BLACKSBURG, April 23, 2001 - Researchers from the Virginia Bioinformatics Institute (VBI) at Virginia Tech, the University of Nevada-Reno, and the Samuel Roberts Noble Foundation in Ardmore, Oklahoma, have formed a partnership to develop a relational database, data processing pipeline, and data analysis system to support gene sequencing and gene discovery.
The three will jointly develop a database and analysis tools for the automatic processing, storage and analysis of genetic data originating from a variety of plant species.
The partnership will aid in the discovery of new genes, which will in turn help Nevada researchers in a number of different areas. For example, John Cushman, professor of biochemistry at Nevada and project leader for UNR, has an emphasis in research in methods of genetically engineering plant types that are more drought-, cold-, and salt-tolerant.
"But in order to [discover new genes], we need genetic resources," Cushman said. "Our agreement with the Virginia Bioinformatics Institute and the Samuel Roberts Noble Foundation is not only for researchers in this particular area, but for anyone on our campus doing genomics-related research."
Cushman said the practical applications of the agreement are immense. In irrigated agriculture, for example, soil experiences a buildup of salt, reducing crop yield and ultimately eliminating the growth of certain plants completely.
"This problem affects about 42 percent of all worldwide irrigated agriculture," Cushman said. "It's a huge problem. That's why we want to genetically engineer salt-tolerant plants. For drought, there are certain plant models where the vegetative tissue will completely dry out, but you water them again and they come back to life.
"We want to figure out how these plants are able to do this. If we are able to do that, then will be able to make drought-tolerant plants."
Cushman said the agreement also significantly helps speed the process for genomics and gene sequencing researchers in the search for new gene types.
"The process of data collection, cleaning and polishing, is tremendously labor-intensive if you were to attempt to do it by hand," he said. "Our job will be made a whole lot easier. We generate data very well - but this frees up to focus more on the biological significance of the data."
The initial focus of the agreement will be on gene sequence data, but the system is being designed to eventually extend to genomic, genetic mapping and markers, gene expression and protein data. Software design and development will occur at VBI, while data generation and pipeline testing will be done at Nevada and the Noble Foundation. The software will also form a critical part of VBI's Core Laboratory Facility infrastructure.
"This arrangement reduces the resource burden for each partner," said Gregory May, Associate Scientist at Noble. "Allowing new partners to join the collaborative effort leverages costs in adding new functionalities to the program." The Noble Foundation's activities related to this project will focus on gene discovery in economically important forage grass and legume species. Traits of major significance to scientists at Noble include disease resistance, nutrient uptake, forage quality and health-promoting plant chemicals.
"Partnering with VBI will allow us to focus on what we do best," said May. "Addressing complex biological phenomena using a global approach afforded by the power of genomics."
"The true power (in the agreement) will lie in allowing a diverse group of scientists access to a wide range of data to explore and synthesize into new knowledge," said Jennifer Weller, project leader at VBI, home to a world-class research program in bioinformatics.
Bruno Sobral , Director of the VBI, described this type of collaboration as "a new business model for bioinformatics software development - one that is distributed, effective and economical. It brings together the strengths of biologists and software developers and has them work as peers to contribute equally in the areas they know best. This is also an open participation model, allowing new groups to enter the collaboration and bring new ideas for its improvement. All software in bioinformatics is incremental and evolutionary, and this model leverages that reality".
April 21, 2001