Tests commissioned by Greenpeace, shown that Pepsico’s Doritos Corn Chips contains Genetically Modified Mon 863 and NK 603 variety corn ingredients.

Both Mon 863 and NK 603 are Monsanto’s genetically modified corn varieties. Mon 863 has a bacterial gene to give pest tolerance, while NK 603 has a bacterial gene for herbicide tolerance. An Independent analysis last year, done by the Committee for Independent Research and Information On Genetic Engineering and French National Committee For Risk Assessment of GMOs had concluded that both Mon 863 and NK 603 pose serious health impacts.

The find comes from India by Greenpeas after  an independent laboratory in germany conducted Tests on products picked up randomly from a supermarket in New Delhi.

Under existing Indian laws this is illegal practice. Every importer is required to label the products containing any GM content as well as get prior approval from the Genetic Engineering Approval Committee which falls under the environment ministry.

Surprisingly in 2007 United Arba Emirates have confirmed that 40% of the food in the UAE is genetically modified yet is sold to the end users without proper labelling.

While in Europe if an item contains more than 0.9 per cent of GMOs it is required to carry a label.

Its growing concern among many developing countries that import products from US where Monsanto dominates the food chain with its GM seeds. And it is going to create more controversy as Monsanto has aggressive plans in milk production. It already has a product on Bovine somatotropin a natural protein produced in the pituitary glands of all cattle which helps adult cows to produce milk. Monsanto’s version of Bovine somatotropin is a leading dairy animal health product in the United States and many other countries.

Microsoft is now offering its Amalga health-care software in Europe.  now Known as Microsoft Amalga has many components, from PACS solutions, Managing patient care records to tracking research projects and finance department tasks.

Microsoft Amalga  was previously known as Azyxxi which was acquired from General Datomics and  MedStar Health in 2006. This was positioned as a health intelligence Software.

But the New Amalga is more powerful and it bring the synergies of various microsoft acquisitions. It now Has a Hospital Information System (HIS) earlier known as Hospital 2000 “hospital information system for developing and emerging markets acquired from the  Thai developer Global Care Solutions (GCS) in 2007.

Amalga also boast of a Microsoft Amalga RIS/PACS earlier  known as GCS Amalga.

Amalga is being used by eight hospitals in MedStar Health’s network, which covers the Washington, D.C., and Baltimore areas, as well as Johns Hopkins Hospital, among others.

Cambridge based Helicos Bioscience announced the publication of a report in Science Magazine demonstrating the first single molecule sequencing of an organism (M13 virus genome) examining more than 280,000 strands of captured DNA.

Helicos’ uses a proprietary form of sequencing-by-synthesis called True Single Molecule Sequencing(tSMS)™. Unlike other methods, the technique builds up the sequence of each strand of DNA one base at a time.

After a brief hiatus am back to work, Microarray blog is chugging along slowly though I get very less time now a days to write , I have no plans to stop the blog. But reaching out to more people is an issue If I cant post atleast once a week.

Still I am going to take the challenge of writing another blog this time on the The Science Advisory Board website for microarray. Am happy the folks at SAB are using wordpress platform, so no hickups there.

I am going to maintain both the blogs for a while and perhaps spend more time on this blog on other subjects that I am interested in bioinformatics other than microarary such as Pharmacogenomics, Clinical genomics, SaaS in bioinformatics, Opensource and Adoption of technology among biologists to name few.

The new post in microarray is available at http://microarray.scienceboard.net

Surface plasmon resonance (SPR) reflectivity measurements are surface-sensitive, spectroscopic methods that can be used to characterize the thickness and/or index of refraction of ultrathin organic and biopolymer films at gold, silver  surfaces.

The probes can be proteins, peptides, nucleic acids, sugars, membranes, or any other molecule. GWC Technologies is one such company that offers the services in this field

SPR imaging detects the presence of a biopolymer on a chemically modified gold surface by the change in the local index of refraction that occurs upon adsorption.

Research Papers are on , Uiversity of California, Irvine page   and also at

UC Davis Biophotonics center web page                  

Benjamin Franklin said “As we enjoy great advantages from the inventions of others we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously.” - Any one listening !

Leaders and veterans in Biotechnology and Health care research industry may not be welcoming open source ideals. But IT industry has set new benchmarks and proved that open source brings in much needed new ideas and innovation. So hear out loud from none other than chairman and former CEO of Mozilla. The article is published for free at the Mckinsey quarterly

Mitchell comments that Mozilla’s real contribution isn’t just the browser but the model of participation.

In 2005 annual report on Association of American Medical Colleges acknowledged that industry, academic and government researchers can and must work together to remove scientific hurdles in drug development.

For hte uninitaited a look at the article published in Nature Magazine in 2006 with help from Pharma major Eli Lilly-Open source R&D and collaborative drug discovery and other related blogs  MnDoci FuturePundit

And don’t think these are just rants of an overenthusiastic researchers, who doesn’t know the dynamics of business, why because Director-General of the Council for Scientific and Industrial Research (CSIR) in, India unveiled a USD $34 million plan for Open Source Drug Discovery. CSIR is one of the world’s largest publicly funded R&D organisations 38 laboratories working on a range of subjects from molecular biology to road research to Himalayan bio-resources. The Council has more than 4,000 scientists working for it at these 38 labs.

The January 18 2008 meeting in NewDelhi in India was organized by Knowledge Commons, Delhi Science Forum, IIT Delhi, Red Hat and Sun on Free and Open Source model of knowledge. The highlight of the event was opensource drug development — make sure you read the Opensource India blog by Venkatesh

CSIR’s chief Sameer K. Brahmachari says, he looks for “taare zameen par” (stars on earth, a reference to one of Bollywood’s latest blockbusters), in large numbers

OSDD has the support of Sun Microsystems Inc. Hewlett-Packard, IIT Delhi, Red Hat and Indian corporate houses like TCG Life Sciences.

Related Topics Video: open source drug discovery for neglected diseases from google tech talks , Articles: The Ecconomist -An open-source shot in the arm

If you still think open source has no place in biotechnology and life science its not likely that you would listen to Alexander Graham Bell

“Great discoveries and improvements invariably involve the cooperation of many minds. I may be given credit for having blazed the trail, but when I look at the subsequent developments I feel the credit is due to others rather than myself.’

If you are on linkedin take a look at the question posted by Jake Chen, Founding Director at Indiana Center for Systems Biology and Personalized Medicine.

One area where bioinformatics havn’t experimented a lot is probably adopting SaaS (software as a service) methodology for growth. Software being developed for scientists is still not that user-friendly. Bioinformatics have evolved; but has it been hijacked by engineers?.

Though bioinformatics companies have lost the sheen, the growing need for data analysis is unmistakable , with more large genome projects being announced everyday.

1996-2002 was a period when bioinformatics was the darling of budding entrepreneurs and scientists the world over. Depending on your point of view the industry is now either passé or futuristic. The only ones that made money were the equipment companies and the those making reagents. Propelling the acquisitions phase that is still going on, transforming most of the erstwhile famous names from pure play bioinformatics to drug discovery/development services companies.

The future is there as a CEO puts it “We’re just at the tip of the iceberg of addressing the real problem — helping scientists understand how to use software to make a discovery,”

surprisingly given below is a quote I found in the website of the Stanford University Center for Molecular and Genetic Medicine , for the class on introduction to bioinformatics for fall-quarter 2007. here is the actual link . I hope am not going to be denied an admission there for posting this. But I agree with it completely, and its time for the industry to take note

“There are a wide variety of companies trying to commercialize bioinformatics. Some of these businesses have been around for many years, but a lot of them are just jumping in with nothing but hype to sell, trying and gain some market share and position themselves as “leaders” in the new area of genomics, hoping to become profitable or get bought out before the venture capital funds dry up”.

The study published in Jan. 23 issue of the Journal of the American Medical Association  is a thumps up for those interested towards personalized medicine, a small but important step.

A person’s genetic make-up seems to influence how he or she reacts to certain hypertension medications. The new study focused on the NPPA (atrial natriuretic precursor A) gene, which is involved in forming atrial natriuretic polypeptide, which acts as a diuretic.

n all, 38,462 people with hypertension underwent genotyping [genetic testing] and were randomly assigned to receive a diuretic (chlorthalidone) or one of the following three drugs: a calcium channel blocker (amlodipine); an angiotensin converting enzyme inhibitor (lisinopril); or an alpha-blocker (doxazosin).

people with hypertension and two different NPPA genotypes (known as NPPA G664A and NPPA T2238C) responded differently to different medications.

The 1000 Genomes Project, led by an international research consortium, will
sequence the genomes of at least a thousand people from around the world to create the most detailed and medically useful picture to date of human genetic variation.

The international research consortium draws support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).

The other participants include from as many as 35 Institutions such as the

Sanger Institute, BGI Shenzhen and National Human Genome Research Institute’s Large-Scale Sequencing Network,  Broad Institute of MIT and Harvard; the Washington University Genome Sequencing Centre at the Washington University School of Medicine in St. Louis; and the Human Genome Sequencing Centre at the Baylor College of Medicine in Houston. European Bioinformatics Institute near Cambridge, UK, and the National Centre for Biotechnology Information in the USA

Using standard DNA sequencing technologies, the effort would likely cost more than £250 million. However, leaders of the 1000 Genomes Project expect the costs to fall to as little as £15 million by the use of new sequencing technologies.

The scale is immense. At 6 trillion DNA bases, the 1000 Genomes Project will generate 60-fold more sequence data over its three-year course than have been deposited into public DNA databases over the past 25 years.

Among the populations whose DNA will be sequenced in the 1000 Genomes Project are: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States.

Alan Lambowitz, director of The University of Texas at Austin’s Institute for Cellular and Molecular Biology and Senior researcher Paul Paukstelis and his team has found the missing links in evolution of life from the simple to the complex and involvement of RNA.

By crystallizing a fungus the team of researchers were able to visualize the process of moving from RNA to RNA and proteins and then to DNA.

The crystal structure provides a snapshot of how, during evolution, protein molecules came to assist RNA molecules in their biological functions and ultimately assumed roles previously played by RNA quoted by Purdue structural biologist Barbara Golden

The study is published at January edition of Nature

University of California, Irvine researchers  Philip Felgner and Huw Davies with the Department of Medicine found that the modified vaccinia virus Ankara (MVA) produced the same antiviral response in human and animal studies as the current smallpox vaccine Dryvax.

Smallpox was declared eradicated worldwide in 1980; the last naturally occurring case in the world was in Somalia in 1977. and last I heard of it was when I watched the zombie movie I am Legend  last year,

In the study, Researchers applied blood serum samples taken from both humans and animals to microarray chips containing more than 200 vaccinia virus proteins, on which they simultaneously studied how the serum antibodies responded to all the vaccinia proteins

Details are on the UCI website press release 

The Uk government backed UK Household Longitudinal Study to use genetics analysis of British citizens (previous post on UK BioBank) to assess impact of Genetics and lifestyle in health and medical treatment and how it affects people’s social and economic status over time, is turning into controversy. The expansion of the program to cover “nature versus nurture” questions through genetic and medical testing has raised fears among civil liberties campaigners.

More than 100,000 people, including children as young as 10, will be asked to provide saliva tests and DNA samples in a new annual survey of the lives, behaviour and beliefs of people in the United Kingdom.

I thought of how we are going to look at privacy concerns at such government backed studies, Take a look at the blog by Deepak Singh Your personal health: The internet and privacy

Even though participation is voluntary The plan has been denounced by civil rights campaigners. ‘I would not let my DNA details be taken in this way,’ said Richard Clayton, the barrister representing the rights group Liberty in its fight to prevent police from keeping DNA samples of suspects later cleared of wrongdoing as quoted on The Observer

Details of the study is available at the University Essex website of UK Household Longitudinal Study

A service launched by quintiles claims to be one of the first to provide post launch drug safety information about drugs directly to any one who is using them.  iGuard is a web-based services that will help you take medication safety without the help of  healthcare professionals.

You can register on the site for free and record all the drugs you are using, along with  general health profile. When the FDA issues advisories and other safety notices for some 20,000 different marketed drugs, or when new research emerges about drugs or drug interactions that may affect them, iGuard members taking those drugs will get an e-mail alert.

The warning system uses a scale of 1 to 5 and is color-coded in a way that was inspired by the U.S. government’s homeland security alerts.

t’s impossible to gauge how many drugs will be given a “1,” which means suitable for widespread use, or a “5,” which iGuard says should be more carefully considered. Lipitor, for the record, gets a “2” rating from iGuard.

One of the reader had posted a question about my earlier post on genetics of Transplant Organ Rejection so this post is a part answer to her comment, I choose the title american way of life as my first post in 2008 is not mine but an interesting article from Newyork Times

A good article about what can we expect from genomics in clinical decision making and therapeutics

The truth behind the new bill signed into law by President Bush on 26 December 2007, which states that the findings of NIH-funded research must be made freely available to the public within one year of publication.

But all is not Hunky dory , as more obvious once you go through the complete text of the LAW as published in Government website

And it clearly states that copyright law takes precedence over deposition into PubMed Central.

What does that mean, when you publish a research paper it usually belongs to the University or the institution that funded the project. ie if you did sign a copyright transfer agreement with your publisher or sponsor of your funding he can deny the article being published in open source website or journal.

The only surprise is that in future based on the new Law the Director of NIH can prevent publication by grant recipients in journals that don’t allow publications of articles into PubMed Central. Aha now thats not good news for scientists and many are not going to welcome it either

But how many would care NIH is not the lone sponsor of grants, and yes certainly none from healthcare/pharma companies would allow their articles be published at open source journals. that questions how helpful the law would become

But certainly Many Many thanks and Happy New Year to  SPARC and the Alliance for Taxpayer Access  for making the first step, and it sure is a big one

There is certainly going to evoke multiple responses from everyone, wired magazine says its bad news for the science publishing industry, who’ve rallied against initiatives such as PRISM, and other open source websites such as PLOS, to preserve the right of journal publishers to charge for access to federally-funded findings. that means they will find their ways

Am certainly one of those not so politically obsessed persons, and I dont know that many politically savvy lab rats. may be few of those working in stem cell research, cloning or any other controversial topics might be. but I am beginning to like Dubya more. Not a bad a move for someone more associated bad grammar

Happy Christmas and Happy New Year , um now that may not be politically correct statement, as many say it has to be Happy Holidays and Happy New Year. But I just wanted to wish everyone pure unadultered happy holiday wishes and greetings

CombiMatrix  has completed the clinical validation of the  BAC array CGH based clinical microarray tests. ATScan is designed to detect known genomic copy-number variations  associated with Autism Spectrum Disorder and this test is now available to physicians and consumers.

Biotechnological methods can be used for cryptography. DNA binary strands can be used for steganography to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages.

I thought this as an interesting article since my last post was about DNA based security

http://www.cs.mun.ca/~banzhaf/molcomp.html

AUTHORS: Andre Leier, Christoph Richter, Wolfgang Banzhaf and Hilmar Rauhe

SOURCE: BioSystems, 57 (2000) 13 - 22,Extended Manuscript from 6th DIMACS Workshop on DNA Computing, Leiden, 2000

AUTHORS: Andre Leier, Christoph Richter, Wolfgang Banzhaf and Hilmar Rauhe

Applied DNA Solutions is NewYork company that offers DNA-based security solutions to Prevent fraud and theft

Applied DNA Sciences’ technology has been utilized to successfully mark nearly 1 billion items including DVDs and CDs, fine art, prestige wine, luxury and personal care goods botanical DNA encryption, embedment and authentication solutions that can help protect companies, governments and consumers from counterfeiting, fraud, piracy, product diversion, identity theft, and unauthorized intrusion into physical locations and databases.

ADNAS uses DNA segments from one or more botanical sources, rearrange them into unique encrypted sequences, and then implement one or more layers of anti-counterfeit techniques

Researchers from MIT have discovered that bacterial genes, known as the dnd gene cluster, gives bacteria the ability to employ DNA modification by adding sulfur to the sugar-phosphate DNA backbone as a phosphorothioate,

The same method used in laboratories worldwide to modify synthetic oligonucleotide.Why would bacteria conserve this system which requires five enzymes, each with different co-factors?”

Peter Dedon says the modification system might serve as either protection against foreign (unmodified) DNA, or as a “bookmark” to assist with transcription or replication of DNA.