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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.

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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

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UD team finalist in 2011 Illumina Data Excellence Award Challenge

June 15, 2011 under CANR News

A team from the University of Delaware College of Agriculture and Natural Resources (CANR) and Delaware Biotechnology Institute (DBI) has been selected as a finalist in the 2011 Illumina Data Excellence Award (iDEA) Challenge, taking place June 14-15 in San Diego. The team was selected for a project that focuses on developing user-friendly tools for the processing, analysis and visualization of DNA and RNA sequence data.

The iDEA Challenge is designed to inspire the scientific community to develop new and creative visualization and data analysis techniques. Hosted by Illumina, a San Diego-based company with technologies used for the study of genetic variation and function, the program is interested in empowering and accelerating the analysis, visualization and interpretation of data being generated by Illumina technologies.

The project on which researchers from UD and DBI have been working dates back nearly 10 years and, during that time, more than 20 laboratory members have contributed in various ways to the development and improvement of the software, whose database and web tools were arguably the first visualization system and database specifically for next generation sequence data.

Blake Meyers, the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences and chair of the Department of Plant and Soil Sciences, has been working on the project since the outset and said that though the team did not set out to work on the project specifically to enter it in the iDEA Challenge, the contest has helped them to improve their software.

“We have been working on cleaning up and organizing our software code to make it more streamlined, professional, and universally applicable — that is, to make it useful in many other organisms other than those which we study — thus this has been a useful and encouraging project for those other efforts,” Meyers said.

The UD team has developed a series of websites based on a common set of scripts and tools, specialized for different species’ genomes. The websites enable users to analyze, visualize and download various types of Illumina data, and are built on a common set of web interfaces equipped with user-customizable graphical and analytical tools that allow the user to retrieve and analyze the data.

Speaking to biologists who have very complex datasets, Meyers said he has founded that they generally “emphasize the importance of user-friendliness to methods for interacting with their data, and in my opinion, this is something that we have really developed well. Although ten years of development has meant that our website and web-based tools are quite complex, for the biologist that takes the time to learn the power of our options, there are many ways to interpret their data.”

The UD websites have received thousands of hits per day from users all over the globe and the sites and their informatics tools have been integral to numerous manuscripts that have been published in journals such as Science, Nature, Nature Genetics, Nature Biotechnology, PNAS, The Plant Cell, Nucleic Acids Research, and others.

Meyers said that as a biologist, one of the things he enjoys most about the project is “making new insights and discoveries into biological processes. But related to this is the pleasure of seeing the broad utility of the tools we’ve developed, and knowing the deeper understanding of the data that comes from visualization that allows the user to make the discoveries.”

Those currently involved with the project include:

Mayumi Nakano, a staff research associate in the lab, who has done nearly all the programming to develop the visualization tools and web interface.

Kevin McCormick, a doctoral student in the Department of Computer and Information Sciences (CIS), who has led the development of the primary database structure and database loading scripts.

Caghan Demirci, a CIS doctoral student, who has been working on streamlining and standardizing the systems.

Feray Demirci, a CIS doctoral student, who has worked on application development for specialized analyses.

Recent but former members of the lab who worked on the project include:

Gayathri Mahalingam, a CIS doctoral student, who has worked on parts of the database that stores information on DNA methylation.

Guna Gurazada, a former CIS master’s student who now works at DuPont, and who was involved in many aspects of the data handling pipeline.

The UD team attending the iDEA Challenge includes both Caghan and Feray Demirci and Nakano, and they will present from 10:30-11 a.m., Wednesday, June 15.

Article by Adam Thomas

Photo by Danielle Quigley

The original posting of this article can be viewed on UDaily

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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.

Please visit UDaily for the full article by clicking here.

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Students battle rice blast disease with underground microbes

November 30, 2010 under CANR News

Rice is the most important grain consumed by humans, providing more than one-fifth of the calories sustaining the world’s population. By some estimates, however, global production of rice could feed an additional 60 million people, if it weren’t for rice blast disease, caused by the fungus Magnaporthe grisea.

This past summer, four students from the University of Delaware and two of its partner institutions in Delaware’s National Science Foundation EPSCoR program, Delaware State University and Delaware Technical and Community College, found themselves on the front lines of the battle to defeat rice blast.

Those battle lines have been drawn on opposite coasts of the United States, through a collaboration between scientists in Delaware and at the University of California at Davis, the land-grant institution of the UC system. The students therefore split their summer internship between laboratories in both states.

The project is led by Harsh Bais, professor in UD’s Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, and is funded by the National Science Foundation.

The full article with photos can be viewed online on UDaily by clicking here.

Article courtesy of Beth Chajes, DENIN

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UD scientists featured in top environmental science journal

January 29, 2010 under CANR News

Research performed by Matthew Ginder-Vogel, associate scientist in the Delaware Environmental Institute, Gautier Landrot, a graduate student in environmental soil chemistry at the University of Delaware, and Donald L. Sparks, S. Hallock du Pont Chair of Soil and Environmental Chemistry and director of the Delaware Environmental Institute, is featured in this month’s special issue of Environmental Science and Technology, the premier environmental science and engineering journal in the world.

Read the full story online here at UDaily.

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