Sherrier named acting deputy dean of College of Agriculture and Natural Resources

February 14, 2013 under CANR News

Dr. Janine Sherrier, Plant and Soil Science.Janine Sherrier has been named the acting deputy dean of the University of Delaware’s College of Agriculture and Natural Resources (CANR).

Sherrier, a professor in the Department of Plant and Soil Sciences with a secondary appointment in biological sciences, also directs a robust research program at the Delaware Biotechnology Institute (DBI).

Sherrier was one of the earliest hires for the DBI initiative and worked as part of the team to grow DBI into the center of research excellence that it is recognized to be today.

Sherrier earned her bachelor of science degree in biology at Baylor University and her doctorate in biology at Texas A&M University. Subsequently, Sherrier pursued postdoctoral research in genetics at the John Innes Centre, U.K., and postdoctoral research in biochemistry at the University of Cambridge, U.K.

She is a member of the American Society of Plant Biology, the American Association for the Advancement of Science and the International Society for Molecular Plant-Microbe Interactions. She is also currently serving as the leader of a federal program that supports outstanding early-career scientists engaged in agricultural research.

Of the appointment, Sherrier said, “I consider it an honor and privilege to serve my college for a year as acting deputy dean. My highest priority is to provide members of my college with the resources required for high-quality student education, community outreach, and internationally-competitive research programs.”

Sherrier continued, adding that CANR Dean Mark Rieger “brings great ideas and an energizing enthusiasm, and I am pleased to be working as part of his team.”

Rieger said that he is “delighted that Dr. Sherrier has joined the college’s administrative team. As a world-class molecular biologist, she brings a strong background in research, which will be the focus of her appointment. Most importantly, I have found her to be truly passionate about the advancement of the college and agriculture and natural resource issues in general.”

Sherrier currently teaches courses in plant development biology, current topics of plant biology, and mentors undergraduate and graduate students in her research laboratory.

The research being conducted in her laboratory focuses on the beneficial symbiotic relationship between plants in the legume family and the soil microbe rhizobia, and the resulting development of a nitrogen-fixing root nodule. Her research program includes both a strong fundamental research component and the direct application of that knowledge into the development of new resources to address the immediate needs of growers.

Article by Adam Thomas

Photo by Kathy F. Atkinson

This article can also be viewed on UDaily.


UD’s Schmidt studies heat stress, disease resistance in African chickens

February 11, 2013 under CANR News

Last fall, the University of Delaware’s Carl Schmidt took a trip to Uganda with a team of researchers from Iowa State University and North Carolina State University to get genetic samples from African chickens. The goal was to compare and contrast their genes to one another, and also to American broiler chickens, to gauge how the two species’ genetic makeup helps them cope with heat stress, as well as susceptibility and resistance to different diseases.

The trip was part of a five-year, $4.7 million National Institute of Food and Agriculture (NIFA) climate change grant for a project titled “Adapting Chicken Production to Climate Change Through Breeding.”

UD Professor Carl Schmidt studies chickens in AfricaSchmidt explained that the objective of the trip was “to try to identify genes that may be helping these birds survive on different diets, in a different climate, and facing different disease challenges.”

Schmidt, associate professor in the Department of Animal and Food Sciences in UD’s College of Agriculture and Natural Resources (CANR), said that the group gathered more than 100 samples of African chicken DNA from “back yard flocks” of chickens from three cities from different regions of the country: Buwama, Wobulenzi and Kamuli.

Aiding the group in the research being done in Uganda was the organization Volunteer Efforts for Development Concerns (VEDCO), which Schmidt called invaluable as it supplied the researchers with lodging during their time in Kamuli. The group also collaborated with the International Livestock Research Institute (ILRI), which gave them access to samples ILRI had collected from chickens in Kenya.

Now that the researchers have the samples from Africa, researchers at North Carolina State are processing the DNA. Once the DNA is processed, Schmidt will work at the Delaware Biotechnology Institute to handle the sequencing of the genome and the bioinformatics.

Chicken differences

Schmidt said one of the main variances that might have an impact on the genetic differences between the American chickens raised in a production facility and the African chickens, which roam, is diet. The African chickens will eat anything that is available to them, including bugs, whereas the American chickens in production facilities are fed a largely corn-based meal. Schmidt said that he is interested to see “what kind of impact that has had on the genes that are involved in actually getting nutrients out of insects.”

Another difference between the two birds is that whereas American chickens raised in production facilities are relatively sheltered from the elements and from disease, African chickens are pretty much on their own. Schmidt explained that the African chickens are “exposed to the environment — they usually have a small building that they can go into, sometimes they even just go into the homes, but for the most part, they have to fend for themselves.”

Schmidt added that the African chickens also have to deal with predators, theft and “then of course they are also exposed to more disease agents than certainly the birds that are in production facilities here. And the thought is that they’ve been in essence selected to deal with these challenges.”

The group didn’t only get samples from traditional African chickens, however, as Schmidt explained that they also ran into a line of chickens imported from India and they wanted to examine the genome of those chickens, as well.

When it comes to size, Schmidt explained that African chickens are smaller than the American broiler chickens one would find in a production facility or at a grocery store. One reason for this is that whereas the production facility chicken is raised to be eaten, the African chicken is kept alive so it can continuously provide eggs as a food source.

Now that the group has collected samples from American and African chickens, Schmidt is hopeful that he will be able to head to Brazil in the summer — as part of a joint agreement between CANR and the University Federal de Lavras — to collect samples of chicken DNA from South America.

“What we’d like to do is get a couple of different geographic locations,” said Schmidt. “And the interesting thing to me is, Uganda kind of straddles the equator and Brazil isn’t quite straddling the equator but it’s a little more similar to Uganda than it is to the United States, so you can kind of see if there are any similarities.”

Schmidt also said that once he gets samples from Brazil, he would be interested in collecting samples from other locations, as well. “One of the things I’d love to do is go to Central America.”

Researchers and students who went on the trip and are involved in the grant from Iowa State include Max Rothschild, the Curtiss Distinguished Professor in Agriculture and director of the Center for Integrated Animal Genomics, and Angelica Bjorkquist and Damarius Fleming, both graduate students.

Researchers and students who went on the trip and are involved in the grant from North Carolina State include Chris Ashwell, associate professor of poultry genomics, nutrition, immunology and physiology, and Alex Zavelo, a graduate student.

Article by Adam Thomas

Photo provided by Carl Schmidt

This article can also be viewed on UDaily.


University of Delaware plant and soil sciences chair named AAAS Fellow

December 3, 2012 under CANR News

Blake C. Meyers, chair of the Department of Plant and Soil Sciences and the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences at the University of Delaware, has been named a fellow of the American Association for the Advancement of Science (AAAS).

Designation as a fellow of AAAS is an honor bestowed upon members by their peers.

Meyers received the award in large part because of his contributions to bioinformatics and plant functional genomics of model and crop plants, especially in the area of small RNA biology.

Meyers explained that he has been involved in the field of plant genomics for more than 15 years, with the most intensive research taking place at the laboratory he established at UD’s Delaware Biotechnology Institute.

Noting that he has an ongoing and long-running collaboration with Pamela J. Green, the Crawford H. Greenewalt Endowed Chair in Plant Molecular Biology, Meyers said that the collaboration helped him to focus on small RNAs as a particularly productive field in which to apply his work on “next-generation” DNA sequencing technologies.

“Collaborative research is key to our success, as we’ve worked with experts in rice, maize, soybean, model plants such as Arabidopsis thaliana and Medicago truncatula, tomato, numerous other plants, fungi and even chickens, contributing our expertise and tools, and learning from our collaborators, their biological materials, and the comparisons we’ve made across organisms and their genomes,” said Meyers.

Meyers said of the AAAS announcement, “It is really a tremendous honor, because it reflects a recognition by my scientific peers of the quality and impact of both the work of my lab and my own contributions to science. The AAAS is a remarkable organization so I’m really thankful to be elected a fellow.”

He also said the honor would not have been possible without the help of the many researchers with whom he has collaborated over the years. “The honor should be shared with my past and present lab members, as I’ve been lucky to work with excellent lab members over the 10 years that I’ve been at the University of Delaware.”

Meyers said the recognition is to be shared by UD as well, as he has had “strong institutional encouragement and support from the University, the College of Agriculture and Natural Resources and my department, including excellent peers, top-tier facilities in which to carry out our work and access and support with the latest generation of technologies that my lab requires to carry out its work.”

Meyers has also participated in activities shaping the future of bioinformatics in plant biology.

“Like many plant biologists, I feel a responsibility to help advance agriculture which has tremendous challenges due to population growth, environmental pressures and climate change, and increasing demands on natural resources,” said Meyers. “The AAAS has long promoted science as the means to help address issues such as these, so their recognition of my work is quite gratifying.”

Mark Rieger, dean of the College of Agriculture and Natural Resources, said of Meyers, “Dr. Meyers’ work in plant genetics and molecular biology is known around the world and reflects extremely well on the college and the University of Delaware.”

Rieger added he is “thrilled that AAAS has recognized his research. He is one of the youngest faculty that I know to have received this recognition, and I predict he’ll have an even greater impact on his discipline in the coming years.”

About Blake C. Meyers

Blake C. Meyers received a bachelor’s degree from the University of Chicago and his master’s degree and doctorate from the University of California Davis.

He joined the UD faculty in 2002 and was named the Edward F. and Elizabeth Goodman Rosenberg Professor of Plants and Soil Sciences in 2010.

Meyers’ lab has pioneered the application to mRNA and small RNA analyses of what was the first of the now-popular “next-generation” DNA sequencing technologies. Research in his laboratory is supported by the National Science Foundation, the U.S. Department of Agriculture and industry.

About AAAS

The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science around the world by serving as an educator, leader, spokesperson and professional association. In addition to organizing membership activities, AAAS publishes the journal Science, as well as many scientific newsletters, books and reports, and spearheads programs that raise the bar of understanding for science worldwide.

Founded in 1848, AAAS serves some 261 affiliated societies and academies of science, serving 10 million individuals. Science has the largest paid circulation of any peer-reviewed general science journal in the world, with an estimated total readership of one million. The non-profit AAAS is open to all and fulfills its mission to “advance science and serve society” through initiatives in science policy, international programs, science education, and more.

Article by Adam Thomas

Photo by Evan Krape

This article can also be viewed on UDaily.


Researchers reveal the ‘dark side’ of beneficial soil bacteria

September 21, 2012 under CANR News

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Article by Tracey Bryant

Animation and images courtesy of Harsh Bais

This article can also be viewed on UDaily.


UD researchers show how beneficial soil bacteria can boost plant immunity

August 29, 2012 under CANR News

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

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

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

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

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

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

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

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

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

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

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

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

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

Article by Tracey Bryant

Photo by Ambre Alexander

This article can also be viewed on UDaily.


UD, DBI use advanced technology in genomic sequencing

May 22, 2012 under CANR News, Cooperative Extension

The Delaware Biotechnology Institute (DBI) at the University of Delaware has been equipped with a state-of-the-art Pacific Biosciences RS DNA sequencing machine to help researchers obtain genetic information, making UD one of the few universities in the country equipped with the advanced device. In fact, at the time of its installation, UD was the 25th site in the world to house such a machine.

The machine came to UD and DBI thanks to a $744,538 National Science Foundation (NSF) award and is stationed in the UD Sequencing and Genotyping Center, which is run by Bruce Kingham and provides genomic technology services for University research groups as well as outside investigators.

UD is in a unique spot with the machine because, as K. Eric Wommack, professor of environmental microbiology in the Department of Plant and Soil Sciences, explained, “Most of the places that have the Pacific Biosciences machine are large sequencing centers that sequence the human genome through massive amounts of sequencing, or they’re government labs. I believe we are one of the few research Universities without a medical school that has one of these instruments.”

Because of this, the sequencing machine will be used in unique ways, branching out into areas such as environmental and agricultural studies, with Wommack being one of the first UD professors to use the machine for research purposes.

Wommack was awarded a $200,000 NSF EAGER Collaborative Research grant focusing on exploratory application of single-molecule real time (SMRT) DNA sequencing in microbial ecology research.

The grant will focus on three areas of research. The first is in the area of single cell genomics, in which Wommack and his collaborator at the Bigelow Marine Laboratory in Maine will pull a single bacterial cell out of an environmental sample and sequence its genome.

The second has to do with characterizing the composition of a microbial community using a single gene, with the Pacific Biosciences machine enabling Wommack to look at changes in the sequence of a single gene in order to infer information about the species of microbes making up the microbial community as a whole.

The third application is what he calls “shotgun meta-genomics of viral communities,” which is the heart of his research. Explaining further, Wommack said, “The reason it is called ‘shotgun’ is that we literally are randomly sampling sequences from viruses in the environment.”

Piecing together genetic puzzles

Wommack said a problem with obtaining genetic sequence information is that the process takes a long time when in fact it needs to be as fast and accurate as weather predictions. “What if we could only measure temperature once a week? We really wouldn’t know a lot about how the climate and how weather works,” he said. “But of course, we can measure temperature in incredibly small scales of time. That’s where we need to get in the use of genetic data and environmental science and the Pacific Biosciences instrument gets us a little bit closer to that.”

The machines currently utilized at the center — while they each serve their own function — are slower than the new model, which Wommack said, “Allows you to run a lot of samples quickly.” They also provide shorter snippets of genetic sequence.

The current high-throughput DNA sequencers read anywhere from an average of 50 base pairs — that is, DNA “letters” — to 400 base pairs, while the Pacific Biosciences instrument can read anywhere from 1,000-12,000 base pairs.

Kingham said of the longer sequences, “Many times when you’re studying genomics, the length of the DNA sequence is everything, so the longer the DNA sequence read for each sample, the better.”

With the shorter sequences, Wommack explained, researchers have to take the little snippets and match them together, like piecing together a jigsaw puzzle. He compared putting together data on the old machines to solving a 1 million-piece puzzle, while putting together data on the new machine is like solving a 100-piece puzzle.

Kingham explained that another big advantage of the Pacific Biosciences machine is that researchers are able to monitor a single DNA molecule as it’s being replicated, as opposed to the other machines in the lab that rely on making copies of the DNA before it can be analyzed. “If you make a copy of something and then you make a copy of that copy, and then you make a copy of the copy of the copy, ultimately what you end up with is likely going to look somewhat different than what you started with,” said Kingham.  “The same thing can happen when you copy DNA.”

Kingham also said that he encouraged “anybody that’s involved in life sciences research to consider using that Pacific Biosciences sequencer because it’s so new, there’s so little known about how it can be utilized, and through the ability to analyze a single molecule of DNA, it has the possibility to change the face of genomics research.”

Without distinguished faculty at UD involved in genomics research, Kingham said, it may not have been possible to have obtained the machine. “This is a good representation of the prestige of genomics research at the University of Delaware,” he said. “Many of the scientists are internationally renowned in genomics research. Blake Meyers, Pam Green, Eric Wommack, Carl Schmidt, and others — these faculty members are internationally renowned in their respective fields of study.”

Kingham went on to say that the machine is “absolutely the cutting edge of DNA sequencing technologies, and UD is really fortunate to have it.”

About the UD Sequencing and Genotyping Center

The UD Sequencing and Genotyping Center is equipped with three DNA sequencing instruments — the Pacific Biosciences instrument, an Applied Biosystems Sanger sequencer, and the Illumina HiSeq 2000 genome sequencer.

While Kingham said he is thrilled about the new Pacific Biosciences machine, he is also quick to point out that each of the sequencers has its own relevant application area.

The Sanger machine, explained Kingham, “has been around for 40 years, and will probably be around for another 40 years. The advantage to that technology is it produces very high quality data. The disadvantage to it is that it can be very expensive to generate that data.”

The Illumina instrument, Kingham said, generates a large amount of data very inexpensively, but he added that the data might not be of as high a quality as that produced by the Sanger machine.

As for the Pacific Biosciences sequencer, the long length of the sequencing read, coupled with the ability to analyze a single molecule of DNA, cannot be matched by the other instruments.

For more information on the UD Sequencing and Genotyping Center visit the website.

Article by Adam Thomas

Photo by Danielle Quigley

This article can also be viewed on UDaily


Abasht joins the Department of Animal and Food Sciences

February 6, 2012 under CANR News

The Department of Animal and Food Sciences in the University of Delaware’s College of Agriculture and Natural Resources (CANR) has added Behnam Abasht to its faculty.

Abasht, assistant professor in the Department of Animal and Food Sciences, received his bachelor’s degree in animal science from Urmia University and his master’s degree in animal science from the University of Tehran in Iran. He received his doctorate in Quantitative and Molecular Genetics in France from the University of Rennes INRA-Agrocampus in 2006. His travels then took him to Iowa State University where he completed his post-doctoral work before working as a Research Geneticist and Genomics Project Leader at Perdue Farms from 2008 until 2011.

Now, Abasht has brought his expertise in chicken genomics to the College of Agricultural and Natural Resources.

Abasht visited the University of Delaware campus, specifically the Delaware Biotechnology Institute (DBI), in 2009 and in 2010. He said that these visits left no doubt in his mind that he wanted to join the faculty at the University of Delaware.

“That was truly one of the most pleasant visits that I have had to an academic institution,” said Abasht. “I felt that people were friendly and welcoming and was impressed from the outstanding research programs of the faculties and the commitment of both Animal and Food Sciences and DBI to cutting-edge technologies for research.”

Now that he has been on campus working, nothing has changed. “I believe CANR has a nice ambiance with its energetic and welcoming staff. I enjoy speaking with people at CANR and receive positive energy from them. You just feel that it is a great place to be and to work.”

Abasht said that his research at UD focuses on using an integrated, multi-disciplinary approach that will include collaboration with an international team of scientists to help identify genes that explain the differences on fatness between two lines of chickens, the French Fat and Lean chicken lines.

His research interests extend into the “implementation of genomics technologies in commercial chicken breeding programs” and he is hoping to continue this research at the University of Delaware by collaborating closely with poultry industry members.

Abasht also said that he is looking forward to “building a dynamic lab group to conduct research on integrative avian biology, using systems-based approaches.”

Abasht added, “I had no idea that one day I would be in one of the world’s leading animal science departments developing my research program on studying the genetic basis of phenotypic variation in chickens.”

Article by Adam Thomas


UD researchers identify novel regulatory network within legumes

January 26, 2012 under CANR News

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

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

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

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

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

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

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

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

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

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

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

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

Article by Blake Meyers and Laura Crozier

Photos by Evan Krape and Kathy F. Atkinson

This article was originally published on UDaily


Researchers to study positive genetic contributions of viruses

March 21, 2011 under CANR News

The positive genetic contributions of viruses to life on Earth will be explored by researchers at the University of Delaware and the Delaware Biotechnology Institute through a grant from the Gordon and Betty Moore Foundation Marine Microbiology Initiative.

The two-year, $550,000 grant has been awarded to K. Eric Wommack, professor in UD’s Department of Plant and Soil Sciences with appointments in the Department of Biological Sciences and the College of Earth, Ocean, and Environment, and Shawn Polson, research assistant professor in the Center for Bioinformatics and Computational Biology at DBI.

The grant will support the rollout of a computational infrastructure dedicated to the analysis of viral genetic data from environmental samples. The Viral Informatics Resource for Metagenome Exploration (VIROME) is hosted at DBI.

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