UD alumnus finds potentially dangerous fleas on New York City rats

Matt Frye conducts research on fleas in NYCWhen University of Delaware alumnus Matt Frye signed on to work with researchers from Columbia University studying pathogens of Norway rats in New York City, he knew that as the team’s entomologist he would be combing the rats for critters such as fleas, lice and mites.

What he didn’t know was that he would find such a high rate of the oriental rat flea — an insect that hasn’t been documented in New York since the 1920s and is a known vector for several important human diseases such as murine typhus and the plague.

The results of these findings were reported recently in the Journal of Medical Entomology.

Despite their name, Frye explained that Norway rats actually come from Asia and through the years have traveled the world with humans on wagons and trade ships, carrying a familiar set of ectoparasites as they make their way across the globe.

“Studies that are specifically interested in rat ectoparasites tend to find the same cast of characters,” said Frye. For example, researchers in Hawaii — Pingjun Yang, Sandra Oshiro and Wesley Warashina from the Hawaii Department of Health –published a paper in 2009 that found all the same ectoparasites on their rats that Frye and the Columbia research team found in New York.

“We were not necessarily surprised to find any of these critters, but we were surprised at the numbers that we found,” said Frye, an extension educator with the New York State Integrated Pest Management (IPM) Program at Cornell University

The group collected the data over a one-year period from five different sites in the city, specifically areas where rats and humans are most likely to have direct contact with one another.

All told, Frye took samples from 133 rats and collected a total of 545 fleas. Of those 133 rats, he said that about 30 percent were infested with fleas.

“The interesting thing is that the fleas were unevenly distributed by site. At the outdoor site, a single flea was collected from 26 rats. Meanwhile, all 20 rats from another site had fleas, and that site accounted for 94.1 percent of the total 545 fleas we collected,” said Frye. “The implication is that a more thorough survey of rats is needed to understand the distribution of ectoparasites in New York City.”

At the site where all 20 rats had fleas, Frye collected 83 fleas from just one rat, which could be cause for alarm according to plague surveillance literature. Frye said that a flea index — the total number of fleas divided by the total number of rodents captured — below 1.0 represents a remote possibility of a disease outbreak.

“In 1925 in New York, the flea index was 0.22. In our study, the index was 4.1 for all 133 rats, and 5.1 for rats caught indoors. That was surprising,” he said.

However remote, the potential exists for diseases like murine typhus and the plague to surface, Frye said, noting, “We have the rats, we have the vector that can transfer pathogens from the rats to humans, so it’s sort of a recipe for disaster if plague or typhus were introduced.”

Frye is hoping that the revelation of the high numbers of oriental rat fleas discovered in New York City’s rat population will lead to more research on the subject.

“The purpose of this study was to take a first look at what pathogens and ectoparasites are present on Norway rats New York City,” said Frye. “However, our study was limited in scope, and has led to more questions than answers. For instance, we do not know the distribution of these organisms, nor do we know if the conditions are right to sustain something like plague. What we do know is that more work is needed to better understand the risk of exposure to rodent-borne disease for New Yorkers.”

The researchers also discovered several new species of viruses and some pathogens that haven’t been recorded before in New York City. The results of those findings were released in a paper published last year by the American Society for Microbiology.

The viruses are listed as two novel hepaciviruses, one novel pegivirus and one novel pestivirius. Frye explained because the viruses are new and were detected using novel screening methods, the researchers “don’t know much about the viruses and if or how they might impact human health.”

Time at UD

While at UD, Frye worked with Judy Hough-Goldstein, professor of entomology, for six years studying biological control of invasive plants, specifically kudzu, as both a master’s and doctoral student.

As a master’s student, Frye conducted research on a specific insect and its potential to control the plant — which ultimately didn’t work out due to the insect’s appetite for soybeans — and as a doctoral level student, he looked at different types of damage with kudzu to see if any reduced the plant’s growth and reproduction.

Frye said that his time at UD working with Hough-Goldstein and the Department of Entomology and Wildlife Ecology was beneficial to his career.

“Our department at the time was relatively small, so there was a lot of interaction between graduate students and faculty that I found to be exceptionally valuable. I felt very fortunate to have Dr. Hough-Goldstein as an adviser, because she was very organized and helped her students develop as scientists,” said Frye.

In his role with the New York State IPM Program, Frye said that he provides training, demonstrations, workshops and creates educational materials about pest management and specifically structural or urban pest management, which deals with the insects that infest buildings, schools and homes.

He said that his favorite part of his job is “working with people. I get to interact with homeowners, with universities, and pest professionals. Helping people find a solution to their pest problem is a very rewarding experience.”

Article by Adam Thomas

New research characterizes novel aspects of maize reproduction

Blake Meyers, the Edward F. and Elizabeth Goodman Rosenberg Professor and Chair for Plant and Soil Sciences in the College of Agriculture and Natural Resources, along with his research team Kun Huang, Atul Kakrana, Parth Patel, TC, Saleh Tamim, Reza Hammond, and Sandra Mathioni in plots of corn on the UD farm. Dr. Meyers's "research includes programs that emphasize bioinformatics and plant functional genomics."Male reproductive organ development in maize involves a complex array of ribonucleic acid molecules (RNAs) with potentially diverse activities in gene regulation, demonstrated by new research from the University of Delaware and Stanford University.

In addition, this work suggests that the beginning phases of such development in maize and mammals – two very different life forms – have some intriguing molecular parallels.

The research findings have been published in the Proceedings of the National Academy of Sciences (PNAS) by a team of scientists led at UD by Blake Meyers, chair of the Department of Plant and Soil Sciences in the College of Agriculture and Natural Resources and the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences.

The first author on the paper is Jixian Zhai, a former graduate student who worked with Meyers and is now a postdoctoral researcher at the University of California, Los Angeles (UCLA). Zhai was a 2014 recipient of the prestigious Life Science Research Foundation postdoctoral fellowship, sponsored by the Gordon and Betty Moore Foundation.

Meyers collaborated with Virginia Walbot, professor in the Department of Biology at Stanford University, to characterize maize anthers — the male reproductive organs — that had been carefully staged through the developmental transition and were perfect for the molecular studies in which the UD team has specialized.

The Walbot lab has a longstanding interest and expertise in anther development, and they work with a large collection of male-sterile maize mutants with altered anther development. Analysis of a subset of those mutants provided key insights in the study.

With the materials from the Stanford group, Meyers said the researchers put the plant tissues through an analysis pipeline that his lab has developed and refined in the years since he came to UD in 2002. This work involves purifying and sequencing the small RNAs from the anthers and integrating the resulting data into a computational software package

“We were really excited to see the results when we noticed a tremendous increase in the abundance of these molecules that was perfectly timed to developmental transitions that take place in the anther,” said Meyers.

Their work built on and extended findings from data published earlier by other labs in a study focused on rice. That earlier study showed the abundance of some of the same molecules in reproductive tissues, but lacked the temporal resolution of the staged maize anthers used by the Meyers and Walbot labs and the spatial resolution provided by the mutants and other advanced localization techniques they employed.

Because maize has a separate male inflorescence (the tassel) and female inflorescence (the ear), the researchers were able to study the male flower separate from the female flower, a further advantage over working in rice, which has combined male and female flowers.

With Walbot’s lab able to dissect the anthers at very precise stages — from their earliest origins when they are only a fraction of a millimeter in length all the way up to the mature anthers, which are about five millimeters — the research team was able to assess the developmental transition from early anthers to mature pollen.

“We could see that these RNAs fell out into two classes: an early class and a middle-to-late class,” said Meyers.

Meyers explained that the early class corresponds to developmental events in which the cell types are becoming organized, defining the cellular architecture of the anther, whereas the later class corresponds exactly to meiosis, the process of production of the haploid microspores that ultimately mature into the pollen grains.

“We could see that the increases in the abundance of these two groups of small RNAs exactly corresponded with those two developmental phases,” said Meyers.

Maize and mammals

Where this intersects with mammals and animal developmental biology is that there has been a lot of work in mammals on a very unusual class of small RNAs that are particularly abundant and enriched in male reproductive organs during early development.

“These mammalian small RNAs, called piRNAs, have a very unique pathway for their production. Tremendously abundant and in mammals, there are two classes: an early class and a kind of middle to late class. We were intrigued to see in maize several analogous features; yet the plant and animal small RNAs abundant in male reproduction share no apparent common origin,” said Meyers. “We think that they are independently evolved in the lineages of plants and in mammals.”

What the researchers don’t know yet is whether there are analogies of function.

“All we know for now is that there are several unusual similarities between these classes of RNAs. And to use these methods to characterize the unique yet analogous aspects of the plant reproductive small RNAs was a particularly rewarding part of the work,” said Meyers.

Different from Arabidopsis

Maize and rice, the two plant species best characterized for these novel small RNAs, are in the branch of the plant kingdom that’s known as the monocots, one of the major groups of flowering plants.

Another major group of flowering plants — the eudicots — contains the plant species most studied at the molecular level, the model plant Arabidopsis thaliana.

In Arabidopsis thaliana, however, there is no evidence that these two classes of small RNAs exist, let alone are enriched during anther development.

Meyers was able to see this firsthand when he collaborated with a group at Cold Spring Harbor to look at small RNAs in Arabidopsis flowers. “That work gave us many insights into small RNAs and plant reproductive biology,” said Meyers. “In that work, we looked at Arabidopsis flowers including comparable stages of anthers and there was no evidence for these classes of small RNAs that we saw in maize. We can conclude that there are distinct but abundant classes of small RNAs in these different lineages of plants.”

This means that maize and the Arabidopsis diverged in their use of small RNAs during evolution, and yet despite this evolutionary divergence, there are signs of a possible convergence between the grasses (i.e. maize) and animals in the use of small RNAs in reproduction.

Spatial mapping 

The paper also describes the development of a spatial map of the production of those small RNAs, combining their collaborators’ expertise in anther biology with microscopy in the Bio-Imaging Center in the Delaware Biotechnology Institute (DBI).

“Professor Walbot has collected many male sterile mutants of maize, plants defective, for a wide variety of reasons, in the production of mature, fertile pollen,” said Meyers. “She was able to pick from this collection mutants that she thought would be particularly informative to identify the cell layers required for production of these small RNAs.”

A mature maize anther contains five cell types and the researchers looked at mutants that were defective in one or more cell layers to see if the production of the small RNAs was dependent on one or more of these layers.

The researchers then combined that data from the mutant analysis with microscopic visualization techniques called in situ hybridizations that allowed them to probe dissected tissue for the presence of their RNAs of interest.

“We could essentially say, ‘The mutant analysis indicates that small RNA X is found in cell layer Y; if we use the dissected anther and we apply a labeled version of X, do we observe it in that cell layer?’ These images took advantage of the advanced microscopy at DBI,” said Meyers.

With those data, the researchers were able to reveal specific cell layers required for production of the two classes of small RNAs, allowing them to validate the mutant analysis. One discrepancy in the mutant and hybridization results suggested that at least one set of small RNAs might move across cell layers – a result that they can test in future experiments.

Next steps

Meyers said that the next step for the research is to discover the functional roles of these small RNAs.

“We know they’re extremely abundant, we know that they increase in abundance at very particular stages in anther development, and they’re dependent on very particular cell layers in the anther, but we still don’t know exactly what their functions are. That’s a really intriguing mystery because in the functions of almost all other plants, small RNAs are at least generally well-described,” said Meyers.

This research was funded as part of a four-year, $6.5 million National Science Foundationgrant to analyze developmental events in maize anthers and tassels.

Article by Adam Thomas

Photos by Evan Krape

This article can also be viewed on UDaily.

UD’s 2015 Philadelphia Flower Show exhibit to feature plants from Amazon

UD students work on the Philadelphia Flower Show ExhibitThe University of Delaware exhibit at this year’s Philadelphia Flower Show will provide visitors a lesson in the inherent value of abundant plant life, with a focus on useful, edible and therapeutic plants found in the Amazon rainforest.

The exhibit, which has been prepared by students and faculty members in the Design Process Practicum class and the Design and Articulture (DART) student organization, will highlight the diversity of plants found in the Amazon and the capacity of the rich ecosystem to provide medicines for ailments.

The flower show will run Feb. 28 through March 8 at the Pennsylvania Convention Center.

The idea for the theme originated last spring in the interdisciplinary Design Process Practicum class, which is taught by Jules Bruck, associate professor in the Department of Plant and Soil Sciences; Anthony Middlebrooks, associate professor in the School of Public Policy and Administration; and Jon Cox, assistant professor in the Department of Art.

Students in the class split into three groups and each group had to design a flower show exhibit for three separate clients — the Amazon Center for Environmental Education and Research (ACEER), Duffy’s Hope, a service provider for at-risk and hard to reach youth ages 12-17, and Connections Community Support Programs Inc., which provides a comprehensive array of health care, housing and employment opportunities that help individuals and families to achieve their own goals and enhance communities. Through Connections, the students specifically worked with the Sturfels Youth Center, which provides a safe haven for boys and girls who have been arrested but who have not yet been convicted of a criminal offense.

When the professors were unable to choose a winner, they had Sam Lemheney — chief of shows and events for the Pennsylvania Horticultural Society (PHS), director of the Philadelphia Flower Show and an alumnus of the College of Agriculture and Natural Resources (CANR) — pick the project to represent UD. He selected the project of the group that had worked with ACEER.

ACEER is committed to promoting conservation of the Amazon by fostering awareness, understanding, action and transformation, and in keeping with that theme, the UD group decided to highlight the plant life found in that region.

“We’re really going to try to highlight awareness and understanding of the conservation of the Amazon rainforest for the purpose of making sure that we have good access to medicinal plants over time,” said Bruck. “As the forest ecosystems are degraded and eventually lost through poor agricultural practiceswe lose an opportunity to study species and the way indigenous tribes use medicinal plants. The students were really interested in a ‘forest to pharmacy’ concept.”

Paige Gugerty, a senior organizational and community leadership major who is part of DART and is the teaching assistant for the class, said that the forest to pharmacy concept comes from the fact that “in the pharmaceutical industry, a lot of medications that we use, and even some potential cancer fighting drugs, come from plant compounds found in the Amazon. It’s really important to preserve the Amazon because of those plant compounds and the different medicinal and religious uses of what is found there.”

In addition to having an education display, the students were also interested in having a very exuberant, colorful exhibit. To do that, they had to select plants that are both educational and aesthetically pleasing.

To choose the plants for the show, two students — Gugerty and Elinor Brown, a junior in the College of Health Sciences — traveled to Florida in September 2014 with Lemheney to visit nurseries and tree farms.

The fact that Gugerty, a leadership major, and Brown, an exercise science major, were chosen to visit Florida to pick out the flowers speaks to the interdisciplinary nature of the course, something the professors stressed is important to the design process.

“We’re highly interested in crossing disciplines and we’re always trying to get different disciplines to work together to see each other’s perspectives and understand the strengths that each perspective brings that they might be overlooking,” said Middlebrooks. “So the flower show is a perfect opportunity because there are so many details to putting together an exhibit — from the initial exploration of ideas, to generating ideas, to the creative details and the logistics for getting it there, getting it set up, ordering materials, balancing the books, and everything else.”

For their part, the students were thrilled to be selected to travel to Florida.

“I was so grateful that Jules offered up that opportunity to us,” Gugerty said. “The fact that they sent two students was really awesome because neither one of us is from CANR, but we worked together and prepared for the trip and did a lot of our research up front so that when we got to the nurseries, we were able to look at what we wanted to look at and then come back and order pretty quickly.”

Brown added that it was nice to travel with Lemheney and another exhibitor at the flower show because “they have such a connection with people down there and they’re so close. It was really nice being with them and meeting their clients and establishing a connection with them that we can use for the next few years.”

Students prepare for the philadelphia flower show installation, 2015. Sydney Bruck paints laser cut wood plant labels.The students chose most of their flowers from Excelsa Gardens in Loxahatchee as they said Excelsa set the gold standard for nurseries and had a very accommodating staff.

The comprehensive plant list had around 450 plants in total and included bromeliads, gingers, banana palms, orchids, bananas and cocoa.

Cox, who conducted studies in Peru recently, will include in the display some masks and objects from his trip. There will also be baskets that indigenous Peruvians use to gather plants and berries in the exhibit, and ACEER is going to hand out samples of fair trade coffee and promote other fair trade products.

In addition to the plants, the display will also have little bottles hanging from the ceiling to represent the concept of running water, and a CD titled Sounds from the Peruvian Rain Forest will be played. There will also be art from Hillary Parker, an award winning botanic illustrator, with some of her paintings representing this area’s local native plants that have medicinal properties and were once used by indigenous North American peoples.

The theme of this year’s Philadelphia Flower Show is “Celebrate the Movies” and the hope is that people who visit the UD display will walk away knowing that they are in the director’s chair when it comes to conservation and that even though they aren’t in the Amazon, they can have an impact on rain forest conservation by supporting ACEER, buying sustainable products and even planting a forest garden of native plants in their back yards.

“What we want people to walk away with is that everything is connected and that our reliance on medicines derived from tropical plants reminds us to support education and research in products that help conserve and sustain these ecosystems,” said Bruck.

After the show, the plants will be sold at the University’s Ag Day, as most of the items — such as the orchids and the ferns — make for good house plants.

The exhibit is sponsored by PHS and the Hutton Fund, in memory of Richard J. Hutton.

Blake Meyers, chair of the Department of Plant and Soil Sciences and the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences, also contributed to the show.

Middlebrooks said that there is an open invitation to get involved with the project. “This is not a closed project in any way. We are very true to our spirit of creativity and innovation, and anyone who wants to bring their talents or even just their energy and enthusiasm to the group — students, staff, faculty — we’re open to all those kinds of collaborations.”

For those wishing to get involved with the project, contact MiddlebrooksBruck or Cox.

Article by Adam Thomas

Photos by Lindsay Yeager and courtesy of Paige Gugerty

This article can also be viewed on UDaily.

Agriculture, natural resources ranked among highest paying degrees for 2015

According to a recent USA Today article, agriculture and natural resources ranks fifth among the college majors that will likely lead to the highest earnings for 2015 graduates. The others in the top five are, in order, engineering, computer science, math and sciences, and business.

According to the article, students who graduate with a degree in agriculture and natural resources will have a projected average starting salary of $51,220 and average lifetime earnings of $2.6 million. As is the case with other top majors, those who obtain management positions generally have the highest earnings over a lifetime — around $800,000 more than the typical college graduate.

The article drew from census data and an employer survey analysis conducted by the National Association of Colleges and Employers.

At the University of Delaware’s College of Agriculture and Natural Resources (CANR), enrollment is up by (insert stats) and graduates are thriving in careers that are as diverse as they are interesting.

Notable CANR graduates

Mary Ellen Setting, who serves as deputy secretary of the Maryland Department of Agriculture, studied entomology and applied ecology at CANR.

Setting said she had only a brief introduction to agriculture as a youth, visiting the King Street Farmers Market in Wilmington and through deliveries of fresh eggs, fruit and vegetables to her house by a local framer.

Other than that, Setting had very little background in the field when she chose to study entomology at UD.

“Coming to the University of Delaware in the entomology department, that’s really where I got my main introduction to agriculture,” said Setting, who majored in entomology and applied ecology, learning things like wildlife management and ornithology along the way.

Michael Balick graduated with an undergraduate degree in horticulture and plant science from CANR, focusing on ornamental horticultre and plant agriculture.

Through his degree, Balick spent 37 years traversing the globe and studying herbs with medicinal properties within indigenous cultures, co-founded the New York Botanical Garden’s Institute of Economic Botany with Sir Ghillean Prance, and received his doctorate in biology from Harvard University.

Balick currently serves as vice president for botanical science and director and philecology curator of the Institute of Economic Botany at the New York Botanical Garden.

Of his time at UD, Balick said he enjoyed spending time at Longwood Gardens with the Longwood Graduate Program and that he was given the freedom to explore the things in which he was interested, satisfying his curiosity about the different aspects of the plant world.

“Education for me at the University of Delaware was about identifying my passion and sailing in that direction with the encouragement of so many fine professors and a wonderful student body, to whom I am really grateful,” said Balick. “I’d encourage everyone to find something in life that they’re fascinated with and go full speed ahead in that direction because in the end it’s not a job you’re searching for, it’s a career, and it’s just so satisfying to work on something that brings excitement to you on a daily basis. I would say horticulture and agriculture and plant science allow you the freedom to do just that.”

Robin L. Talley received a bachelor of science degree with distinction and graduated cum laude in agricultural economics in 1984. She went on to receive her master of business administration degree from UD in 1996 and serves as the district director for the U.S. Department of Agriculture (USDA) Farm Service Agency. She was the recipient of the 2013 George M. Worrilow Award, presented by the CANR Ag Alumni Association to those who have exhibited outstanding service to the field.

Rachel Acciacca is a Veterinary Corps officer in the U.S. Army and was an Honors Program student who studied animal science as a pre-veterinary major in CANR.

Acciacca said she enjoyed her time at UD, and said that CANR helped set her on the road to success. “The close-knit community at CANR was very supportive and encouraging,” she said. “I still remember individual professors who went out of their way to support me and prepare me for veterinary school. Everyone there was always so approachable, and I truly felt that they were dedicated to seeing me succeed.”

For any UD students currently interested in applying to veterinary school after graduation, Acciacca said, “Don’t ever doubt your ability to become a veterinarian — if you want it badly enough, you will make it happen. Work hard, seek out many different types of animal or veterinary-related experience you can, and keep your mind open. It’s a lot of work, but it’s a blast and I wouldn’t trade my job for anything.”

UD-led study suggests new pathway for phosphorous cycling in Chesapeake Bay

Deb Jaisi, CANR and his associate Sunendra Joshi work with:  1.	Silver phosphate, ultimate analyte for the phosphate oxygen isotope ratios measurement. Phosphorus from sediment is extracted, processed, and precipitated as silver phosphate.In the summer months, phosphorous cycling leads the center of the Chesapeake Bay to suffer from bottom water hypoxia — low levels of oxygen — which makes it hard for oxygen dependent organisms to survive. Conversely, this cycling also causes surface water eutrophication, which leads to phytoplankton blooms.

In a new paper published in the journal Environmental Science and Technology, researchers from the University of Delaware and other institutions have identified for the first time organic matter remineralization as the predominant pathway for the phosphorous cycling that occurs in the Chesapeake.

The research, led by Sunendra Joshi, a doctoral student in the College of Agriculture and Natural Resources, includes UD’s Deb Jaisi, assistant professor in the Department of Plant and Soil Sciences, and Donald Sparks, the S. Hallock du Pont Chair in the Department of Plant and Soil Sciences, Francis Alison Professor, director of the Delaware Environmental Institute (DENIN) and a leader of the University’s Environmental Soil Chemistry Group.

The UD scientists collaborated with David Burdige, professor and Eminent Scholar in the Department of Ocean, Earth and Atmospheric Sciences at Old Dominion University; Ravi Kukkadapu, a senior research scientist at the Environmental Molecular Science Laboratory (EMSL) at the Pacific Northwest National Laboratory; and Mark Bowden, a scientist at EMSL.

Remineralization vs. remobilization

Remineralization is a cycling process that starts with the breaking down of organic matter, in this case phytoplankton blooms that take up phosphorous and live in top level waters that have undergone eutrophication.

When those phytoplankton die, they settle to the bottom of the body of water, break down and release phosphorous, causing hypoxia.

While some believe the dead zone in the center of the Chesapeake during the midsummer months can be attributed to nutrient remobilization — phosphorous entering from terrestrial or atmospheric sources, settling to the sediment and then again mobilizing to bottom water — this research suggests that the problem lies in organic matter remineralization, as it forms the predominant pathway for phosphorous cycling in this section of the bay.

“This remineralization process is more of a natural process of cycling and leans more toward a self-sustaining process than having direct phosphorous coming into the bay from the land,” said Jaisi. “That [remobilization] pathway is almost not there. It is very insignificant because the bulk of land driven phosphorus is buried in the sediment and is inactive. People used to think that that pathway is a significant pathway compared to remineralization, which is not the case. It’s the other way around, and that has a direct impact on how to control the nutrient issue in the bay.”

Seasonal event

The late spring, early summer months are the perfect time for the eutrophication process to begin as they follow the spring when the bay is fed by heavy water flows from the rivers, which bring a substantial amount of nutrients into the Chesapeake. In the early summer, the temperatures are right for organisms like phytoplankton to grow.

Burdige explained that, like every plant, phytoplankton requires several basic things in order to grow, including light, the correct temperature and nutrients.

“It’s similar to how you put fertilizer on your garden to make tomatoes grow, or your grass grow. Plankton need nitrogen and phosphorous,” said Burdige, who added that a spring phytoplankton bloom “is not dissimilar to what happens to your lawn. Your lawn dies in the winter and then, come around March or April, it starts to be green again.”

The phytoplankton contribute to phosphorous cycling because in summer months when they die, they break down and their remains sink to the bottom water and to the sediment column. The nutrients that the phytoplankton took up to form themselves in the first place regenerate and are returned to the bottom water to refuel the dead zone and may diffuse up to the surface water to feed a new generation of phytoplankton.

“So it is a recycling process, a process that reuses the same nutrient multiple times,” said Joshi.

Jaisi added that it is “an efficient system for microorganisms but a great pain for nutrient management.”

Sediment cores

In order to study the processes, the researchers extracted sediment cores from three sites in the Chesapeake — though their study only concentrated on the mid-bay portion — freeze dried them and analyzed the different phosphorous pools, taking the isotopic composition for those different pools and looking at what the isotope means and how the specific range of isotopic composition evolve.

According to the paper, this is the first natural environment where the preservation of the isotopic signature immediately after the remineralization of organic matter has been documented in the world.

“This can only happen under intense remineralization where the released phosphorus is too high to precipitate as a mineral instantly. The beauty of the isotope tool is that once the phosphate mineral precipitates, the isotopic composition is locked in and is now available for us to see what reactions and processes happened in the past,” said Jaisi.

The researchers looked at authigenic phosphorous pools — phosphorous that precipitates as a mineral — and iron oxide-bound phosphorous pools, which largely include phosphorus entering the bay from terrestrial sources and end up in the sediment.

The research showed that the iron oxide dissolution seems to be a minor source of the phosphorous in the area of the bay they studied. This means that a bulk of land driven phosphorus remains in sediment and is not active anymore.

Kukkadapu added that iron oxide bound phosphorus is not reactive as it is commonly anticipated, saying, “The small-particle iron oxides coated with organic matter and phosphorous in the uppermost layer of the sediment are surprisingly stable toward changes under anoxic conditions.”

In addition to looking at current sediments, they were also given historic sediment samples from past years in the Chesapeake thanks to Burdige, who has spent years studying the bay.

“Deb contacted me because he was looking for samples. We’ve done a lot of work in the bay over the years so we have a lot of frozen mud,” said Burdige, who pointed out that these historic sediments were studied to shine a light on legacy nutrients, those that enter the bay because of runoff but remain buried in sediment.

“If, for example, we figured out a way tomorrow to stop all inputs of excess nitrogen and phosphorous from human sources, there would still probably be a declining problem with excess nutrients in the bay because you’ve got this legacy reservoir that’s sitting on the bay floor,” said Burdige. “It’s sort of providing a new source of nutrients. It’s new today, so to speak, but it originally entered the bay 10 years ago, 20 years ago, 50 years ago. So it’s like rooting through your pantry to find a can of soup that you stashed away and forgot about.”

Analytical tools

By using a number of advanced state of the art analytical tools involving field sampling and laboratory work, and examining sediments all the way to the sub-atomic level, using Jaisi’s Environmental Biogeochemistry Laboratory to measure the phosphate oxygen isotopes, Sparks said that “one of the strengths of this work is that we’ve taken multiple approaches and really used some cutting edge techniques to try to get very precise information on the major source and what the cycling is due to.”

Sparks said that his group brought certain spectroscopic tools, collaborating with Bowden and Kukkadapu, who did the Mössbauer spectroscopy portion of the research at EMSL, and then “Deb had the isotope biogeochemistry expertise so it was a nice partnership.”

Burdige said that in a lot of ways, the result of the research is a testament to Jaisi and Joshi’s hard work “in making these difficult and challenging isotope measurements. From that perspective, they should be commended for their persistence and perseverance.”

The Soybean Boards of Maryland, Delaware and Pennsylvania provided major funding for this research, while the United States Department of Agriculture (USDA) and Delaware EPSCoR also helped fund the research.

Article by Adam Thomas

Photos by Kathy F. Atkinson and courtesy of Deb Jaisi

Images courtesy of Deb Jaisi

This article can also be viewed on UDaily.

UD student uses genome annotation to help study crocodiles, alligators, gharials

Computer Science student Colin Kern is working with Carl Schmidt, Professor of Animal and Food Sciences and  Associate Professor of Biological Sciences, on using computers to locate the genes of crocodiles, alligators, and gharials.For the last year and a half, University of Delaware doctoral student Colin Kern has been annotating the genome of the American alligator, the salt water crocodile and the Indian gharial to help researchers from multiple institutions determine the ancestral patterns of evolution among archosaurs, which include crocodilians, dinosaurs and birds.

The results of this study were recently published in the American Association for the Advancement of Science journal Science.

Kern, who is studying in the Department of Computer and Information Sciences, worked on the project with Carl Schmidt, professor in the Department of Animal and Food Sciences, to try to identify where certain genes are located on the sequenced genomes of the three species.

There are two ways to try to determine the location of the genes, Kern said. The first is to predict where the genes are based on current knowledge and the ability to identify sequences of DNA that mark the start of a gene.

The second is to look at known genomic information from other species. “We know that all life evolves, and if you go back far enough, any two species will have a common ancestor,” Kern said, explaining that a researcher who finds a gene in a given animal and sees a very similar sequence in a genome just created can infer that it might be the same gene in the newly-studied animal.

Kern said that for each species, he looked for about 20-25,000 genes.

To comb through such massive amounts of data, Kern used two computer programs. The initial gene prediction was done using a program called Augustus and when it came time to assign a function or a name to the genes, he used a tool called the Basic Local Alignment Search Tool (BLAST), which is used to search for similar genes.

Kern said the researchers took the genes that they predicted from the crocodiles, and about which they were not certain, and ran the BLAST program in comparison to chickens to determine the similarities between the genes of the two species.

“We started with the chicken because birds are the most similar group of species to crocodiles, and chicken is probably the most well-studied bird,” said Kern. “We were able to assign a name — and along with a name comes the function of what those genes actually are — to a lot of the crocodile genes.”

Once the genes were identified at UD, Kern said the results were sent to researchers at other institutions to complete the study.

The results of the study show that the evolutionary rate of crocodilians is exceptionally slow.

For example, Kern said, even though the crocodile and alligator have been separate species for about 80 million years, “they’re more similar than comparing two mammal species that may have only split 20 million years ago.”

The data produced from the study, along with newly published bird genomes, also allowed the researchers to reconstruct the partial genome of the common ancestor of archosaurs, providing a tool to investigate the genetic starting material of crocodilians, birds and dinosaurs.

Article by Adam Thomas

Photos by Lindsay Yeager and Danielle Quigley

This article can also be viewed on UDaily.

Agriculture and natural resources included in list of top 5 paying degrees for 2015

More and more people are earning college degrees. As of 2011, close to one out of every three people over 25 held a bachelor’s degree, according to a U.S. Census Bureau release. “As recently as 1998, fewer than one-quarter of people this age had this level of education.”

Because more of us are college-educated, this makes it so that “just any” degree will not necessarily suffice for some people anymore. People are starting to see that if they’re going to invest all of that hard-earned money, not to mention time and energy, into obtaining a degree, it should be into one that will likely lead to ample job opportunities and higher earnings power.

Click through to the full article on USA Today >>

UD students learn about interesting CANR programs

Students with undeclared majors meet CANR's Dean, Mark Rieger, and pot plants in Fischer Greenhouse.Twenty-three University of Delaware students visited the College of Agriculture and Natural Resources (CANR) campus on Jan. 23 to create dish gardens at the Fischer Greenhouse, learn how ice cream is made at the UDairy Creamery and speak with CANR Dean Mark Rieger about the college’s class offerings and job opportunities for students who graduate with degrees in agriculture and natural resource related fields.

The students toured the CANR facilities as part of UD’s 2015 Study at Home program, which is funded by a Unidel grant and designed to emulate Winter Session study abroad experiences by highlighting exciting venues and activities both on and off the UD campus.

Christina King, Residence Life and Housing complex coordinator, said the program planned nine workshops and events, three of which were trips to Longwood Gardens, to Philadelphia and to the Metropolitan Museum of Art in New York City.

“Study at Home is meant to be a series of events, workshops or trips that can in some ways mirror the experience a student could get if they went abroad, but on campus and in the local area,” said King. “Each trip has something to see and then a cultural meal or an activity that might take students out of their comfort zone.”

In addition to the CANR visit, the students also participated in other on-campus activities, such as a paint night, a yoga workshop, a tour of the University of Delaware Library Special Collections and an Asian cooking tutorial in Vita Nova’s kitchens with representatives of the Department of Hotel, Restaurant and Institutional Management (HRIM).

For their experience at CANR, students began with a tour of the Fischer Greenhouse, where they learned firsthand from Bill Bartz, greenhouse manager, about the facility and the plants grown there. They were then able to make festive dish gardens out of tropical houseplants and interact with Rieger, who was on hand to help out and answer any questions the students had about CANR.

One student was able to learn about the horses on the CANR farm as well as the equine science minor, while another asked about the UDairy Creamery’s new “Science of Ice Cream” course. Another was interested in Rieger’s sustainable and organic agriculture class that will be offered in the spring. 

After spending time at the Fischer Greenhouse, the students moved to the UDairy Creamery, where they were treated to some ice cream and finished their day with a tour led by Melinda Litvinas, creamery manager, and Jennifer Rodammer, supervisor at the facility.

Ariel Ramirez, a sophomore majoring in political science, said that — other than a stop at the popular UDairy Creamery — Study at Home was the first time he had visited the CANR campus and he found it very interesting.

“I think the greenhouse is amazing. I didn’t know this much went into it. I was really impressed,” he said.

Of the Study at Home program, Ramirez said that he participated in the paint night, visited the library’s Special Collections and participated in the trip to New York City. He has found the program beneficial and said he believes it should be carried on into the future.

“It’s really cool because you get to see all the culture and all the things UD has to offer, and all the opportunities that you might not get to see otherwise,” said Ramirez.

McKenzie Tsaousis, a freshman mechanical engineering major, said she really enjoyed her time at CANR and, like Ramirez, had never been inside any of the buildings on the CANR campus, although she had been at the site for ice cream and to see the cows.

Tsaousis said she is interested in taking the “Cow to Cone” class.

“I think that would be really interesting. I’ve milked a cow before, but obviously not thought about making ice cream, so I think it would be really cool — especially since I love the ice cream here — to get involved in the whole thing,” said Tsaousis.

Of the Study at Home program overall, Tsaousis said, “I absolutely love it. I’ve actually been to every single program. It’s a really awesome opportunity because I’m from Raleigh, North Carolina, so I haven’t been to a lot of the things that are up here. We went to Longwood Gardens and I’ve never been, so it’s really cool to expose yourself to all these different things.”

King said that throughout the experience, “The students have been delightful to work with. To see them do this has been very rewarding because it was very hard to plan and we weren’t sure if people were going to do it and it’s been great. The students have been wonderful and really enjoyed it.”

For more information on the Study at Home program, visit the Winter Session Learning Activities website.

Article by Adam Thomas

Photos by Kathy F. Atkinson

This article can also be viewed on UDaily.

10th annual Delaware Agriculture Week concludes with breakfast event

10th Agriculture Week wraps upThe 10th annual Delaware Agriculture Week, a celebration of an industry vital to the state’s economy, wrapped up on Jan. 16 with the Friends of Ag Breakfast.

This year, Delaware Agriculture Week — held Jan. 12-16 at the Delaware State Fairgrounds in Harrington — welcomed a record 2,085 visitors to learn best practices and new technologies, expand existing networks and make connections with leading vendors.

U.S. Rep. John Carney attended the Friends of Ag Breakfast, saying, “As Delaware’s largest industry, agriculture plays a central role in our state’s economy. Each year, Ag Week is a great opportunity for all those involved in Delaware’s agricultural industry to come together to share information and collaborate on new ways to support and strengthen agriculture in our state. I always look forward to attending events during Ag Week to discuss the challenges facing farmers and to find opportunities to grow Delaware’s economy through agriculture.”

Cara Cuite, associate research professor in the Department of Human Ecology at Rutgers University Cooperative Extension, was the keynote speaker at this year’s breakfast and discussed “GMO’s and Public Perception in the 21st Century.”

Cuite spoke about a survey on genetically modified foods that she and two Rutgers colleagues — William K. Hallman, professor and chair of the Department of Human Ecology, and Xenia Morin, associate dean and liaison for sponsored programs — conducted in fall 2013.

She began by explaining how people have been working to improve plant and animal species through techniques such as selective breeding and crossbreeding for much of human history.

“However, genetic engineering is different from this. Genetic engineering allows scientists to select specific genetic traits from one organism and insert them into the genetic code of another organism,” said Cuite.

The results of the survey found that for many people, opinions about genetically modified foods are not strongly held, and that many people base their opinions on feelings and that opinions change as they learn more specifics.

Cuite’s group concluded that how the genetic modifications are referenced — whether as GMOs, genetically modified foods, genetically engineered foods or agriculture biotechnology — makes a big difference in how people respond.

“We’ve done research that finds people respond differently to different terms. ‘Agriculture biotechnology’ people seem to like better than ‘genetic engineering,’ so it really matters what we call it. And we know that most of the world uses the term ‘genetic modification’ and uses ‘GMOs’ to describe the product of this process,” she said.

Cuite said the group found that out of all the terms, the one most frequently searched online was GMO.

“GMO is clearly what most people are thinking about and searching for when they are thinking about this issue,” said Cuite.

National award

At the breakfast, Dave Marvel, a grain and vegetable farmer from Harrington and the vice president of the Fruit and Vegetable Growers Association of Delaware, was recognized with the 2014 National Epsilon Sigma Phi Friend of Extension Award.

Susan Garey, a Delaware extension agent, presented Marvel with the award and talked about how he was instrumental in “working with UD Cooperative Extension to establish a Produce Food Safety (GAP/GHP) training program for Delaware growers and has helped us receive over $45,000 in grants to support Produce Food Safety programs.”

On receiving the award, Marvel thanked Cooperative Extension, saying, “Cooperative Extension touches our lives in a lot of ways that we don’t realize. When it comes to food, to health, to agriculture, to people, to animals and plants, Cooperative Extension plays a role in it to better the lives of Delawareans.”

About Delaware Agriculture Week

Delaware Agriculture Week provided numerous sessions that covered a wide array of topics including small fruits, fresh market and processing vegetables, small flock and commercial poultry, grain marketing, grain crops, hay and pasture, beef cattle, irrigation, direct marketing, and much more. Nutrient management, pesticide, and certified crop adviser continuing education credits were offered.

Agriculture is an $8 billion industry in Delaware, according to a 2010 University of Delaware report, which factored in the agriculture jobs and related production, goods and services that support the largest industry in the First State.

Delaware Agriculture Week is sponsored by University of Delaware Cooperative Extension, Delaware State University Cooperative Extension and the Delaware Department of Agriculture.

This article can also be viewed on UDaily.

Environmental concerns, awareness grow in South Wilmington community

Environmental concerns, awareness grow in South Wilmington communityAn interdisciplinary research team from the University of Delaware, which is working with Wilmington’s Southbridge community on environmental issues, has released results of a survey showing that more than half the residents have serious concerns about pollution and sea level rise.

The survey, which was administered at various community events in the South Wilmington neighborhood, found that 50.6 percent of residents who responded were greatly concerned about pollution and that about 59 percent described sea level rise as a very serious or extremely serious issue.

The low-income, largely African-American community of about 2,000 residents is the type of neighborhood that often is left out of discussions about topics such as sea level rise, said Victor Perez, assistant professor of sociology and criminal justice, who has been working with the team and local residents for about 18 months.

“Coastal communities with higher-priced homes are more often at the center of sea level rise concerns,” Perez said. “But it’s well documented that Southbridge is extremely vulnerable to sea level rise.”

Not only would much of the area be flooded if water levels rose significantly, he said, but Southbridge already has a large amount of pollution in its soil from industries such as tanneries and chemical companies once located there. The community, which is the oldest historically African-American neighborhood in the city, is south of the Christina River.

The UD research team is exploring the complex, interrelated issues involving sea level rise, environmental pollution and human health in Southbridge. The potential for sea level rise in the area is a pressing issue, Perez said, which is gaining more attention and awareness with the work of state agencies, as well as local organizations, community members and the researchers from the University’s Delaware Environmental Institute (DENIN).

The research team — made up of experts in soil chemistry, hydrology, engineering, economics and sociology — is attempting a novel interdisciplinary approach to study the potential for pollution in the soil to become mobile by way of projected sea level rise in the area. The approach seeks to integrate each respective discipline into the research design, complementing and informing each other, and has a strong community focus, Perez said.

Members of the team, led by Donald Sparks, S. Hallock du Pont Professor of Plant and Soil Sciences and DENIN director, also includes Kent Messer, associate professor of applied economics and statistics, and Holly Michael, associate professor of geological sciences, in addition to Perez.

Perez’s focus in working with residents is to determine their level of concern and awareness of sea level rise, flooding and pollution in the area, as well as the community’s perceptions of the health effects of their local environmental burdens.

The community’s battles with pollution are well known to many in the area, and residents have completed surveys and participated in focus groups. The research efforts are intended to also inform the community and will be reported back to residents on an ongoing basis, Perez said, noting that about 63 percent of those sampled reported knowing nothing to only a little about the specifics of sea level rise.

UD researchers also are creating a baseline of knowledge of the environmental burdens in the community by way of state reports, soil sampling and local community knowledge and experiences of these issues; this knowledge will continue to inform research approaches and policy recommendations for sea level rise and pollution mitigation and remediation.

The goal is to allow the community’s perspective to help inform the research approach, which considers the local knowledge of these issues vital to the success of the research, Perez said.

The research is funded by NSF-EPSCoR, the Experimental Program to Stimulate Competitive Research, grant No. IIA-1301765, and the state of Delaware. EPSCoR is a federal grant program led by the National Science Foundation to help states develop their research capabilities and institutions.

More about the community

Though Southbridge struggles with environmental and health issues, unemployment and a level of poverty nearly four times that of the state’s, in recent years it has made significant gains in addressing these issues, Perez said. He gave these statistics:

  • From 2000 to 2010, South Wilmington saw a significant decline in unemployment, from 15.7 percent to 7.5 percent, though unemployment did return to 14 percent in 2012.
  • While South Wilmington’s high school graduate rate of 60 percent (of those 25 and older) was considerably less than that of the entire city of Wilmington in 2000, it has increased to 78 percent in 2012, nearly even with the city as a whole.
  • The percentage of households with a female head and no husband present has declined precipitously, from 50 percent in 2000 to 29 percent today.
  • Southbridge is now one of the safest communities in Wilmington, with low crime rates attributed to the efforts of generations of families living there and community police officers.
  • Southbridge is a well-organized community with a rich history and deep ties between citizens, and for the past six years, the community and service agencies have held a free, well-attended community event, “Southbridge Weekend,” every summer.

For more information on the community and its recent accomplishments, check out the links available on Perez’s website.

Community liaisons Stan Salaam and Rysheema Dixon, a 2009 College of Arts and Sciences graduate, contributed information to this article.

This article can also be viewed on UDaily.

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