BLACKSBURG, Sept. 28, 2001 - The National Science Foundation has awarded $3.5 million to The Virginia Bioinformatics Institute (VBI) and the Noble Foundation for a four-year project on functional genomics and bioinformatics of the model legume Medicago truncatula.
The funds come from the Plant Genome Research Program at NSF's BIO division. The project's principal investigators are Dr. Pedro Mendes at the Virginia Bioinformatics Institute (at Virginia Tech) and Dr. Richard Dixon at the Plant Biology Division of the Samuel Roberts Noble Foundation (Ardmore, Oklahoma). Four other senior researchers are involved: Drs. Jennifer Weller (VBI), Lloyd Sumner, Greg May (Noble) and Tim Smith (Southeastern Oklahoma State University).
The ambitious four-year project will carry out a comprehensive measurement of thousands of molecules in a plant cell culture originated from the legume M. truncatula (a forage legume closely related to alfalfa). It combines DNA microarrays, proteomics, and seven different metabolic profiling approaches to measure in great detail how the plant cells respond to metabolic perturbation by microbial signal molecules. The team will also look at the effects of ultraviolet light and the plant hormone jasmonic acid on the plant cells. This requires extensive computational support, to organize and analyze some 120 gigabytes of data. A relational database will be developed to support this research as well as a flexible and extensible analysis system, all to be accessed through the Web.
The software will be made available to the scientific community for managing other similar projects. The novelty of this project is the combination of microarray gene expression with proteomics and metabolomics to provide a highly detailed molecular dynamic picture of the relationships between transcription, translation and metabolic flux.
Mendes, PI on the project, stated: "A major feature of the project is the combination of microarrays with proteomics and metabolomics to create an unbiased systems view of biology and create predictive computer simulations of the underlying biochemistry that will be used for hypothesis generation. This collaboration is the best way to achieve our scientific objectives. Each senior researcher brings in their unique expertise and this type of project could not be done by a single team as it requires very specialized skills." Dixon pointed out that: "The project provides opportunities for a truly global understanding of the genetic and metabolic changes that result from biotic and abiotic elicitation, in addition to facilitating the discovery of important new genes for manipulation of natural product pathways for crop improvement."
The aims of the project are to reveal the identity of the genes that provide disease resistance to the plant, to reveal novel metabolic pathways for synthesis of natural products, to develop novel computer algorithms to integrate the analysis of gene expression, proteomics and metabolomics data, and, finally, to be able to construct a causal simulation model of metabolism and gene expression. The project will also manage a yearly summer course in legume genomics and bioinformatics to take place in the Noble Foundation's conference center in Ardmore, OK.
The NSF funding leverages previous investments at both VBI and the Noble Foundation. VBI is currently setting up its Core Computational Facility which will be used by the project, and the Noble Foundation has already established a Center for Medicago Genomics Research with state-of-the-art equipment for microarray, proteomic, and metabolic profile analysis.
September 27, 2001