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Foodborne illnesses and the 100K Genome Project
Bart Weimer, professor in the UC Davis School of Veterinary Medicine, serves as director of the 100K Genome Project and co-director of the recently established BGI@UC Davis facility, where the sequencing will be done. Other collaborators include the U.S. Centers for Disease Control and Prevention and the U.S. Department of Agriculture.
The new five-year microbial pathogen project focuses on making the food supply safer for consumers. The group will build a free, public database including sequence information for each pathogen's genome — the complete collection of its hereditary information. The database will contain the genomes of important foodborne pathogens including Salmonella, Listeria, and E. coli, as well as the most common foodborne and waterborne viruses that sicken people and animals.
The project will provide a roadmap for developing tests to identify pathogens and help trace their origins more quickly. The new genome database also will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing bacteria in the food chain.
"This landmark project will revolutionize our basic understanding of these disease-causing microorganisms," said Harris Lewin, vice chancellor for research at UC Davis.
The sequencing project is critically important for tackling the continuing outbreaks of often-deadly foodborne diseases around the world. In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the CDC.
"The lack of information about food-related bacterial genomes is hindering the research community's ability to improve the safety and security of the world food supply," Weimer said. "The data provided by the 100K Genome Project will make diagnostic tests quicker, more reliable, more accurate and more cost-effective."
"We see this project as a way to improve quality of life for a great many people, while minimizing a major business risk for food producers and distributors," said Mike McMullen, president of Agilent’s Chemical Analysis Group.
A consumer-focused article about the project is available on the FDA website.
(This article was condensed from a UC Davis news release. Read the full press release and watch a video of Bart Weimer giving an overview of the project.)
First draft of genome of wheat stripe rust published in Public Library of Science
The stripe rust disease of wheat caused by the highly specialized fungal pathogen Puccinia striiformis f. sp. tritici has been responsible for recurrent episodes of large yield losses and economic hardship among grain-based agricultural societies for centuries. Current epidemics of new aggressive races of Puccinia striiformis that appear after the year 2000 pose significant threats to food security worldwide and, in particular, in developing countries in Africa and central Asia. In spite of its economic importance, the Puccinia striiformis genomic sequence is not currently available.
In order to get access to the genes of this pathogen, a team of researchers – including Professor Jorge Dubcovsky (also a Howard Hughes Medical Institute researcher) and Professor Richard Michelmore, director of the UC Davis Genome Center, Project Scientist Dario Cantu and Manjula Govindarajulu, a postdoctoral researcher in Michelmore’s lab - used cutting-edge technology to rapidly sequence a large portion of the genome of one of the Puccinia striiformis more virulent and aggressive races. They assembled long stretches of the Puccinia striiformis genome and established a preliminary automatic annotation of its genes, with a special focus on those likely to be involved in pathogenicity.
This information is available in the open-access article published by the Public Library of Science and made publically available through the National Center of Biotechnology information and a dedicated web page.
“This shotgun sequence assembly does not substitute for the need of a complete and annotated Puccinia striiformis genome, but it provides immediate access to a large proportion, more than about 88 percent, of the genes from this pathogen,” said Cantu. “This public information has the potential to accelerate a new wave of studies to determine the mechanisms used by this pathogen to infect wheat, and hopefully to reduce current yield loses caused by this pathogen.”
These researchers, in collaboration with others at the John Innes Institute in the UK, are currently sequencing new and old races of Puccinia striiformis to investigate their differences in virulence and aggressiveness.
This project was supported in part by funds provided through a grant from the Bill & Melinda Gates Foundation, and the National Research Initiative Competitive Grants from the USDA National Institute of Food and Agriculture.
New funding to study wheat and forest genetics
Roger Beachy, the director of the USDA National Institute of Food and Agriculture, was at UC Davis yesterday to announce grants for agricultural research amounting to $40 million, calling them "significant investments," said a UC Davis news release.
Together with UC Davis officials, Beachy announced that:
- Wheat geneticist Jorge Dubcovsky will receive $25 million to develop new varieties of wheat and barley. Dubcovsky and his 55 university and USDA colleagues will focus on biological and environmental stresses to wheat that are caused, at least in part, by global climate change.
- Forest geneticist David Neale will receive $14.6 million to head a team that will work to sequence the genomes of loblolly pine and two other conifers. Neale and his research colleagues plan to accelerate breeding efforts for fast-growing varieties of these trees to enhance their use as feedstocks for biofuels and biopower.
"We look forward to the practical solutions for agriculture and for the environment that will arise from these collaborative projects," UC Davis Chancellor Linda Katehi said at the press conference.
A story about the grants written by Rick Daysog of the Sacramento Bee said they come as UC Davis has stepped up efforts to attract research grants following Katehi's appointment as chancellor in 2009. During its fiscal year ending June 30, 2010, the university received a record $679 million in research grants.
Left to right: David Neale, Jorge Dubcovsky, Linda Katehi, Roger Beachy, Neal Van Alfen.
More federal funds for California farm research
The economy is floundering, but federal money is still flowing. Last week, the U.S. Ag Secretary, Tom Vilsack, announced $7 million in grants for research on the biology of plant processes and traits which can be used to breed crops with greater value and resilience to climate stress, according to a USDA press release.The release said $448,000 of the funds go to UC Davis, where scientists will use the money to better understand plant biology "from the genome to the field."
The "genome" refers to all of the hereditary information encoded in DNA. The phrase "genetic makeup" is sometimes used to mean the genome of a particular individual or organism.
In what may or may not be related to the USDA genome-to-field funding release, the National Science Foundation announced yesterday it has made 32 new awards totaling $101.6 million during the 12th year of its Plant Genome Research Program. The NSF news release says UC Davis and UC Berkeley will recive a share of the funding to address new, testable hypotheses for the mechanism of hybrid vigor in plants.
According to NSF, the development of genomics tools and sequence resources enables "exciting, new comparative approaches and predictive modeling to uncover gene networks that regulate plant development and growth in changing environments."
If that's the news release, can you imagine how complex the research reports must be?
USDA photo.
