 |
|
'Library on a Slide': whole genome microarrays for comparative genomics
March 18, 2004A 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."
BioMed Central Limited
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."
BioMed Central Limited
DNA Current Events and DNA News RSSPossible Link Studied Between Childhood Abuse and Early Cellular Aging
Children who suffer physical or emotional abuse may be faced with accelerated cellular aging as adults, according to new research from Butler Hospital and Brown University.
Biologists discover bacterial defense mechanism against aggressive oxygen
Bacteria possess an ingenious mechanism for preventing oxygen from harming the building blocks of the cell.
Just like old times: Generating RNA molecules in water
A key question in the origin of biological molecules like RNA and DNA is how they first came together billions of years ago from simple precursors.
Gene mismatch influences success of bone marrow transplants
A commonly inherited gene deletion can increase the likelihood of immune complications following bone marrow transplantation, an international team of researchers reports in the November 22 advance online issue of Nature Genetics.
Scientists at UA, collaborating institutions decode maize genome
Scientists from the University of Arizona led by Arizona Genomics Institute director Rod A. Wing and from collaborating institutions have deciphered the complete genetic code of the maize plant for the first time.
Ancestry attracts, but love is blind
People preferentially marry those with similar ancestry, but their decisions are not necessarily based on hair, eye or skin colour.
Scientists unlock clues for tailoring corn plant for food, energy needs
Scientists have long known that the offspring of two inbred strains tend to be superior to both their parents. Now, a team of researchers including a University of Florida geneticist has discovered clues to why that might be the case for one of the most important crops in the world: corn.
Cigarettes Harbor Many Bacteria Harmful to Human Health
Cigarettes are "widely contaminated" with bacteria, including some known to cause disease in people, concludes a new international study conducted by a University of Maryland environmental health researcher and microbial ecologists at the Ecole Centrale de Lyon in France.
Technique finds gene regulatory sites without knowledge of regulators
A new statistical technique developed by researchers at the University of Illinois allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors.
Unknowlingly consuming endangered tuna
While most of us would never willingly consume a highly endangered species, doing so might be as easy as plucking sushi from a bento box.
More DNA Current Events and DNA News Articles
 |
Thames & Kosmos Genetics and DNA by Thames & Kosmos In depth investigation of genetics and DNA. Isolate the DNA from a tomato, learn about inheritance and how traits are expressed, build a DNA model, breed bacteria to experiment with genetic engineering. The full-color, 48-page manual guides your experiments. |
 |
DNA: The Secret of Life by James D. Watson (Author) James Watson, the co-discoverer of the structure of DNA and author of the international bestseller "The Double Helix" tells the story of the amazing molecule since its discovery fifty years ago, following modern genetics from his own Nobel prize-winning work in the fifties to today's Dolly the sheep, designer babies and GM foods. Professor Watson introduces the science of modern genetics, along with its history and its implications, in this magnificent guide to one of the most triumphant achievements of human science. |
 |
Science Wiz DNA Kit by Sciencewiz The central concepts of molecular biology becomes child's play in this set of camp favorites. 40 Page science book and materials with 8 Major Activities. Makes the DNA revolution accessible. Extract DNA from a fruit Probe and spool real DNA Build a double helix Solve a chromosome puzzle Is it a boy or a girl? Play the gene construction game Country of Origin: U.S.A., China & Hong Kong. |
 |
DNA Science: A First Course, Second Edition by David Micklos (Author), Greg A. Freyer (Author) This is the second edition of a highly successful textbook (over 50,000 copies sold) in which a highly illustrated, narrative text is combined with easy–to–use thoroughly reliable laboratory protocols. It contains a fully up–to–date collection of 12 rigorously tested and reliable lab experiments in molecular biology, developed at the internationally renowned Dolan DNA Learning Center of Cold Spring Harbor Laboratory, which culminate in the construction and cloning of a recombinant DNA molecule. Proven through more than 10 years’ of teaching at research and nonresearch colleges and universities, junior colleges, community colleges, and advanced biology programs in high school, this book has been successfully integrated into introductory biology, general biology,... |
 |
K'NEX Educational DNA, Replications and Transcription Set by K'NEX K'Nex kits inspire young minds and satisfy kids' curiosity on how to build simple creations. Each innovative kit keeps young builders busy and intrigued for hours on end. This K'Nex Kit allows one to two kids to work as a team. Models demonstrate the structure and processes of DNA and mRNA molecules. Everything comes in a large compartmentalized storage case with snap-on lid. Curriculum sold separately. |
 |
Genes and DNA (Kingfisher Knowledge) by Richard Walker (Author), Steve Jones (Author) Genes & DNA explores modern genetics, from an investigation of genes and their function, to forensics, therapy, and cloning. |
 |
DNA on DNA by DNA Previously released on CD by No More Records, now issued on a limited edition 2LP featuring newly-discovered songs exclusive to this LP: "Pompeii," "Shrinking Thing," "Drinking Water," plus two encores from DNA's final performance at CBGB's. Definitive collection of studio and live recordings by New York's seminal no wave band DNA. Surviving two line-ups over a brief period of four years; this highly influential, strikingly original and extremely under-recorded band left a huge void in its wake. Formed in 1978, Brazilian-raised singer/guitarist Arto Lindsay hastily assembled an international trio of non-musicians. Robin Crutchfield played keyboard and Japan's Ikue Mori played drums. DNA played their first gig within weeks and recorded their first 7" shortly afterwards. The ear of Brian... |
 |
NOVA - Cracking the Code of Life Starring: Robert Krulwich Directed By: Betsey Arledge; Elizabeth Arledge Does it amaze you that yeast is your very close relative? That you possess roughly the same number of genes as a mouse? That you are 99.9% genetically identical to every other human? ABC Nightline correspondent Robert Krulwich lends a lighthearted touch to genetic science in this provocative two-hour NOVA special that takes you inside the amazing, complex and contentious race to decode the human genome. The Human Genome Project was born in 1990, when an international consortium of labs set out to sequence all 3 billion letters of our DNA, predicting they’d finish by 2005. Halfway through their schedule, controversial scientist and entrepreneur J. Craig Venter threw the genome world into turmoil, when he announced his for-profit company Celera could finish the job in just two years.... |
 |
The Stuff of Life: A Graphic Guide to Genetics and DNA by Mark Schultz (Author), Zander Cannon (Illustrator), Kevin Cannon (Illustrator) The Stuff of Life gives readers a complete introduction to the history of genetics that's as easy to understand as it is entertaining to read. |
 |
Discovery Exclusive DNA Explorer Kit by DISCOVERY CHANNEL Explore one of the newest frontiers in science - DNA mapping. From science labs to courtrooms, few discoveries are as exciting as the world of DNA. With this deluxe, first-of-its-kind kit, you can extract, view and map real DNA yourself. Ideal for budding forensic-scientists or secret agents, the working lab and tools are just like the real thing. Plus, you |
| © 2009 BrightSurf.com |