Library On A Slide Microarray Puts 30,000 Genomes On A Single Slide

CLONE AGE

illustration only

Ann Arbor - Mar 23, 2004
A novel application of microarray technology, where up to 30,000 whole genomes are printed on a single slide, is described in the journal BMC Microbiology this week.

The 'Library on a Slide' will help researchers compare the genetic make up of large numbers of bacterial strains to discover which genes are responsible for causing disease.

Even within one species of bacteria, the genetic content can vary by as much as 25% between individual strains. These differences can determine how virulent a particular strain is or which organisms it can colonise.

To make significant claims about which genes play a role in which biological processes, researchers must compare large numbers of bacterial genomes and see which genes are associated with a particular trait.

Dr Lixin Zhang and his colleagues from University of Michigan have made this sort of experiment much easier, by developing the 'Library on a Slide' technique.

They predict that their high-throughput method will be, "an efficient and cost effective way for sharing and utilizing large strain collections in various comparative genomics studies."

The 'Library on a Slide' is based on current microarray technology � the printing and probing of the slide are carried out largely as usual. The most significant difference is that each spot on the slide contains the genomic DNA of one bacterial strain, rather than containing multiple copies of a single gene.

The researchers describe how they adapted a high-throughput method for isolating small DNA fragments to efficiently isolate high quality genomic DNA, and how they optimized the conditions for printing this genomic DNA at high density onto a glass slide. They also tested techniques for identifying individual target genes at high sensitivity using fluorescently labelled probes.

To test the 'Library on a Slide' method the group created a sample array using a collection of E. coli genomes, and probed this to discover which genomes contained the hemolysin gene � a known virulence factor. The results from the array experiment matched perfectly with results from experiments using dot blot and Southern hybridisation methods.

The researchers can envisage other ways that their technique could develop: "A single 'Library on a Slide' could also be constructed with isolates from several related species, or species that are part of a microbial ecosystem. Such a platform would enable us to examine the extent of shared genetic elements across species � especially horizontally transferred virulence factors and antibiotic resistance genes."

Library on a slide for bacterial comparative genomics Lixin Zhang, Usha Srinivasan, Carl F Marrs, Debashis Ghosh, Janet R. Gilsdorf, and Betsy Foxman BMC Microbiology 2004, 4:12 To be published 22 March 2004 Upon publication this article will be available free of charge according to BMC Microbiology's Open Access policy here.

TERRADAILY

Reflections On Life..In The Jungle

Edwards - Mar 16, 2004
Brilliantly colored strawberry poison dart frogs singing in the jungle below didn't notice the NASA DC-8 flying laboratory passing overhead. After all, there is little disturbance to the rain forest by an aircraft far above.

Thanks for being here; We need your help. The SpaceDaily news network continues to grow but revenues have never been harder to maintain. With the rise of Ad Blockers, and Facebook - our traditional revenue sources via quality network advertising continues to decline. And unlike so many other news sites, we don't have a paywall - with those annoying usernames and passwords. Our news coverage takes time and effort to publish 365 days a year. If you find our news sites informative and useful then please consider becoming a regular supporter or for now make a one off contribution.
SpaceDaily Contributor $5 Billed Once credit card or paypal		SpaceDaily Monthly Supporter $5 Billed Monthly paypal only

The content herein, unless otherwise known to be public domain, are Copyright 1995-2016 - Space Media Network. All websites are published in Australia and are solely subject to Australian law and governed by Fair Use principals for news reporting and research purposes. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA news reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement, agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement All images and articles appearing on Space Media Network have been edited or digitally altered in some way. Any requests to remove copyright material will be acted upon in a timely and appropriate manner. Any attempt to extort money from Space Media Network will be ignored and reported to Australian Law Enforcement Agencies as a potential case of financial fraud involving the use of a telephonic carriage device or postal service.