Navigation Links
Penn, Georgia collaboration awarded $14.6 million to expand pathogen database
Date:12/10/2009

PHILADELPHIA - Researchers from the University of Pennsylvania and the University of Georgia have been awarded a five-year, $14.6 million contract from the National Institute of Allergy and Infectious Diseases, part of the US National Institutes of Health, to expand and extend work on the Eukaryotic Pathogen Genome Database Resource, http://EuPathDB.org. This revolutionary open database enables scientists to examine genes, genomes, isolates, and other attributes related to a variety of important human pathogens. By helping to identify potential vaccine antigens and drug targets, EuPathDB facilitates the search for effective diagnostics and therapeutics.

This award continues NIH funding for a production database system integrating diverse genomic-scale datasets. EuPathDB has been expanded several times based on its success in expediting infectious disease research. The latest release supports a total of 27 species, providing bioinformatics tools for researchers targeting biodefense and emerging and re-emerging pathogens.

Originally developed for Plasmodium falciparum, a microbe responsible for the most severe form of human malaria, EuPathDB has been expanded several times based on its success in expediting infectious disease research. The latest release supports a total of 27 species, providing bioinformatics tools for researchers targeting biodefense and emerging and re-emerging pathogens.

The database also targets:

  • Pathogens that threaten public water supplies, including Cryptosporidium, Giardia and Toxoplasma, with additional components dedicated to Entamoeba and Microsporidia to follow over the coming months.
  • Opportunistic infections associated with AIDS and other immunosuppressed conditions, including Cryptosporidium, Microsporidia and Toxoplasma.
  • The congenital pathogen Toxoplasma gondii, a leading source of neurological birth defects. Toxoplasma and Neospora caninum are also economically important as sources of congenital infection in farm animals.
  • Trichomonas, a widespread cause of vaginitis in women.
  • The parasites responsible for kala azar (Leishmania), African sleeping sickness (Trypanosoma brucei), and Chagas disease (Trypanosoma cruzi), which have been incorporated into this resource with support from the Bill & Melinda Gates Foundation.

The EuPathDB database is one of four Pathogen Bioinformatics Resource Centers supported by the NIH and is directed by principal investigator David S. Roos, E. Otis Kendall Professor of Biology in the School of Arts and Sciences at the University of Pennsylvania. Co-investigators include Christian Stoeckert of the School of Medicine at Penn and Jessica Kissinger of the University of Georgia. Roos and Stoeckert are also affiliated with the Penn Center for Bioinformatics and the Penn Genome Frontiers Institute, and Kissinger with the Center for Tropical and Emerging Global Diseases.

Understanding the genes of an organism and how they are expressed is a critical first step in preventing or treating disease. EuPathDB provides researchers with a database that catalogues every accessible step in the chronicle of disease pathogenesis. This database and its component web sites have been used by more than 42,000 scientists over the past six months, from more than 100 countries worldwide. Meeting presentations and workshops help to ensure effective use of this resource by the scientific community.

Advances in genome technology have dramatically increased both the scale and scope of information now available for human pathogens. For example, the first Plasmodium parasite genome sequence was completed in 2002 after six years of work and a cost of $35 million. Scientists can now sequence additional strains of the parasite in just a few days, for a few thousand dollars but the raw data for a single genome can generate terabytes of data, easily overwhelming a personal computer. Additional large-scale datasets supported by EuPathDB include DNA sequence polymorphisms from the wider population, chromosomal modifications, comprehensive studies on RNA transcription and protein expression, analysis of protein-protein interactions and metabolic pathways.

Consider a researcher working to develop a malaria vaccine. First, this scientist must identify which genes are active when the parasite is living in a human host, rather than when it lives in the mosquito. They must then determine which of those genes encodes protein antigens likely to be recognized by the immune system. By taking all of these factors into account plus many more the researcher can narrow the many thousands of genes in the parasite genome down to a few dozen candidates for further testing.

"It has been remarkable to witness the rapid growth of biomedical research in recent years, fueled by the genomic revolution" says Roos, "and it is particularly gratifying to see the impact of bioinformatics tools such as EuPathDB. By integrating diverse sources of information -- all the genes in the genome, all the proteins in the cell, all patient responses in a population -- these databases offer great promise for improved human health."


'/>"/>

Contact: Jordan Reese
jreese@upenn.edu
215-573-6604
University of Pennsylvania
Source:Eurekalert

Related biology news :

1. Georgia State researcher to use $1 million grant to improve computer models for fighting wildfires
2. New center at Georgia Tech aims to improve recovery of soldiers with severe injuries
3. Georgia goes bananas
4. Georgia Stem Cell Initiative meets on MCG campus Feb. 10
5. MIT Holding, Georgia Southern University, and MEVLABS successfully test the PROVECTOR
6. Flu vaccine in painless skin patches under development at Emory, Georgia Tech with NIH grants
7. Georgia Tech/Emory Center to study origin of life
8. Tropical crab invades Georgia oyster reefs -- but the long-term impact cant be predicted
9. Synthetic biology offers new opportunities for interdisciplinary collaboration
10. NanoString Technologies announces research collaboration with the Broad Institute
11. £7.5 million ($12.6 million) collaborations lead UK research communitys response to H1N1 pandemic
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/23/2017)... N.Y. , June 23, 2017  IBM (NYSE: ... dairy research, today announced a new collaboration using next-generation ... chances that the global milk supply is impacted by ... Cornell University has become the newest academic institution to ... a food safety initiative that includes IBM Research, Mars, ...
(Date:5/16/2017)... DALLAS , May 16, 2017   ... for health organizations, and MD EMR Systems ... certified development partner for GE, have established a ... Patient Portal product and the GE Centricity™ products, ... Centricity EMR. These new integrations ...
(Date:4/18/2017)... Calif. , April 18, 2017  Socionext Inc., a global ... of a media edge server, the M820, which features the company,s ... recognition software provided by Tera Probe, Inc., will be showcased during ... at the NAB show at the Las Vegas ... ...
Breaking Biology News(10 mins):
(Date:7/18/2017)... ... 2017 , ... G-CON today announced that it has received ... Patent Applications 14/858,857 and 13/669,785 both entitled Modular, Self-Contained, Mobile Clean Room. The ... protection of G-CON’s R&D investments and validate the G-CON platform as a novel ...
(Date:7/17/2017)... ... July 17, 2017 , ... Whitehouse Laboratories ... capabilities to encompass the full series of ISO 80369 standard test procedures. The ... medical device and drug delivery systems. With this recent expansion, Whitehouse Labs becomes ...
(Date:7/17/2017)... ... July 17, 2017 , ... Neurodevelopmental disorders (NDDs) ... of overlapping clinical features. The advancement of targeted next-generation sequencing (NGS) has been ... and testing. , However, designing a custom panel for disease research requires ...
(Date:7/16/2017)... ... July 16, 2017 , ... OHAUS Corporation, a leading worldwide ... its new line of Rocking and Waving Shakers today. , Five New Models ... and digital) for laboratory applications in a variety of environmental conditions. Rocking shakers ...
Breaking Biology Technology: