Navigation Links
Bioinformatics technology developed at Argonne provides new insight into microbial activities
Date:3/14/2008

ARGONNE, Ill. (March 14, 2008) -- Scientists may gain a new insight into the relationship between viruses and their environments thanks to a new computational technology developed by researchers at the U.S. Department of Energys (DOE) Argonne National Laboratory. This technology has already been used to identify subtle differences in the metabolic processes of microbial communities.

The ability to determine such differences may help scientists detect environmental changes at early stages and identify previously unknown pathways for treating disease.

The researchers analyzed the frequency distribution of more than 14 million microbial and viral sequences from almost 90 different ecological communities, called metagenomes. By doing so, they hoped to produce a biological profile for the samples taken from diverse environments ranging from underground mines to sea and fresh water.

Metagenomics enables the DNA from all microbes to be sequenced at once, without any culturing, said Robert Edwards, a computational biologist at Argonne and San Diego State University and one of the projects principal investigators. Such an approach was impossible even a decade ago.

While the researchers had expected to find similar lifestyles among the viral metagenomes in every environment, they instead found that the metagenomes have distinctive metabolic profiles. Researchers may be able to use these profiles in the future to answer questions about the viral dynamics in, for example, the lungs of cystic fibrosis patients.

Argonne has become a world leader in metagenomics, said Edwards. The bioinformatics technology developed by Argonne researchers and their collaborators is being used by hundreds of researchers worldwide. This work demonstrates the practical basis for the multimillion-dollar effort by the National Institutes of Health to understand the benign and malign roles of microbes in health and disease.

As the use of metagenomics has become increasingly common, scientists have had to address the challenge of analyzing an enormous number of genomic sequences. To ease this process, scientists at Argonne and the Fellowship for Interpretation of Genomes (FIG) developed a system that contains all known DNA and protein sequences. Using this directory, known as SEED, biologists can identify matches between metagenomes and profiles already in the SEED database.

For this study, DNA sequences first were analyzed by using a high-throughput pipeline called the metagenomics RAST (Rapid Annotation using Subsystem Technology) server (http://metagenomics.theseed.org/), developed by researchers from Argonne in collaboration with FIG, the University of Chicago, San Diego State University and Hope College.

Comparing such a huge number of metagenomes is an enormous computational task, said Rick Stevens, a principal investigator in the project and associate laboratory director of Computing, Environment, and Life Science at Argonne. This automated technology revolutionizes the steps needed to acquire an accurately annotated genome.

The sequences then were compared to the SEED platform by using the compute cluster at the National Microbial Pathogen Data Resource. The database allows an overview of the microbial communities and the ability to focus on one metabolic area and detect differences in the proteins being used by the microbes in each environment.

The initial analysis took months of computer time, said Stevens. We eventually determined that more than 1 million sequences from the microbial metagenomes and more than 500,000 from the viral metagenomes were significantly similar to functional genes within the SEED.


'/>"/>

Contact: Steve McGregor
smcgregor@anl.gov
630-252-5580
DOE/Argonne National Laboratory
Source:Eurekalert

Related biology news :

1. Yale scientists use nanotechnology to fight E. coli
2. Voice Biometrics Gains Traction as Most Accurate and Convenient Technology to Secure Customer Privacy
3. M2SYS Partners with SecuGen Corporation to Support Market Leading Hamster Plus Fingerprint Reader with Auto-On Technology
4. Silicon Valley Technology Leaders LaserCard Corporation and Tesla Motors Sign LaserPass Secure Access Deal
5. Nanotechnology: Whats that?
6. UCs NIH grant brings technology from outer space to playgrounds
7. BIO-key(R) International to Showcase Deployed Biometric Security Applications at 2007 Biometric Technology Expo
8. Cogent Systems and Northrop Grumman Reach Agreement to Settle Automated Fingerprint Identification Technology Suit and Create Strategic Alliance
9. UCLA/VA partners with ASU to advance biosensor technology for urinary tract infections
10. Herr receives Heinz Award for Technology, the Economy and Employment
11. Singapore National Science and Technology Awards
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/7/2017)...   MedNet Solutions , an innovative SaaS-based eClinical ... research, is pleased to announce that the latest release ... flexible and award winning eClinical solution, is now available ... is a proven Software-as-a-Service (SaaS) clinical research technology platform ... also delivers an entire suite of eClinical tools to ...
(Date:2/3/2017)... 3, 2017  Texas Biomedical Research Institute announced that its ... Schlesinger as the Institute,s new President and CEO. Dr. ... 31, 2017. He is currently the Chair of the Department ... for Microbial Interface Biology at Ohio State University. ... President and CEO of Texas Biomed," said Dr. James ...
(Date:2/2/2017)... Feb. 1, 2017  Central to its deep ... advances worldwide, The Japan Prize Foundation today announced ... have pushed the envelope in their respective fields ... Three scientists are being recognized with the 2017 ... not only contribute to the advancement of science ...
Breaking Biology News(10 mins):
(Date:2/22/2017)... , ... February 22, 2017 , ... ... is has acquired Kendall Research Systems, LLC (KRS) clinical development program. ... develops neural interface technology for research and clinical applications. The terms of the ...
(Date:2/22/2017)... 22, 2017  PrimeVax Immuno-Oncology, Inc. announced today its ... the Annual Biocom Global Life Science Partnering Conference.  The ... AM, at the Torrey Pines Lodge, in San Diego.  ... at Biocom who have chosen our company, amongst numerous ... companies, investors, and clinical researchers," said Mr. Chen. "In ...
(Date:2/22/2017)... (PRWEB) , ... February 22, ... ... Collaborative (TOPEC), the leading medical education provider of women’s health, primary ... by the Accreditation Council for Continuing Medical Education (ACCME). ACCME’s Accreditation with ...
(Date:2/22/2017)... ... February 22, 2017 , ... ... engineers, and scientists from around the world, is pleased to announce the 2nd ... and 23, 2017. This premier, online-only conference focused on the development and advancements ...
Breaking Biology Technology: