multipathogen- and chemical-detection Microarray.

CombiMatrix announced that the DoD has awarded a one-year, $2.2 mln contract to CombiMatrix for further development of its microarray technologies for a multipathogen- and chemical-detection system.

IS Microarray facing the DOOM….Invading microarray turf……….

ChIP-sequencing (ChIPSeq) – a combination of chromatin immunoprecipitation and next-generation, or parallel, sequencing. The feat was performed “with a speed and precision that goes beyond what has been achieved with previous technologies,” comments University of Washington geneticist Stanley Fields, in an accompanying essay in Science.

hIP is a well-established lab technique to identify those specific sites where proteins latch onto the DNA. Cells are treated with a chemical to fossilize the links between DNA and protein, the chromatin is then isolated, the DNA broken up, and the attached proteins immunoprecipitated. Finally, the DNA stuck to the protein can be released and analyzed. Until now, the most high-throughput application of this technique involved using microarrays containing thousands of gene spots able to identify binding sites for transcription factors and the like.

Next-Generation Sequencing Invades Microarray Turf By Kevin Davies June 14, 2007 | Two new papers unveil a new dimension to commercial next-generation sequencing applications – one that could potentiallypose a threat to more-established microarray technologies. Using theGenome Analyzer from Illumina/Solexa, two groups working independentlyhave been able to map the locations across the genome where a specific
DNA-binding protein latches onto the DNA.

ChIPSeq is a cost-effective alternative to microarray methods, with a significant upside. “Other ultrahigh-throughput sequencing platforms, such as the one from 454 LifeSciences, could also be used to assay ChIP products, but whatever sequencing platform is used, our results indicate that read numbercapacity and input ChIP DNA size are key parameters,” Johnson et al. writes.ChIPSeq might be an order of magnitude cheaper than microarray alternatives, with the eight flow cell lanes in theGenome Analyzer offering excellent design flexibility. Fewer materialsare required, and the method can be applied to any organism – it is not restricted to available gene arrays.

Changing ChIPs
The advantages of ChIPSeq over ChIP-chip include the ability to interrogate the entire genome rather than just the genesrepresented on a microarray. (For example, Johnson et al. point out thata similar experiment using Affymetrix-style microarrays would requireroughly 1 billion features per array.) There is also the benefit of
sidestepping known hybridization complications with microarrayplatforms. “Perhaps most usefully,” writes Fields, “ChIPSeq canimmediately be applied to any of those [available] genomes, rather thanonly those for which microarrays are available.”

Gone in 60seconds-

Personalized Medicine in 60 Seconds

Bioinformatics was a BOOM its was predicted to be next big thing, yet the industry which had hundereds of fragmented mom and pop kind small companies are now under mergers and acquisitions, Does everyone got their money back.

Bioinformatics is yet to become the big Billion billion Dollar, and on the door step the next big thing is ready for its journey

Personalized Medicine in 60 Seconds is the article published in Wired magazine

Affymetrix expands into personalized medicine The next big thing

Affymetrix expands into personalized medicine! Why because The next big thing in health care? is You the individual

personalized medicine is the place step every one wants to be. Roche recently went after Nimblegen for a small foothold in this developing ssicne field, Now its the turn of Affymetrix the leader in microarray DNA chips.

The company is trying to get ahead of the market curve by partnering with drug companies that are making precisely targeted medicines, tailored for patients who have specific gene variations

the company opened the Affymetrix Clinical Services Laboratory to analyze the genes in blood and saliva samples for pharmaceutical companies, diagnostic laboratory businesses and hospitals

Chikken Tikka and Alzheimer’s !!

Does eating a lotf of spicy curry eliminates the chances of geting cancer and diseases like Alzheimer’s thats a yummy proposition, I wish it was that easy, but apparently the Indian curry cuisines has the capacity to prevent the onset or delay the disease, but dont reach out for the qwik e mart yet. The curry doesnt do the job all by itself ,one of the key spices used ‘the Turmeric’ does that work, Ayurvedic medicine practioners has known the value of turmeric for a very long time, the stuff even finds its ways into soaps and cosmetics           

Scientists have for the first time isolated bisdemethoxycurcumin, the active ingredient of curcuminoids, a natural substance found in turmeric root that stimulates the immune system to destroy brain-clogging proteins that cause Alzheimer’s.

Researchers found that bisdemethoxycurcumin boosted immune cells called macrophages to clear amyloid beta. Amyloid beta is a peptide that forms the plaques found in Alzheimer’s disease.

Amyloid plaques are found outside the neurons. Two major pathways are involved in breakdown of APP (amyloid precursor protein) which makes the protein called B-amyloid protein. responsible for plaques .One pathway is normal and causes no problem. The second results in the changes seen in Alzheimer’s and in some of the other dementias.

Collaborative Drug Discovery

Collaborative Drug Discovery Releases Next Generation Database for Both Private Collaborations and Public Open Access

Collaborative Drug Discovery enables scientists to archive, mine, and collaborate to more effectively develop new drug candidates for commercial and humanitarian markets.

 The technology enables novel community-based research efforts that become more and more useful as additional participants contribute data. Publicly available data sets currently in the system include the FDA orphan and approved drugs and small molecule drug discovery data dating back over half a century. These data sets pertain to a diverse group of neglected diseases, including malaria, tuberculosis, African Sleeping Sickness, Chagas Disease and Leishmania.

Hocus Locus Spins out of University of Albany

Hocus Locus, a bioinformatics company which is part of the $225 million Gen*NY*Sis   Programe (Generating Employment through New York State Science) is located at the Center for Excellence in Cancer Genomics in University of Albany, it makes products to help small drug discovery companies speed up development of new drugs.

Affymetrix microarrays in mental retardation research

Affymetrix is collaborating with the University of Nijmegen in the Netherlands, the University of Tuebingen in Germany and the NHS Regional Genetics Laboratory in Birmingham, U.K. for the European Cytogenetic Research Initiative to investigate causes of mental retardation,

microarray technology will be used to try to identify the specific causative mutations in mentally retarded children.

Currently, cytogeneticists use karyotyping and FISH technologies to study deletions, amplifications and other chromosomal rearrangements..

The company is also a particpant of the Encode consortium that studies the junk DNA. http://www.affymetrix.com/corporate/events/2007_7_encode.affx

Tougher times for Drug Resistant Bacteria

The Secret of how to prevent bacteria from developing drug resistance has been revealed in a new study.Drugs called bisphosphonates, widely prescribed for bone loss has been found to help in preventing an enzyme that helps in conjugation of bacteria, by help of which it derives drug resistance.

Many highly-drug resistant bacteria rely on an enzyme, called DNA relaxase, to obtain and pass on their resistance genes. Relaxase  plays a crucial role in conjugation as it is the gate keeper that starts and stops the movement of DNA between bacteria durig conjugation.

researchers at the University of North Carolina at Chapel Hill, have stopped the microbes’ ability to spread, among other advantageous mutations, resistance to antibiotics, by disabling the enzyme using molecules known as  bisphosphonates

The study by Matthew Redinbo and his associates is published in this week’s Proceedings of the National Academy of Sciences USA

The antibiotic-resistant Escherichia coli bacteria that were trying to pass their genes along, actually died when their DNA relaxase was shielded thus preveinting the spread of drug resistant bacteria andpossibility of more mutations.

The news is will bring fresh hopes at a stage when drug–resistant strain of the bacteria Staphylococcus aureus infects over 1 million US hospital patients every year.

Microarray to detect mutations in largest Human Gene

The average human gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases. Residing at Chromosome 4 it has long been of interest to the medical community because its the gene responsible for huntington’s disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence – a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

Now reseacrhers at Emory university has developed a microarray based test to chek for mutations in this gene. The current test do not detect all types of mutation that affects 1 in 3500 males according to the university wesbite.

Mutations in the dystrophin such as point mutations in a sequence of DNA can result in mistakes in gene  expression and nonfunctional proteins that causes Duchenne muscular dystrophy (DMD).

A detailed presentation of the advantages of the test is available at the Emory Genetics Testing website. The test offeredon the Nimblegen CGH array platform gains more prominance as the company is now being acquired by Roche who has plans to dominate the clinical microarray market with its products in genetics testing space

The emory university Genetics testing lab offers numerous other genetic tests

New horizons ahead

Its been two years since I have been with Ocimum Biosolutions ,the India HQ company serving bioinformatics and microarray market in US with office in Indianapolis and another lab in netherlands, I have been working in the business development of the company’s microarray arm in US which was acquired from MWG biotech, we had tasted success,

I have been busy lately as I have resigned from the company now that explains the absence of any new posts for few weeks now. Ocimum is one of the unique bioinformatics oraganization to make its mark in this industry, because unlike many new companies .  it was started by people with no biological background but has been selected as one of fastest growing life science company in India and Asia many times by Deloitte ranking and many other independent agencies. apart from winning awards from government and even a funding fro world bank. So what makes them so sucessful

Ocimum offers services in bioinformatics oligo microarray and R&D but its the presence of its labs near to its customers and the company’s software development division housed at Hyderabad India that makes the difference. Coupled with India’s cost efficiency, it has many advantages

Bioinformatics industry is going through a face of consolidation, marketed in India in its infancy as a glamorous field to work many who jumped into the fray has burned their hands. and industry analysis in 2000 predicted the industry to become a 100 billion worth by 2004, yet even in 2007, majority of the biologists are yet to warm upto the industry in a way predicted by the software pundits

Research and Markets (http://www.researchandmarkets.com/reports/c59429) has announced the addition of “Biomed Outsourcing Report: An Overview of the Life Sciences and Outsourcing Landscape in India: Spotlight on Bangalore” to their offering.