UD professor seeks holistic understanding of disease resistance in maize

February 25, 2014 under CANR News

UD professor seeks holistic understanding of disease resistance in maizeThe University of Delaware is leading an interdisciplinary project aimed at unraveling the biology of a durable form of disease resistance in maize.

A grant from the National Science Foundation Plant Genome Research Program (NSF-PGRP) has brought together a team of experts in breeding, genetics, pathology, bioimaging and computer science to generate new knowledge that can be leveraged in the staple crop when breeding for disease resistance.

Randall Wisser, assistant professor in UD’s Department of Plant and Soil Sciences is leading the five-year, $3.9 million project.

Working with seven other investigators at Iowa State University (ISU), Cornell University, North Carolina State University (NCSU), and the U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Wisser explained that the group is trying to gain a holistic understanding of disease resistance.

“To date, we’ve focused on dissecting the genetics, trying to figure out what the genes are,” said Wisser. “In some cases we’ve been successful, but there are many more genes we have not yet identified; we still don’t understand how the genes work or how they act together to cause resistance.”

How cells react

A significant component of the project at UD consists of the researchers adapting bioimaging technologies to study natural genetic variation in disease resistance. For this, three of the labs are collaborating.

In controlled environments, Rebecca Nelson, professor at Cornell University, and Peter Balint-Kurti, research geneticist with USDA-ARS at NCSU, perform genetic experiments from which infected tissue is sampled and shipped off to UD.

Wisser and Jeff Caplan, director of the BioImaging Center at the Delaware Biotechnology Institute (DBI), work together to analyze microscopic images of the samples.

Studying hundreds of tissue samplesthe team captures numerous snapshots across each sample in microscopic detail and in 3D. Then, from more than 1,000 separate images taken on each sample, the researchers use computational techniques to reconstruct the images into their original form.

With these large format images, the team initiated a collaboration with Chandra Kambhamettu, professor in UD’s Department of Computer and Information Sciences and director of the Video/Image Modeling and Synthesis (VIMS) Laboratory, to adapt methods from computer vision research that allow features within the images — such as the number of cells the pathogen has infected — to be characterized.

In the end, the team is able to gain an understanding of how a specific resistance gene or a group of resistance genes act to cause resistance.

Wisser summarized the technique’s important effect, saying, “We’re not just taking a picture of the surface, we’re actually taking pictures as though we are peeling layers off the tissue one at a time. Also, because of the relatively large area of the leaf we can now image, we can observe plant-pathogen interactions at an unprecedented scale and gain a better understanding of variation in the interactions between pathogens and plants.

“Essentially, what we’ve been able to achieve is the development of an imaging and analysis platform that allows us to quantitatively examine the effects of different genes at the tissue and cellular level. It’s eye-opening, and we’ve only begun scratching the surface.”

Gene identification

The team is simultaneously trying to shine light on the specific genes that underlie disease resistance.

Jim Holland, research geneticist with USDA-ARS at NCSU, leads a component of the project on genetic mapping. Holland, Balint-Kurti, Nelson and Wisser collaborate on sequencing and comparing the genomes of over 250 maize varieties using advanced techniques in genetic mapping, when researchers try to determine the specific genes that control a characteristic like plant disease resistance.

There is typically uncertainty in the process. Therefore, Balint-Kurti and Nick Lauter, assistant professor from ISU, are validating the effects of these genes by searching for extreme mutations and deregulating the gene. If disruptions of the gene cause a change in the plants’ resistance to disease, then they know they are onto something.

Lauter and Alicia Carriquiry, professor from ISU, are also working with Cornell and NCSU to study how the genes are regulated when the pathogens infect. A gene may be turned on or off in response to infection, which further clues the researchers in to the genes that underlie resistance.

Looking at all of these results together allows the researchers to understand the genes associated with resistance, how they function in terms of their internal wiring, how they connect to each other to form a network, and how that network gives rise to disease resistance or susceptibility.

An applied impact

The work on this project addresses issues that relate to the global sustainability of agriculture. Pathogens often evolve quickly to overcome the resistance genes in the cultivars breeders produce, resulting in a constant tug-of-war between the breeder and the pathogen.

This basic research project intersects with applied efforts to have greater durability in disease resistance. The knowledge, methods and resources from the project can be leveraged in the breeding of varieties that have longer lasting resistance, resulting in better food security.

Wisser said that while the group is using maize for its study, the results could have positive effects on many plants. “The things we find are not just applicable to maize and diseases we’re working on here, but there are also some general rules that are likely to surface. So we think that our project has more to offer than helping to solve the issues associated with these specific diseases and the crop that’s the focus of the project.”

Article by Adam Thomas

Photos by Danielle Quigley

This article can also be viewed on UDaily.

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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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