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:2/2/2016)... YORK , Feb. 2, 2016 ... of the bioinformatic market by reviewing the recent ... enabled tools that drive the field forward. Includes ... to: Identify the challenges and opportunities that ... providers and software solution developers, as well as ...
(Date:2/2/2016)... Technology Enhancements Accelerate Growth of X-ray Imaging ... and computed radiography markets in Thailand ... Indonesia (TIM). It provides an in-depth analysis ... as regional market drivers and restraints. The study offers ... market attractiveness, both for digital and computed radiography. Market ...
(Date:2/2/2016)... Calif. , Feb. 2, 2016  Based ... market, Frost & Sullivan recognizes US-based Intelligent Retinal ... Frost & Sullivan Award for New Product Innovation. ... in North America , is ... the rapidly growing diabetic retinopathy market. The IRIS ...
Breaking Biology News(10 mins):
(Date:2/8/2016)... Inc. (NYSE: DPLO) announced today that its new website has gone live. On Thursday, Feb. 4, ... Visit the new site: www.diplomat.is ... ... ... "The goal was to reimagine the website and create a smarter, ...
(Date:2/6/2016)... ... ... The Center for Excellence in Education (CEE) will sponsor a Bite of Science ... 2016. This Bite of Science session, hosted by the Smithsonian-Mason School of Conservation, ... in Front Royal, VA from 5:00 p.m. to 8:00 p.m. The dinner is for ...
(Date:2/5/2016)... ATCC, the premier global biological materials resource ... and life science researchers that are working to address ... CDC website . --> CDC ... a single-stranded RNA virus of the Flaviviridae family, genus ... Chikungunya Viruses. Zika virus is transmitted to humans primarily ...
(Date:2/5/2016)... 5, 2016 On Thursday, February 11, ... for community, health and disaster services, and the ... to enhance care coordination and service delivery for the ... need and to better connect service providers to the ... San Diego has handled more than ...
Breaking Biology Technology: