UD researchers’ website tracks genetic sequence data from unknown viruses

UD researchers' Wommack and Polson's website tracks genetic sequence data from unknown virusesUniversity of Delaware researchers Shawn Polson and Eric Wommack have received a three-year, $867,661 National Science Foundation (NSF) Advances in Biological Informatics (ABI) grant to continue and expand the work being conducted on their Viral Informatics Resource for Metagenome Exploration (VIROME) website.

The web-application site is designed to help researchers explore sequence data collected from environmental viruses or, as they describe it, to “shine a little bit of light into the unknown.”

The project began in 2008 with funding from the Gordon and Betty Moore Foundation and came about when Delaware Biotechnology Institute-based researchers Polson and Wommack discovered the lack of computational tools for analyzing DNA sequences from environmental viruses.

“One big problem we ran into when looking at microbes in the environment is if you want to grow them, only about 1 percent of them are going to be culturable. For the vast majority, the only way we really have to look at them is to try to isolate a sample from the environment and sequence the DNA that’s there and attempt to identify the little pieces,” said Polson, a research assistant professor in UD’s departments of Computer and Information Sciencesand Biological Sciences and coordinator of the Center for Bioinformatics and Computational Biology’s Core.

Wommack, a professor who holds joint appointments in the departments of Plant and Soil Sciences and Biological Sciences and the College of Earth, Ocean, and Environment, added that the field of microbiome research, in which researchers randomly sample microbes without any sort of laboratory cultivation, is relatively new.

“Ninety-nine percent of the microbes can’t be grown in the lab so when you look at only the microbes you can grow, you’re vastly restricted in your understanding of what is really there and what they are really doing,” said Wommack. “It wasn’t until sequencing became cheap enough that we could even contemplate doing things this way. Now that DNA sequencing is affordable, we can start to apply it to these questions, and UD is pretty well positioned with regards to sequencing and computation.”

Metagenomics

Using the technique known as metagenomics, which was established in the mid-2000s to study bacteria in the environment, Polson explained that he and Wommack are interested in viruses that infect microbes like bacteria and microalgae. These sorts of viruses account for most of the viruses in natural systems.

In essence, metagenomics requires lots of sequencing of genomic DNA taken directly from microbes in environmental samples such as water, air or soil. Metagenomics is also being applied to samples from humans, plants and animals to uncover the diversity of microbes associated with larger organisms.

Once the metagenomic sequence data is obtained, a complex analysis of the data is necessary to uncover what the genes do and which organism or virus they came from. Usually with sequence analysis, researchers will compare the sequences to known things that have been seen before and are stored in a database. The problem with studying environmental viruses is that so few known viral genomes have been sequenced.

“With bacteria, that strategy worked pretty well. You might get 70 percent of your sequences matching a gene that had been seen before. With viruses, at first we were seeing 5 percent of our sequences hitting something that had been seen before,” said Polson. “We really had to come up with a way to analyze that data and, at first, it was just for our own use but then we built a tool to grab every little piece of information we could. From there, we realized that other people might be interested, so that’s when we started building the website and talking to the Moore Foundation.”

Now people submit their sequence data to the VIROME website and it is processed through an analysis pipeline. The process involves a great deal of computational work, which Polson and Wommack have been providing through a computational grid supported by the National Science Foundation.

While the funding from the Moore Foundation got the site started, with this new NSF ABI grant, Polson and Wommack are seeking ways to sustain the website and grow the program to evolve with the changing technologies.

Evolving technologies

When VIROME first started, sequencing was expensive and people were sequencing long pieces of data but they were not doing a lot of sequences in bulk. Now, things have swung in the other direction, with tens to hundreds of millions of short sequences. Because the cost of sequencing has gone down, a lot of data can be produced and sequences are much shorter so the researchers need to evolve their pipeline to assemble the little pieces into longer stretches and then provide the analysis.

“One of the challenges in big data science is to make the data easily available,” said Wommack. “It’s a lot to ask an individual principal investigator to maintain a site for sharing this data. Part of our model going forward is that the users will support the computation but we’ll maintain the shared data resource so that hopefully the data and, more importantly, the analysis has a long term life beyond their immediate scientific needs.”

While the two researchers and Daniel Nasko, a doctoral student in the bioinformatics and systems biology program, are currently processing all of the data, Anup Mahurkar, their collaborator at the University of Maryland’s Institute for Genome Sciences, is trying to take that work and package it in a way that allows the users to handle some of the computational requirements, as well.

“It’s called a virtual machine so essentially you create software that makes a computer think that it’s something else,” said Wommack. “It’s sort of like a computer running an image of another computer.”

Viral dark matter

The other aspect to the research is the creation of a database of viral dark matter to help identify unknown proteins in datasets.

“At first we could only identify about 5 percent of the genes that we were finding in these datasets and we wanted to create a database specifically for this viral dark matter — these genes are very abundant and we don’t know what they do. The goal of the database is to give more meaning to the dark matter, to see if we can figure out what these genes might be doing,” said Polson.

Wommack said that when the researchers go out and get a water sample or soil sample to get sequence data out of the viruses and compare them to other known virus sequences, most of the time they do not find a match.

“There’s a vast amount of genetic novelty among viruses and so we have to start somewhere and the ‘starting somewhere’ is to leverage the VIROME pipeline and our big data resource to begin to at least classify where and when these unknown viral genes have been observed,” said Wommack. “It’s somewhat reassuring when you do see the gene again within another, different viral sample, at least you know it’s a gene that belongs to viruses. You don’t know what it does, but it occurred more than once.”

The goal is to track these occurrences to see if they are happening in certain types of environments more frequently than others, which can give the researchers clues as to where to start looking for the unknown viruses.

“You start with these guilt by association sorts of findings,” said Wommack. “I might not know what it does, but I know we always find it in ecosystems like the Chesapeake Bay and we don’t see it in the deep ocean, we don’t see it in soils. The hope is by building this database that it will start to point the way to genes that we have no idea of their function but they happen to be really important to what viruses do. We hope it gives us a process of being able to shine a little bit of light into the unknown.”

Article by Adam Thomas

Photo by Lindsay Yeager

This article can also be viewed on UDaily.

UD’s Seyfferth to create rice paddies to study ways to lower arsenic levels in rice

UD's Seyfferth to create rice paddies to study ways to lower arsenic levels in riceThe University of Delaware’s Angelia Seyfferth has received a prestigious five-year, $465,000 National Science Foundation (NSF) Faculty Early Career Development Award for studies on arsenic in rice, and the funding will provide for the installation of the first rice paddies in the state. 

The rice paddies, to be created on the College of Agriculture and Natural Resources (CANR) campus in spring 2015, will not only aid Seyfferth’s research on potential methods to lower arsenic levels in rice – a staple crop for nearly half of the people on Earth – but they will also provide an important teaching tool for UD graduate and undergraduate students, and local high school and middle school students, as well. 

Seyfferth, assistant professor in CANR’s Department of Plant and Soil Sciences, is the first recipient of an NSF Career Award in the college and CANR Dean Mark Rieger said he is thrilled that Seyfferth has received the award.

“To my knowledge it is the first one that has been awarded to our college, so it’s definitely a milestone and a reflection of the caliber of our most recent hires,” said Rieger. “The best part of the NSF Career program is the intentional and thorough integration of teaching and research, which means that students will also benefit from this award.”

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, added that the award shows the great work and research conducted by Seyfferth.

“Her work is exceptional, focused on the coupled effects of plant and soil processes on trace element and nutrient cycling in the rhizosphere,” said Meyers. “Through her research and teaching supported by the NSF Career award, she will bring together and build on many aspects of our departmental expertise in plants and soils. I’m thrilled for her and to have her as a colleague in our department.”

Research and teaching

Seyfferth said the award requires almost equal weight to be put on the research and teaching components.

“With all NSF awards, the broader impacts of the research are important, but this particular award is about the integration of the research with the education,” Seyfferth said. “It’s not just doing research but really how you integrate education into the research.”

As such, a major component of the project will be the establishment of a dozen small rice paddies at a new outdoor research education laboratory – the Rice Investigation, Communication and Education (RICE) Facility – to be built in cooperation with students in UD’s landscape design program.

The facility will enable field experiments and integrate research with educational outreach, and Seyfferth said plans are in the works to involve high school and middle school students.

Arsenic research

Arsenic is a cancer-causing compound that can show up in drinking water or food. Humans can get exposed to arsenic through ingesting food or water that has arsenic, and the toxic effects depend on the concentrations of arsenic in the food or water as well as the dose – the amount of food or water that is ingested.

Rice tends to have more arsenic compared to other cereal crops and arsenic in rice is an especially important issue for people who eat a lot of rice. Since over half the world’s population depends on rice as a staple food, finding ways to lower arsenic in rice is extremely important.

Seyfferth’s research will look at different ways to decrease arsenic concentrations in rice grains while also increasing yield. Her research will consider arsenic dynamics in the soil solution as well as within the plants themselves, from the water the plants are in contact with to the grains that people eat.

It will also look at how management practices could affect the biogeochemistry of carbon and iron dynamics. For example, iron oxides precipitate on the outside of a plant’s roots and are thought to absorb arsenic before it can get taken up by a plant, and adding organic matter into the soil as a way of soil management could enhance carbon cycling and methane production.

“If we were to incorporate a material into the soil with the goal of decreasing arsenic levels in rice, we want to be sure we are not creating another environmental problem in the process – by increasing greenhouse gas emissions from soils. We are ultimately looking for an economical and sustainable solution that could be adopted by farmers in the U.S. and especially in developing countries where arsenic contamination and poisoning is a critical issue,” said Seyfferth.

UD rice paddies

Seyfferth is already growing rice in rice chambers at UD to conduct the research, but she will be aided in an important way with the construction of the RICE Facility paddies on UD’s Newark farm in the spring of 2015.

“Some people might laugh and say, ‘Why would you want to grow rice here?’ Well, there’s no reason that you can’t grow rice here in Delaware,” said Seyfferth. “As long as everything more or less stays the same, we can expect to have relatively humid summers. In terms of the growing season, we’d only be able to grow rice in the summer but we’d be able to have enough time to grow a four-month rice crop.”

The RICE Facility’s 12 paddy mesocosms were designed in conjunction with Carmine Balascio, associate professor of plant and soil sciences, and his students in a landscape design course.

Seyfferth said the students came up with a grading plan and a design for building the rice paddies with water management in mind. In addition to the excavating team Seyfferth is hiring, some of the students from the class will have a hand in the actual construction of the RICE Facility.

Seyfferth and her team will grow different varieties of rice each year and at the end of the study they will have a large data set of several globally important rice varieties. Plants will be grown in the RICE Facility in summers, and in environmental chambers in the Fisher Greenhouse Laboratory in the fall and winter.

“Specifically, we will grow varieties that are important for both the U.S. and for Southeast Asia, where arsenic in rice and in drinking water is a huge problem affecting more than 100 million people,” said Seyfferth.

Teaching component 

Graduate and undergraduate researchers in Seyfferth’s laboratory will work on the rice paddy fields and students from her class, Humans and Environmental Sustainability, will also have a chance to learn about the paddies.

In addition, students from Newark High School will have the opportunity to work on the paddies in the summer and middle school students from Serviam Academy will have a one day summer camp – called Soil is Life – to learn about the importance of soil in food production.

Seyfferth said that the grant has funding to pay the high school students to work on the research project. This will provide a unique opportunity for these young students eager to pursue scientific interests.

“When I was a student, I wish I had an opportunity like that but I always had to get a side job and work, so the high school students are actually going to get paid hourly to work in the summertime,” said Seyfferth. “I don’t want them to have to make a choice between having that hands-on experience and working so they can do both at the same time.”

Article by Adam Thomas

Photos by Lindsay Yeager and courtesy of Angelia Seyfferth

This article can also be viewed on UDaily.

New equine science minor open to all UD students

New Equine Science minor open to all UD studentsA new equine science minor has been established at the University of Delaware’s College of Agriculture and Natural Resources (CANR) for students in all majors across UD with an interest in horses. 

The program was created with a generous gift of support from University Trustee and CANR student Stuart M. Grant and his wife, Suzanne.

The minor was designed for students who have no prior experience with horses but are interested in learning about the animals as well as those who have previous experience and want to further their education.

It will start with an introduction to equine science course as the foundation on which to build.

Other courses in the minor include behavior and nutrition, equine health and lameness, and equine management.

The courses are currently being taught by UD faculty members and Annie Renzetti, a local equine veterinarian associated with the Department of Animal and Food Sciences.

Courses with laboratory components will utilize the CANR horse herd on the Webb Farm.

Students can go into UDSIS and declare the minor at any time. Four of the courses required in the minor will be offered in the spring 2015 semester.

This article can also be viewed on UDaily.

In Memoriam: Memorial service for Mark Manno set Oct. 20 in Clayton Hall

In Memoriam: Mark MannoThe University of Delaware College of Agriculture and Natural Resources will hold a memorial service for Mark J. Manno, a long-time leader in the Cooperative Extension Service, at 1 p.m., Monday, Oct. 20, in Clayton Hall on the University’s Laird Campus. Friends and family may begin visiting at 11 a.m. 

Mr. Manno, who was state 4-H program leader, died suddenly on Saturday, Sept. 13. He was 64. 

“Mark Manno left an indelible impression on the University of Delaware and our state’s 4-H Program,” said Mark Rieger, dean of the College of Agriculture and Natural Resources. “His commitment to Cooperative Extension, its volunteers, staff and youth was unparalleled. We are grateful for his vast contributions and the precedent that he set as part of his legacy.”

“Mark was a blessing to UD Extension and to many of us personally,” said Michelle S. Rodgers, associate dean for Extension and outreach in the college and director of UD Cooperative Extension. “I am grateful that the 4-H staff celebrated with him this past week as he prepared for retirement. Please lift up Sandy and the Manno family in your thoughts and prayers.”  

Mr. Manno began his career with the 4-H Youth Development Organization in 1974, working as an extension agent in Virginia, Maryland and finally Delaware. He most recently served as program leader for the entire state of Delaware. 

His dedication to 4-H was more than a career obligation; it was a way of life. He had an impact on the lives of thousands of children who participated in 4-H programs over the years.

In 2008, Mr. Manno was awarded the Ratledge Family Award for Delaware Public Service by the University of Delaware. The award recognizes significant public service by the members of the UD community that contributes to the overall well-being of all Delawareans. 

Mr. Manno frequently said that his greatest career satisfaction came from the former 4-H’ers who would thank him for the impact that he had on their lives.

Born in Wilmington, Delaware, Mr. Manno was a 1967 graduate of Salesianum High School and was enlisted in the U.S. Army National Guard from 1971-1972. 

He received his bachelor’s degree in animal science and agricultural education from UD in 1971, his master’s degree in dairy science from Virginia Tech in 1974; and his M.P.A. degree in personnel from UD in 1988.

His work with 4-H afforded him the opportunity to travel to each state in the continental U.S., and he took several trips to Europe. He enjoyed gardening and stamp collecting and was an avid fan of UD sports, especially football and basketball – both the men’s and women’s teams. 

Mr. Manno was involved in the Knights of Columbus and was a devout parishioner at St. Johns-Holy Angels Church. 

His dedication to 4-H was exceeded only by his dedication to his family, as a devoted husband, loving father and adoring grandfather.

He is survived by his wife of 42 years, Sandy (Smith); his daughter, Nikki Szymurski and her husband, Jared; his sons, Tony and Mark, and Mark’s wife, Kim; his grandchildren, Mason and Everly; his brother, Fran Manno Jr. and his wife, Helen; his sister, Joan Haizlip and her husband, Chris; and several nieces and nephews.

Family and friends are invited to visit from 5-8 p.m., Friday, Sept. 19, at the Doherty Funeral Home, 3200 Limestone Road, Pike Creek. A Mass of Christian Burial will be celebrated at 10 a.m., Saturday, Sept.  20, 2014 at Holy Angels Church, 82 Possum Park Road, Newark. Burial will follow at All Saints Cemetery.

In lieu of flowers, the family suggests contributions be made to the Delaware 4-H Foundation, 113 Townsend Hall, Newark, DE 19716. 

Fighting Poisons With Bacteria

 The effort to save rice is but one use of microbial bacteria in protecting or enhancing agricultural plants. Credit Harsh Bais/University of Delaware
The effort to save rice is but one use of microbial bacteria in protecting or enhancing agricultural plants. Credit Harsh Bais/University of Delaware

Excerpt from The New York Times

When Harsh Bais grows rice plants in trays of water in his greenhouse at the University of Delaware, he can easily spot the ones that have been exposed to arsenic: They are stunted, with shorter stems and shrunken, yellow-tinged leaves.

Dr. Bais is working to develop rice plants that take up less arsenic, a common contaminant in the fields of his native India and other Asian countries. Chronic exposure to arsenic has been linked to heart disease, diabetes and genetic damage associated with elevated risk for cancer.

Read more on The New York Times website.

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UD’s Brannick named American Veterinary Medical Association Future Leader

Erin Brannick named American Veterinary Medical Association Future LeaderThe University of Delaware’s Erin Brannick has been named one of the American Veterinary Medical Association’s (AVMA) 2014-15 Future Leaders. 

Brannick, assistant professor in the Department of Animal and Food Sciences in UD’s College of Agriculture and Natural Resources, was one of 10 Future Leaders selected nationally.

The leaders represent a wide range of veterinary medicine disciplines, spanning from the military service to private laboratories to diagnosticians to small or mixed animal practitioners.

“I think that’s one of the powers of the program — that we’re bringing together such a breadth of our profession on this small team,” said Brannick. “We will bring all those different perspectives into moving a project forward, as well as helping each other gain leadership experience and skills.”

Nominated by the American Association of Avian Pathologists (AAAP), Brannick said that it was a tremendous honor to be selected as a Future Leader.

“It is definitely an honor to be named one of the Future Leaders, especially knowing that I was selected from all of my peers across the country. I’m very thankful and grateful to the AAAP for that honor,” said Brannick.

As a Future Leader, Brannick will participate in a yearlong leadership-training program as well as a project that will end up feeding back to the AVMA as a whole.

For this year’s project, Brannick said that the group wants to focus on the theme of workplace wellness, specifically wellness of the veterinarians themselves.

“Our particular group decided that we wanted to focus on workplace wellness and so we’re thinking across the breadth of veterinary workplaces, from academia to pharmaceutical or industry to private practices, and what individual veterinarians need to be able to work in a healthy way in that environment,” said Brannick.

Brannick said that creating a healthy work environment could encompass working on interpersonal relationships, balancing work with private life, taking time out to exercise, and learning how to cope with being a compassionate caregiver every day, as well as figuring out ways to handle potential emotional stress in their clients or staff.

A private consultant has been brought in to lead the workshops that will develop further leadership skills within the group and get the group working as a team.

In addition, the leaders completed a “360 assessment,” in which they received leadership commentary, completed self-reviews and got feedback from peers, supervisors and superiors within their organizations.

“That is supposed to give us a more rounded approach to how to best develop our unique leadership skills and talents,” said Brannick. “The hope, ultimately, is that these future leaders will truly become the leaders in local, state and national organizations so that it will end up benefiting veterinary medicine as a whole by developing individuals who will take the charge and lead our organizations to the next phases.”

Brannick said she had not considered applying for the program until she happened to see a photograph of Barbara Schmidt, a former mentor from a high school veterinary internship and the current treasurer of the AVMA, gracing the cover of one of the organization’s journals.

“I had shadowed her on multiple farm visits and then one day here at UD, I ended up grabbing one of the AVMA journals and there on the front cover was her picture. I started reading and it really got me thinking. Even though I felt like I was just one person — what could I possibly do? — I realized that if everyone felt like that, nothing would get done, so maybe it was time to take my leadership to a national level and show that to others,” said Brannick.

Having taken her leadership to that next level and received national recognition, Brannick is hoping to have the same impact on some of her pre-veterinary students that Schmidt had on her.

“I’m very grateful to have this opportunity to show my students leadership at a national level,” she said. “I hope that as my pre-veterinary students come up into veterinary medicine, they’ll consider what they can do to give back to their profession and how they can make an impact at a regional or national level.”

Article by Adam Thomas

This article can also be viewed on UDaily.

New book by UD professor highlights latest work in land economics

Josh Duke editor of new Oxford Handbook of Land EconomicsWhen Oxford University Press set out to publish a handbook in each field of economics, they selected the University of Delaware’s Josh Duke to be a co-editor of the volume focused on land economics.

The work, titled The Oxford Handbook of Land Economics, was edited by Duke, professor in UD’s Department of Applied Economics and Statistics (APEC), and Junjie Wu, the Emery N. Castle Endowed Chair in Resource and Rural Economics at Oregon State University, and joins 44 other economics handbooks currently available as part of the Oxford Handbooks in Economics series. 

Duke said that putting the book together was a five-year process, which started with a successful refereed editorial proposal and the recruitment of leading thinkers in the field to write the chapters.

“Although the book is aimed at documenting state-of-the-art knowledge and research methods for academic economists and doctoral students, policy makers and others with basic economic training will find the results useful for improving land use policy and understanding how economists think about land use problems,” said Duke.

The book includes chapters featuring the latest research in different application areas, with many – such as ecosystem services and climate change – concerning the environment.

Land economics

As for what land economics entails, Duke explained that it is how humans make decisions about using natural resources and how society can adjust rules to improve the performance of land markets.

“For instance, should a parcel be put to agricultural use, or should it be put to industrial use or commercial use? The problem with land markets, and land use decisions in general, is that they often have implications that affect people who are not the landowner,” Duke said. “When I make a decision about how to maintain my house and manage my yard, it affects my neighbors — both positively and negatively. There are a lot of interdependencies associated with land use.”

Duke pointed out that wars are fought over land and that people’s wellbeing is tied to the land, noting the security that comes from land ownership.

“To the owner, land is a special type of commodity and yet the way you use your land affects other people and vice versa,” said Duke. “Every society, over centuries, has developed institutions, or rules, to manage land use decisions. In the U.S., you can’t do whatever you want with your land, even if you’re the owner. You can’t convert a farm — in many jurisdictions — into a housing development without some form of governmental permission. There is a range of processes that society has decided upon for what ends land will be put to. Obviously, these processes can be very controversial, and this handbook provides economists’ perspectives.”

Duke explained that economists study the performance of these institutions and make recommendations on new institutions, something with which the book deals.

“In these chapters, the authors talk about how ecosystem services are produced from land and what kinds of policies are available to direct or incentivize land owners to enhance those services,” he said. “For instance, how can society protect prime farmland from urban encroachment? How can society best adjust land management behavior to protect water quality? This is a small sample of topics addressed by the handbook.”

Property rights and law also affect land use economics. “Several chapters address when land use regulation goes too far,” said Duke. “Our society vigorously debates the conditions under which an environmental regulation unduly restricts landowner options, and when confiscating urban business is permissible using eminent domain. Economists contribute insight by assessing the efficiency of those laws that determine what is private property.”

Top authors

The Oxford Handbook of Land Economics authors come from all over the world, representing institutions such as Ohio State University, Oregon State University, the University of Cambridge, and the University of California, Berkeley. International contributions come from researchers in Nigeria, South Korea and Italy.

Kent Messer, the Unidel Howard Cosgrove Chair for the Environment in the Department of Applied Economics and Statistics, was one of the contributors.

“The book features a lot of the best people in the field. It is a great group of contributors,” said Duke.

As for how he and his co-editor came to work on the book, Duke explained that Wu is “a leading thinker on land economics from Oregon State University who I’ve known for a while and this seemed like a great opportunity to collaborate, not just because I think he’s an excellent scholar, but because he covers a lot of the urban economic models that I don’t know as much about.”

Oxford Handbook

Oxford Handbooks offer authoritative and up-to-date surveys of original research, providing scholars and graduate students with compelling new perspectives on a wide range of subjects in the humanities, social sciences, and sciences.

The first Oxford Handbook in Economics was published in 2009. For more information on the series, visit the website.

Article by Adam Thomas

Photo by Lindsay Yeager

This article can also be viewed on UDaily.

UD professor touts benefits of adding meadows to landscapes

UD's Sue Barton touts the benefits of meadows over lawnsInstead of simple traditional lawns, the University of Delaware’s Sue Barton is asking local homeowners to consider meadows to increase ecosystem services and add aesthetic beauty to landscapes. 

Barton, associate professor in the Department of Plant and Soil Sciences in UD’s College of Agriculture and Natural Resources, said that homeowners with larger yards — one or more acres — should especially consider growing meadows instead of lawns. 

The benefits of having a meadow include more plant and wildlife diversity, better water penetration and deeper root systems to filter water, Barton said. Meadows also increase pollinators and are beautiful if properly maintained.

Some people may hear about installing a meadow and assume that it means they can just stop cutting their grass, letting it grow long and wild, but Barton said that’s not the case.

“The real key is not to just stop mowing your grass but to mow edges, mow a path, have a curvy line at the edge, something that makes the meadow look very purposeful,” said Barton.

Meadow versus lawn

A lawn is defined as something that is routinely cut and maintained at a height somewhere between two and five inches. It is most desirable when it consists of a cool season turf grass species, but the definition of a lawn doesn’t mean that it has to be grass.

“Usually, it’s primarily grass,” Barton said. “My lawn is pretty much all clover and weeds, but it’s still a lawn because it’s mowed regularly and kept short.”

A meadow, on the other hand, includes taller, warm season grasses. Examples of those native to this region include Indiangrass, switchgrass, prairie dropseed and little bluestem.

Meadows can also have blooming perennials, such as butterfly weed and black-eyed Susans.

But what plants grow in meadows will depend on soil types and the amount of available moisture.

Installing a meadow

In order to install a meadow, Barton said that there are two main strategies — stop cutting a lawn, while still maintaining a perimeter, and allow cool season grasses and plants such as Queen Anne’s lace and goldenrod to come into the meadow, or start from scratch and seed a meadow.

In order to do this second method, Barton explained how a meadow was installed on a property in the Applecross neighborhood in Greenville.

“We seeded that meadow, so we had to kill the existing vegetation. Then the strategy was to mix desirable warm season grass and a few perennial forb seeds with sawdust and spread that layer of seed and sawdust,” said Barton. “The sawdust does two things — it prevents light from hitting the soil to avoid crabgrass and foxtail, which are often problem weeds in a new meadow, and it also provides a moist germination medium for the desirable seed. It’s a good way to get a meadow started.”

Meadow alternatives

For those homeowners with smaller yards or yards with big, mature trees such as can be found in North Wilmington, sometimes, a meadow just isn’t practical or even possible.

Robert Finocchiaro, president of Finocchiaro Landscape Co., said that for those who have smaller yards or yards where grass won’t grow, it is best to consider all options that increase biodiversity.

“Plant bushes and groundcovers that will complement the look. There are a lot of landscapes up in North Wilmington where the trees have matured so much that you can’t grow grass,” said Finocchiaro. “The big thing is that they use mulch. What Sue is trying to say is maybe we can use leaves for mulch and do perimeter mulching, where you mulch right along the flowerbed. Maybe we can plant some understory bushes that will attract certain insects, which of course attract birds, and then have this little habitat in your front yard that looks very nice instead of just having mulch.”

Finocchiaro also said that he realizes that in New Castle County, “somebody’s meadow might be somebody else’s un-cut yard,” but he wants people with the space to accommodate the option to keep an open mind.

“If you have an isolated area in the back yard and it’s not a huge yard and you want to have the grass grow a little bit, I don’t see any problem with it. It’s kind of like a little transition zone,” said Finocchiaro. “What Sue’s trying to tell people and what I am trying to tell people is you don’t need two acres of maintained lawn any more. There are alternatives and what’s nice is this creates a little bit of a habitat that wouldn’t exist if you cut the grass every week.”

Changing perception

Barton pointed out that one way in which people can change their perception of meadows is to visit Longwood Gardens and tour its newly installed meadow garden that spans 86 acres and contains three miles of walking trails.

Article by Adam Thomas

Photos courtesy of Sue Barton

This article can also be viewed on UDaily.

Researchers find first evidence of fat-regulating hormone in avian species

Research team discovers first sign of Leptin in avian speciesA team of researchers that includes Larry A. Cogburn, professor in the Department of Animal and Food Sciences at the University of Delaware, recently found leptin in the rock dove, or pigeon.

The team includes scientists from the Agricultural Research Organization in Israel led by professors Miriam Friedman-Einat and Eyal Seroussi and four Israeli colleagues: Sara Yosefi, Gideon Hen, Dima Shinder, and Andrey Shirak.

The work is documented in a paper, “Discovery and Characterization of the First Genuine Avian Leptin Gene in the Rock Dove (Columba livia),” which was recently published in the September issue of Endocrinology.

Leptin and its receptor play critical roles in the control of food intake and energy expenditure, thereby affecting body weight, abdominal fatness, thermogenesis, insulin sensitivity, and lipid metabolism.

Since leptin was discovered 20 years ago, more than 115,000 papers have been published on this protein in humans, and another 5,000 have appeared on leptin in mice.

Leptin’s popularity is not surprising, as the hormone is the principal marker for the development of morbid obesity in humans.

Despite the attention focused on leptin in mammals over the past two decades, many questions remain unanswered about its role and mechanism, especially in non-mammalian species, and documentation of its presence in birds has proved particularly elusive.

“We’ve finally solved a 20-year mystery with the discovery and functional characterization of the first leptin gene in any bird,” Cogburn says. “Our hope is that further study of leptin in birds could identify novel mechanisms controlling appetite and energy balance and one day help solve the problem of obesity in humans.”

For more information on the study, check out the article by Diane Kukich on UDaily.

UD students honored by International Association for Food Protection

Patrick Spanninger and Qing Wang were among 16 students from around the world who received travel awards from the International Association for Food ProtectionUniversity of Delaware doctoral students Patrick Spanninger and Qing Wang were among 16 students from around the world who received travel awards from the International Association for Food Protection (IAFP) to attend the organization’s annual meeting held Aug. 3-6 in Indianapolis. 

The conference brought together more than 2,800 of the top industry, academic and government food safety professionals from six continents.

Spanninger and Wang, both in the Department of Animal and Food Sciences in UD’s College of Agriculture and Natural Resources, said that one of the most beneficial aspects of the conference was the networking, as both were paired with mentors from the food industry.

The mentors shared valuable work experiences with the students, who had an opportunity to follow their mentors and learn about their careers in the industry.

Spanninger’s mentor was Ed Wellmeyer, vice president of quality assurance and food safety at Ventura Foods, a leading manufacturer of products such as custom and branded dressings, sauces, mayonnaise varieties and margarines.

“He was an awesome guy,” Spanninger said. “He introduced me to everybody and took me to all of his meetings, and really took me under his wing. I wouldn’t have gotten half the business cards if I hadn’t been with him.”

Wang’s mentor was Michele Gorman, senior manager of food safety and microbiology for the yogurt company Chobani.

“My mentor had lots of working experience in food microbiology and she shared with me her work experience and also introduced her friends to me, so I felt like it was really good to have a mentor there,” said Wang. “I felt like it gave me a better understanding of the industry to help better my future career.”

Conference activities

In addition to providing mentors, the conference also featured talks, presentations and roundtable discussions.

“You can learn a lot during the talks and I went to several that were related to my studies. I also went to several that were just interesting, so it was pretty cool,” said Wang.

Both students presented their research at the conference. Spanninger’s dealt with his laboratory study on evaluating survival of pathogenic bacteria within different types of wildlife manure to assess the possible transmission of E. coli and Salmonella.

Spanninger said provisions of the new Food Safety Modernization Act includes information on reducing risk from animal intrusion and learning more about how pathogens survive in wildlife feces is an important aspect of this.

Wang’s study focused on the inactivation of foodborne viruses in alfalfa seeds by aqueous ozone. This was done by measuring the efficacy of aqueous ozone to disinfect alfalfa seeds contaminated with norovirus and norovirus surrogates.

Wang focused on alfalfa sprouts because they have been associated with a number of foodborne outbreaks where seed contamination was identified as the source.

Kali Kniel, professor in the Department of Animal and Food Sciences who accompanied the students to the conference along with numerous fellow faculty members from the department, said that it is an exciting time for students like Spanninger and Wang to be studying food safety issues pertinent to pre-harvest food safety.

“We are at the intersection of changes that were 70 years in the making. The FDA proposed produce rules will impact growers across the country and in order for the FDA to have the best science on which to base these rules, young developing scientists like Pat and Qing are involved in identifying that science,” said Kniel. “Both students presented work that is important to understanding the variable risks that affect fresh produce growing in fields and also alfalfa sprouts, which have a long history of transmission of foodborne illness.”

Article by Adam Thomas

Photo courtesy of Patrick Spanninger

This article can also be viewed on UDaily.

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