hot moments” for their short time span, but disproportionate impact on water and ecological processes.

With regard to autumn leaf fall, Inamdar said, “When leaves fall into the stream, they are providing a carbon source, so the moment they fall into the stream, the bacteria kick in and start consuming the nitrogen. So the stream’s inorganic nitrogen drops as the autumn leaf fall occurs.”

Inamdar cautioned that if climate change were to occur and alter the seasons, it could disrupt these processes. “With the autumn leaf fall and the spring leaf emergence, climate change is going to change the dynamics of how these ecological process effect the carbon and nitrogen cycling in watershed systems.”

The researchers also look at where the carbon and nitrogen comes from, as well as the individual flow paths they take on their way to the stream. “What we are seeing is a lot of the carbon is coming from the forest floor, where the leaves have accumulated and are decaying and decomposing,” said Inamdar, noting that they are seeing a lot of the carbon and nitrogen being transported by surface flow paths.

The group not only looked at the amounts of carbon being put into watersheds, they also studied the carbon quality being put into the watersheds. “Is the carbon easily degradable? Is it bioavailable? We are making that level of distinction as well,” said Inamdar, noting that fresh leaves are extremely degradable while a substance like the tree bark and stems in the forest floor take a longer time to degrade.

Teaching resource

For many undergraduate and graduate students, the outdoor watershed laboratory has served as an extremely valuable learning experience. A total of 12 graduate and undergraduate students have used the Fair Hill watershed site for their research. Six different courses from departments across the University have also used the watershed site for hands-on field visits to study the characteristics and functions of watersheds, soils, streams, and the forest canopy.

European and U.S. scientists and NSF program officers visited the Fair Hill site in November 2011 as a part of the International Critical Zone Observatory meeting, and Inamdar and Levia have also been successful in using the site as a recruitment tool for new students.

The study site is used for outreach activities with the Fair Hill Nature Center, a non-profit entity located near the study site, responsible for educating about 8,000 kindergarten through eighth grade students annually about responsible environmental stewardship. Levia has shared his knowledge of the meteorological station with the general public through the Nature Center and led field trips to highlight how water and soils can be studied in a natural setting.

The Fair Hill watershed site is now helping spawn new ideas and research partnerships. For example, Inamdar intends to study how invasive plants may be invading mid-Atlantic forested landscapes and how they may be altering the soil and water chemistry of these important ecosystems, while Levia plans to seek additional funding to establish a flux tower in the forest to study atmospheric-canopy gas exchange.

Article by Adam Thomas

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UD’s Schmidt studies genome of crocodile family in evolution research

June 14, 2012 under CANR News

University of Delaware scientist Carl Schmidt is working to identify genes in crocodiles, alligators and gharials as he searches for links between the creatures that could give clues as to how they evolved over the years in relation to one another.

Schmidt’s effort is part of a National Science Foundation-funded project being conducted by a team of researchers assembled by David Ray, an evolutionary biologist at Mississippi State University.

Schmidt, a professor in the Department of Animal and Food Sciences in UD’s College of Agriculture and Natural Resources (CANR), explained that his role in the study is to receive DNA sequences from researchers who collect samples from the three species.

Instead of trekking through the wetlands tracking down alligators, crocodiles and gharials — a crocodilian native to the Indian subcontinent — Schmidt is conducting all of his research on dry land in the safe confines of CANR’s Charles C. Allen Laboratory, with much of the DNA sequencing being done at the Delaware Biotechnology Institute (DBI). “They don’t let me chase the crocodiles,” he joked.

Along with Colin Kern, a UD doctoral student in the College of Engineering, Schmidt receives the DNA sequences and then uses different informatics approaches to identify the genes.

By identifying the genes that are commonly found in the DNA of the three creatures, Schmidt said that the researchers are able to predict where the genomic changes may have taken place.

This is particularly important when it comes to the gharial, which is an endangered species whose total world wide population numbers in the hundreds. “One of the things that I think is still a little unclear is the relationship of the gharials to the other crocodilians,” said Schmidt. “So one of the things we’re trying to tease out is the actual relationship between the gharials and the crocodiles.”

Because the gharial is so scarce, researchers have only been able to collect blood samples from the creature. In the case of the other two species, scientists have a variety of tissue samples, which allows for a broader array of DNA to be studied.

Despite the lack of tissue samples, the researchers are still confident that they will be able to discover the genomic changes, which in turn could lead to better conservation efforts to help the gharials avoid extinction.

Birds as Relatives

Schmidt’s work will eventually dovetail with a study being headed by Erich Jarvis, associate professor of neurobiology at Duke University Medical Center, and Mississippi State’s Ray that focuses on the genetic evolution of the closest living relative of the crocodilian family — birds.

Of the relationship between birds and crocodiles, Schmidt said, “It goes back to evolution in terms of crocodiles appearing to be the closest existing relatives of the birds, and the birds being modern dinosaurs, basically.”

Schmidt said that he is interested to see what genes are shared between birds and crocodiles, and which ones are unique to each creature — such as feathers for the birds — and he is hoping that they will be able to tie the results from the two studies together.

“A lot of it relates to how evolution has affected these two different lines of animals that share a fairly recent common ancestor,” Schmidt said, adding, “One of the things that I’m curious to find out is what the genome of that common ancestor looked like.”

Article by Adam Thomas

Photo by Danielle Quigley

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Reducing fertilizer use through beneficial microbe reactions

May 8, 2012 under CANR News

Janine Sherrier, professor in the Department of Plant and Soil Sciences at the University of Delaware, is part of a team that has been awarded $6.8 million from the National Science Foundation (NSF) to study the legume Medicago truncatula.

Sherrier leads one of four research groups participating in this project, which represents a collaborative effort between researchers at the Noble Foundation, the Boyce Thompson Institute at Cornell University, the University of Delaware, and the University of North Texas.

“The aim of this large project is to generate resources for the U.S. and international research communities. We will generate resources to help accelerate the transfer of fundamental laboratory research results into useful applications for crop production,” said Sherrier.

In past years, the NSF has supported projects to sequence the complete genomes of organisms, including M. truncatula. The resources generated by this new NSF grant will help researchers define the roles of all of the individual genes within the genome and to elucidate how they are important for legume growth.

“Legumes, such as beans and lentils, provide one third of the protein consumed as part of the human diet globally. Legumes also contribute fiber and micronutrients to the human diet and are utilized widely as forage crops for livestock,” said Sherrier.

M. truncatula has been selected as a research model to study the symbiotic relationships that are characteristic of legumes. Unlike many species of plants, legumes rely on interactions with rhizobia (naturally-occurring beneficial microbes) to supply them with nitrogen. Many crop plants are supplemented with industrially produced nitrogen fertilizer, and the synthesis of the fertilizer is an energy-intensive process.

“As much as four percent of the world’s natural gas is consumed in the production of nitrogen fertilizers, releasing carbon dioxide by-products into the atmosphere,” said Sherrier.

When nitrogen is not present at sufficient levels in the soil to support plant growth, legumes create a home for beneficial bacteria in their roots. The plant develops a novel root organ where bacteria can grow, multiply and enter the plant cell, and within the plant cells the bacteria convert atmospheric nitrogen into a fertilizer for the plant. This greatly reduces the amount of fertilizer and energy necessary to produce a successful crop, lowers production costs for farmers and reduces runoff of fertilizers into the groundwater.

The focus of Sherrier’s research program is on the protein-to-protein interactions that are necessary for such beneficial plant-bacteria relationships to occur.

“If the plant lacks a specific protein, then this can allow bacteria to enter the plant and simply take the sugar without producing anything in return. This would be detrimental for a crop,” she explained.

As part of the NSF-funded project, Sherrier’s team will also be developing and teaching a 4-H summer camp across Delaware to teach children about how different microbes are important for agriculture. Campers will participate in science-based activities, such as using microscopes and making yogurt. The camps will contribute to the development of future growers in all three counties.

Article by Jacob Crum

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Delaware EPSCoR announces 2012 seed grant recipients

March 7, 2012 under CANR News

The Delaware EPSCoR program has awarded seven seed grants to University of Delaware faculty whose projects address current environmental issues within the state.

EPSCoR, the Experimental Program to Stimulate Competitive Research, is a federal grant program of the National Science Foundation (NSF) that helps states develop their research capabilities so that they may compete for further federal funding.

Seed grants are typically in the $50,000 range and help researchers set the stage for applications to larger federal funding programs. Seed grant proposals are solicited annually during the fall semester. The selections were made by a committee of five senior faculty affiliated with the Delaware EPSCoR program and two external reviewers representing the Delaware Department of Natural Resources and Environmental Control (DNREC). This year’s funded projects are as follows:

Microbes that remove arsenic from rice

Rice is a staple in diets across the globe, but it is commonly contaminated by arsenic (As) in many developing nations. To solve this problem, University of Delaware scientists Harsh Bais and Janine Sherrier of the Department of Plant and Soil Sciences have proposed that the inoculation of rice with the bacterium EA106 will reduce arsenic accumulation within the edible portion of the plant, simultaneously improving quality and yield. Arsenic-contaminated rice represents a significant health risk to millions of people worldwide; in their research Bais and Sherrier plan to “systematically dissect the overall mechanism in As absorption and translocation in rice.” Their efforts will further probe the field of plant-microbial processes and how they may be used to agricultural advantage.

Impact of terrestrial phosphorus on eutrophication in the Chesapeake Bay

Principal investigator Deb Jaisi, assistant professor, and Donald Sparks, S. Hallock du Pont Chair of Soil and Environmental Chemistry, both of the Department of Plant and Soil Sciences, will investigate the concentrations of terrestrial and nonterrestrial phosphorus (P) input into the Chesapeake Bay over time. The prevailing notion is that the level of nonterrestrial P has remained constant since early civilization, and thus terrestrial P is the sole culprit in the eutrophication (increased concentrations of nutrients which result in algae blooms and fish kills) of the Chesapeake Bay. However, observed changes in the bottom water environment indicate that this is unlikely. Their study will influence future management strategies to limit nutrient pollution, with regulations possibly addressing both terrestrial and nonterrestrial P input. Sparks is director of the Delaware Environmental Institute.

Article by Jacob Crum

Photos by Ambre Alexander and Kathy F. Atkinson

For the complete article and list of seed grant recipients, view the full story on UDaily

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UD’s Meyers receives NSF grant to study genetic impact of corn mutation

July 19, 2011 under CANR News

In an attempt to understand the genetic impact of a mutation in corn that turns the crop orange and stunts growth, researchers from the University of Delaware and Penn State University have received a $1.2 million grant from the National Science Foundation (NSF).

Leading the UD team is Blake Meyers, Edward and Elizabeth Goodman Rosenberg Professor and chair of the Department of Plant and Soil Sciences in the College of Agriculture and Natural Resources.

The researchers are studying a mutation known as unstable factor for orange1, or Ufo1, which not only impacts the color of the corn, turning the ears from the standard yellow to an orange hue, but has more severe impacts ranging from stunted growth to “whiplash,” a growth defect in which the corn stalk is bent backwards towards the ground.

One important aim of the project is the basic research to understand how gene silencing functions and how it can impact different cellular pathways. This mutant is of interest because it has an “epigenetic” effect on other genes, meaning that Ufo1 produces inherited states in other genes that are caused not by altered nucleotides in the DNA, but by reversible modifications of the DNA.

The research on Ufo1 is being conducted on two fronts, with Surinder Chopra, associate professor of maize genetics at Penn State, working to identify the specific gene that is the Ufo1 mutation and Meyers trying to understand the genetic and genomic impacts of that mutation.

“Basically one gene is altering the expression of many other genes through some sort of epigenetic modification,” Meyers said. “I’m trying to understand, in a global genomic context, what is the impact of this mutation.”

Meyers said he hopes for a happy convergence of the projects, with Chopra pinpointing the gene and Meyers identifying all of the genes or regions of the genome that are showing epigenetic alterations.

“Then we’d like to connect those back to the phenotypic differences that we observe in this mutant,” Meyers said. “There are lots of different effects that are a consequence of this mutation — it’s not just color — and we’d like to understand which genes are causing those phenotypic differences and why those genes are the subject of regulation by this Ufo1 gene.”

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Article by Adam Thomas

Photo by Danielle Quigley

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