The Staphylococcus aureus microarray Database inching closer to Staph Infection Vaccine

MRSA the very name send shudders to any one working in a hospital setup, the aggressive Methicillin-resistant Staphylococcus aureus (MRSA) , is a bacterium responsible for some difficult-to-treat infections in humans.

The organism is often the cause of community-acquired MRSA (CA-MRSA) or hospital-acquired MRSA (HA-MRSA) depending upon the circumstances of acquiring disease,

University of Southern Mississippi biological science professor Dr. Mohamed Elasri and student Vijayaraj Nagarajan, a doctoral student have developed an online database that holds collected data on genes related to stap.The Staphylococcus aureus microarray meta-database, known as SAMMD

There are more than 400 SAMMD users from 23 countries with numbers increasing daily. As researchers work to find a vaccine for MRSA, Elasri said this program can cut a significant amount of time it takes to find information about staphylococcal genes

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New Microarray technology replacing PCR and speed up HTS

Dr. Richard Gibbs, director of the Baylor College of Medicine Human Genome Sequencing Centre and his researchers along with the help of  NimbleGen Systems the  company recently acquired by Roche Applied Science has developed a new technique that combines gene chip technology with the latest generation of gene sequencing machines to allow fast and accurate sequencing of selected parts of the genome

 The technology, called “sequence capture,” enables fast and accurate enrichment of thousands of selected genomic regions, either contiguous or dispersed, such as segments of chromosomes or all genes or exons uses , The study had uses NimbleChip™ microarrays in preparation for a high-throughput 454 Sequencing™.

The study Direct Selection of Human Genomic Loci by Microarray Hybridization presented on October 10, 2007, at the J. Craig Venter Institute’s Genomes, Medicine, and the Environment (GME) conference, Roche NimbleGen and 454 Life Sciences, working with Dr. Richard , will create a whole-genome human exome (all exons) microarray, with the goal of resequencing the entire human exome faster and cheaper.

Till now researchers relied upon PCR for selection of specific genomic regions for resequencing

Limitations of PCR  meant the length of sequence it can amplify was small, is difficult to scale or multiplex for the enrichment of thousands of fragments, and has limited performance in the repetitive regions typical of complex genomes, such as human.

The sequence capture microarray technology bridges the gap between next-generation DNA sequencing technology and current sample preparation methods by providing an adaptable, massively parallel method for selective enrichment of genomic regions of interest.

The new process is simpler, more accurate and efficient than the multiplex PCR . In one experiment, more than 6,400 exons (the part of the genetic code that carries the instructions for making proteins), were analyzed. Using the old technology this would have taken at least six months.

Transposon insertion site profiling chip (TIP-chip)

Transposon insertion site profiling chip (TIP-chip) was invented by Researchers at the Johns Hopkins’ High Throughput Biology Center. Tip-chip can be used to help identify otherwise elusive disease-causing mutations in the 97 percent of the genome long believed to be “junk.”

TIP-chip (transposable element insertion point) can locate in the genome where so-called jumping genes have landed and disrupted normal gene function. This chip is described n the Proceedings of the National Academy of Sciences. the article titled Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposon insertion site profiling chip (TIP-chip

The most commonly used gene chips are glass slides that have arrayed on them neat grids of tiny dots containing small sequences of only hand-selected non-junk DNA. TIP-chips contains all DNA sequences. Because each chip can hold thousands of these dots – even a whole genome’s worth of information – scientists in the future may be able to rapidly and efficiently identify, by comparing a DNA sample from a patient with the DNA on the chip, exactly where mutations lie.

Jef Boeke, Ph.D., Sc.D, professor of molecular biology and genetics and director of the HiT (High Throughput Biology Center), who spearheaded both studies at the Institute of Basic Biomedical Sciences at Hopkins, and his team have focused particularly on transposable elements, segments of DNA that hop around from chromosome to chromosome.

These elements can, depending on where they land, wrongly turn on or off nearby genes, interrupt a gene by lodging in the middle of it, or cause chromosomes to break. Transposable elements long have been suspected of playing a role vital to disease-causing mutations in people. Boeke hopes that the TIP-chip eventually can be used to look for such mutations in people.

The new TIP-chip contains evenly sized fragments of the yeast genome arrayed in dots left to right in the same order as they appear on the chromosome. Boeke’s team used the one-celled yeast genome as starting material because, unlike the human genome, which contains hundreds of thousands of transposable elements of which perhaps a few hundred are actively moving around, the yeast genome contains only a few dozen copies.

Like a word-find puzzle, where words are hidden in a jumbled grid of letters, the TIP-chip highlights exactly where along the DNA sequence these elements have landed. By chopping up the DNA, amplifying the DNA next to the transposable elements and then applying these amplified copies to the TIP chip, the researchers were able to map more than 94 percent of the transposable elements to their exact chromosome locations.

double-tiled DNA chip 

Standard chips contain one layer of DNA dots that read from left to right, like the across section of a crossword puzzle. Boeke’s new double-capacity chips hold two layers of dots, a bottom layer that reads across and a top layer that reads down, again using the crossword analogy. So if their experiment lights up a horizontal row of dots, the researchers learn that the data maps to the region of the genome contained in the bottom layer; likewise, if the experiment highlights a vertical row, the data correspond to the top layer.

Says Boeke, “It’s so easy to differentiate the top and bottom layers. Next we’re going to try adding another layer reading diagonally” to triple the amount of genomic information packed onto the tiny chips.

Authors of the TIP-chip and double-tiled DNA chip papers are Sarah Wheelan, a new faculty member in the Department of Oncology, Lisa Scheifele, Francisco Martinez-Murillo, Rafael Irizarry and Boeke, all of Hopkins.

Microarrays in daily life

Accurate assessment of a calf’s future performance may soon be possible by using microarrays.

By 2010, less than three years away,
Australia’s largest integrated beef research program, the Beef Cooperative Research Centre (CRC) anticipates cattle breeders may be able to get an accurate assessment of a bull or a dam’s future performance within a few months of its birth

Professor John Gibson, Beef CRC Adaptation and Cattle Welfare Research Leader, says microarray technology has enabled the entire 23,000-odd separate genes of the bovine genome to be printed on one microarray plate the size of a microscope slide. 

“Research overseas indicates that how an animal expresses its genes in early life provides an accurate picture of its gene expression at breeding age.” 

This leads to the prospect of microarrays being printed that carry genes of commercial interest, which could be then used to predict the breeding performance of young animals well before they reach breeding age.

 Prof. Gibson observes that this would help breeders quickly eliminate genetically dud bulls and cows early in their life, without the costs of feeding and progeny testing now required to determine the duds. 

Microarray based DRUG DISCOVERY and CLINICAL DIAGNOSIS and biosensor designed to identify viruses

 Prof. David Dandy of Colorado State University chemical and biological engineering has proven that called microarray assays can be used for biomedical disease and drug screening assays could rapidly increase drug discovery,

Although not ready for hospital or office use, microarrays represent a novel miniaturized multi-spot diagnostic format that has huge potential for patient diagnosis if found reliable and approved.

Smaller is often better, according to a new scientific study that appears this week in the Proceedings of the National Academy of Sciences by Professor David Dandy, Dr. David Dandyhead of the Department of Chemical and Biological Engineering at Colorado State. Dandy co-wrote the paper with David Grainger, a former chemistry professor at Colorado State who now is chair of the Department of Pharmaceutics & Pharmaceutical Chemistry at the University of Utah.

The study was funded by a multi-year, $2.5 million grant from the National Institutes of Health.

“This work is extremely useful from an industrial perspective,” said Michael Lochhead, chief scientist at Accelr8 Technology Corp., a Denver-based developer of innovative materials and instrumentation for advanced applications in medical instrumentation, basic research, drug discovery, and bio-detection.

The critical importance of this work is illustrated by the fact that, to date, a single microarray-based test has been approved by the FDA for clinical use.

According to Roche, the manufacturer of this diagnostic microarray, “This test analyzes a patient’s Cytochrome P450 2D6 and 2C19 genotypes from genomic DNA extracted from a blood sample. Test results will allow physicians to consider unique genetic information from patients in selecting medications and doses of medications for a wide variety of common conditions such as cardiac diseases, pain and cancer.”

 

 

Scared of GMO and GM food

 Detecting Genetically Modified Organisms with Microarrays

Is Genetically modified Food a health Hazard ? according to many it seems so. European union has always taken a stringent rules against GM food. A microarray was developed for detecting the presence of Genetically modified organisms some time back a pdf of the article can be downlaoded from http://www.springerlink.com/index/C888146870511P6U.pdf

For example U-Vision Biotech offers a DNA microarray based GMO detection system for detecting

  • Brassica napus

  • Zea mays L.

  • Gossypium hirsutum L.

  • Linum usitatissimum L.

  • Carica papaya L.

  • Solanum tuberosum L.

  • Oryza sativa

  • Glycine max L.

  • Cucurbita pepo

  • Beta vulgaris

  • Lycopersicon esculentum

  • Triticum aestivum

similar products are also offered by Eppendorf   through its dual chip GMO  kit allowing the detection of the EU-approved genetically modified organisms (GMOs) by identifying their genetic elements

Whole Genome microarray @ 99 USD

Ocimum Biosolutions is offering whole genome microarrays at 99 USD as part of its 6th year celebration, The limited period marketing offer is available for many cataloge whole genome microarrays at 99 USD irrespective of the number of microarrays ordered.

The company now offers one of the best cost effective microarray prices in the market

To get more information on microarray price please contact Ocimum Biosolutions web  http://www.ocimumbio.com/web/promo/array99.asp


 

 

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