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USDA: New Gene Data Center and Gene-Analyzing Machines Will Speed Discoveries / January 17, 1999 / News from the USDA Agricultural Research Service

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USDA: New Gene Data Center and Gene-Analyzing Machines Will Speed Discoveries

By Marcia Wood
January 17, 1999

SAN DIEGO, Jan. 17--The U.S. Department of Agriculture announced here today that it will establish a new gene data research center at Cornell University in Ithaca, N.Y. USDA also will acquire eight new automated machines allowing the department's researchers to speed their analyses of plant, animal and microbial genes, said Judy St. John. Based in Beltsville Md., she is Associate Deputy Administrator for Crop Production, Product Value and Safety with USDA's Agricultural Research Service.

"Together, these two initiatives will accelerate genetic discoveries to benefit our agriculture, food supply, environment and consumers," St. John said at the Plant and Animal Genome VII Conference held today through Jan. 21 at San Diego's Town and Country Convention Center.

"The new DNA analyzers are very fast, highly automated machines," St. John said at a conference workshop on federal funding of plant gene research. "These state- of-the-art tools will make USDA's Agricultural Research Service the single most powerful force in genome sequencing within the public agricultural research sector." The analyzers should begin arriving this spring at ARS labs in California, Florida, Georgia, Iowa, Maryland, Nebraska, New York and Pennsylvania.

ARS will operate the new Center for Bioinformatics and Comparative Genomics at sites in Ithaca and Geneva, N.Y., where ARS already has research labs, St. John said.

Genomics is the study of the genome, which refers to essentially all the genetic material of an organism. Bioinformatics is the use of computers to help researchers answer life-science questions, mainly through studying genetic information in electronic databases.

"The USDA-funded center at Cornell," she said, "will aid researchers around the country and the world in the quest to discover all the genes in grains--like corn, wheat and rice--and plants in the family that includes tomatoes, potatoes and peppers."

"ARS and Cornell," she said, "already maintain the foremost computerized, publicly accessible data bases for information about the structure of genes in grain crops and the Solanaceae family that includes tomatoes, potatoes and peppers. The center will establish a new partnership to strengthen this effort."

"This partnership will bring in the expertise of Cornell's computer theory center to apply advanced computer tools to analyze gene information. This research is urgent, because databases are required that can handle the deluge of information these gene data banks will receive as a result of increased federal funding of gene-sequencing projects," St. John said.

Once a gene's structure is discovered, scientists can use computers to look for similar structures in genome databases of plants, humans, mice and other life forms.

Similar structure often connotes similar function, thus shortening the time to find out what job a gene performs. And once a gene's function, such as disease-resistance, is identified, biotechnologists can begin experiments to see if that gene can be re-built to make it more effective.

Plants with improved resistance to disease, for example, should require less chemical pesticides. Or, the genes could be moved into plants that currently lack resistance.

St. John said plans for the Center for Bioinformatics and Comparative Genomics at Cornell will be implemented through increased ARS funding, with the addition of several ARS bioinformatics specialists. Cornell faculty in the Department of Plant Breeding and Biometry and the Cornell Theory Center will join the ARS staff in the new genomics center.

ARS bioinformatics specialists and Cornell faculty in the Plant Breeding and Biometry Department currently maintain the gene data banks known as GrainGenes, SolGenes (for solanaceous crops) and RiceGenes.

The ARS labs receiving the new DNA analyzers are in Albany, Calif.; Ft. Pierce, Fla.; Athens, Ga.; Ames, Iowa; Beltsville, Md.; Clay Center, Neb.; Orient Point, N.Y.; and Wyndmoor, Pa.

"The machines will greatly accelerate the speed at which the researchers discover the structure of genes of plants, farm animals and other living things, such as microorganisms important in food safety," St. John said.

At ARS' Plum Island Animal Disease Center in Orient Point, N.Y., scientists will use the new instrument to detail the genetic makeup of microbes deadly to livestock. "Discovering the genetic structure of those microbes," said St. John, "could enable researchers to develop new, more effective techniques to protect farm animals."

At ARS' Beltsville (Md.) Agricultural Research Center, researchers in the Livestock and Poultry Sciences Institute will put their DNA analyzer to work on genes important in cow mammary glands. The scientists want to find genes responsible for resistance to diseases of the mammary gland.

In Albany, Calif., biotechnologists will use one of the instruments at the ARS Western Regional Research Center and at the Plant Gene Expression Center operated by ARS and the University of California, Berkeley. The scientists will examine genetic material from microbes as well as from rice, wheat and a flowering plant called Arabidopsis thaliana, a member of the mustard family. "Arabidopsis has become a premier model for hastening discovery of important genes in crop plants," said St. John. "The new DNA analyzers should enhance USDA's contribution to international projects to sequence all the genes in Arabidopsis and rice."

The Perkin-Elmer ABI model 3700 DNA sequencers purchased by ARS can boost a lab's productivity an estimated 50 times and decrease costs, according to Perkin-Elmer Corp., Norwalk, Conn. The sequencers can run unattended for 24 hours, enabling labs to process tens of thousands of samples a week.

ARS research on plant genomes is a critical federal component in support of the National Plant Genome Initiative. Through research in the public and private sectors, the initiative aims to improve plants to address regional, national and global problems. These include problems of food supply, human nutrition and health, environmental quality, agricultural and forestry resource supply and quality, energy supply, and rural economies.

The NPGI is coordinated by an interagency working group of the cabinet-level National Science and Technology Council. Federal competitive grant funds in support of the initiative come largely from USDA, the National Science Foundation, the Department of Energy and the National Institutes of Health.

More than 1,000 scientists and others from around the country and the world have registered to attend the Plant and Animal Genome VII Conference. USDA is a co-sponsor along with universities and nonprofit and industry groups.

Scientific contacts: Judy St. John, ARS Associate Deputy Administrator for Crop Production, Product Value and Safety, Beltsville Md., phone (301) 504-6252, fax (301) 504-6191, jsj@ars.usda.gov; Caird E. Rexroad, Jr., ARS Associate Deputy Administrator for Animal Production, Product Value and Safety, Beltsville Md., phone (301) 504-7050, fax (301) 504-6720, cer@ars.usda.gov.

During the Plant and Animal Genome VII Conference, St. John may be reached from Jan. 17-21 at the Town and Country Hotel, phone (619) 291-7131. The number for the conference registration desk in the hotel's Atlas Foyer is (619) 291-7131, ext. 3939.

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