Genetics Influence Blood Preassure medication

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.

So Thats how Humans Evolved! – Now we can begin to answer the big question

Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates the question have been answered by a team of scientists from University of Washington School of Medicine and University of California, San Diego.The research published by Evan Eichler from the University of Washington School of Medicine provide the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations.

Evan Eichler has analyzed segmental duplications in the human genome and have successfully pinpointed the ancestral origin of each and identified the newly named core duplicon.

The study presents a comprehensive global analysis of the evolution of segmental duplications in the human enome. The authors identify the origin of ancestral duplication loci, regions of clustered duplicons, and evidence upporting a punctuated model of evolution.

This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations.

Apart from the above study  the recently completed (check previous blogs) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences the study helps to explain the evolutionary origins of human DNA and the role played by transposons

Genomes can duplicate long stretches of DNA from one chromosome and insert the duplication in another area of the genome. The resulting segments of DNA are called segmental duplications.  They are important because they hold evolutionary secrets

Finding answers to questions such as, Which set came first? What changes were innovated, when and why? What was sacrificed when an innovation took effect? What is the connection between disease and innovations within segmental duplications?, are important because researchers can then design specific medical treatments and can lead to ket discoveries in  Pharmacogenomics research

Download the Research Article

Transplant Patients Could Live Free of Anti-Rejection Drugs

Scientists from the Lucile Packard Children’s Hospital and the Stanford University School of Medicine have identified a pattern of gene expression shared by a small group of patients who beat the odds and remained healthy for years without medication, after undergoing Organ transplant.

The findings made by Minnie Sarwal, MD, PhD, a pediatric nephrologist at Packard Children’s is a major advantage in organ transplantation treatment. Transplant recipients who share the same pattern of genes but are still on conventional medication may be able to reduce or eliminate their lifelong dependence on immunosuppressive drugs. The study may also help physicians determine how best to induce acceptance, or tolerance, of donor organs in all transplant patients, regardless of their gene expression profiles.

Although the anti-rejection medications, known as immunosuppressants, tamp down the immune system enough to permit lifesaving organ transplants, their benefits come at a price. They also quash the body’s natural response to dangerous invaders, such as bacteria and viruses, and to rogue cancer cells. Transplant physicians prescribing immunosuppressants to their patients walk a fine line between avoiding organ rejection and increasing the risk of infection and cancer

The researchers used microarray, or gene chip, technology to compare gene expression patterns in blood samples from 16 healthy volunteers with those from three groups of adult kidney transplant recipients from the United States, Canada and France

Microsoft life science

Well every one is writing about google and its foray into biology and life science, so what is going on with Other companies .

Microsoft started its BioIT alliance During 2006 and guss what Bill Gates said during the launch “Advances in our understanding of the human genome promise to revolutionize medicine and open the door to therapies that are tailored to individuals”,  means they have bigger plans. just like google entered 23andME

Founding members of the alliance include Accelrys Software, Affymetrix, Amylin Pharmaceuticals, Applied Biosystems and The Scripps Research Institute, among more than a dozen other life sciences and IT companies.

and the last month Microsoft has released Microsoft Computational Biology Web Tools as open-source some code for analysis of antiviral immunity

Hmm interestingly I found the project details hosted in Codeplex the open source project hosting the details are on at MSCompBio

And then there is Stochastic Pi-Machine the programming language to model and simulate biological systems- a research funded as part of the European Science Initiative

And then there is the webpage at Microsoft research for bioinformatics

But my favourite is this

Towards 2020 Science microsoft

to define and produce a new vision and roadmap of the evolution, challenges and potential of computer science and computing in scientific research in the next fifteen years.

and this beautiful image from the microsft website

The IBM Clinical Genomics for targeted clinical research

THe Haifa Lab of IBM provides the Technlogy for Clinicalgenomics and leads the research in lifesciences fieds.

The Clinica, Genomics division plans to provide technology to integrate clinial genomics data and HL7 and other complaince protocls followed in clinical research and clinia, trial and integrate them to provide better and focused clinical trials

Clinical genomics for biopharmaceuticals from IBM

the main advatages as per IBM website is that

• Encapsulate raw genomic data into an HL7 Clinical Genomics message, including transformation services of proprietary data formats to standardized formats like MAGE and BSML
• Access patient’s clinical history stored in an enterprise EHR system
• Access all major ontologies that provide genotype-phenotype relationships like OMIM, PharmGKB, etc.
• Parse the encapsulated raw genomic data and bubble-up selected genomic data items based on ontological knowledge as well as the patient clinical data
• Compare two Genotypes (the data model at the heart of the HL7 specs) in order to provide case-based reasoning services to decision support application that will use CGL7 as a specialized clinical genomics middleware
• Find a similar pedigree in case base of pedigrees in order to support risk assessment applications that base their assessment on family history

Girls Really Do Prefer Pink? Yes Owe to evolutionary influences

Ok I did laugh a bit at that story, but interesting ha. according to a study outlined in a report in the Aug. 21 issue of the journal Current Biology Females do have a preference for pinkish colors that males don’t.

So whats the evolutionary reason , well the same old story females used to collect food, the study says Females were the ones who gathered red fruit against a green background,” she said. “Red is healthy in faces and in fruits

so intrigued read on at USNEWS website

Google Health -health information storage

interestingly I found this image from an earlier post of Bertalan at scienceroll

The story according to the blog Google Blogoscoped, Google’s nascent Google Health product, codenamed “Weaver”, will offer consumers the opportunity to create a central repository for their health records, including medications, history, test results and allergies. The blog has a number of screenshots of the program in development.

Well google certainly has more up its sleeve, doubt it, chek the google labs page,

Passionate about these topics? You should work at Google. among others listed is interest in genetic algorithms

Pharmacogenomics has started

IT been a long time since my last post, So I thought of catching up with other blogger before going to do anything myslef. So here is what got my attention from Alla Katsnelson blog on the scientist magazine  that  USFDA approved updated labeling for the widely used blood-thinning drug, Coumadin, to explain that people’s genetic makeup may influence how they respond to the drug.

so whats going to be good for common man, the next time (not very soon) you are going to be under treatment of a controversial drug you might get to know how your genetics makeup can affect the treatment, thats going to be a good relief especially cancer patients and those who undergo HRT

while Frost&Sullivan reports in its latest industry update that  genomics platforms that are too inefficient and expensive for ultra-high throughput comprehensive genome-wide analysis are hindering the realization of personal genomics.

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.

ENCODE consortium: forming background of why 3 billions bp are required for a human to survive not just the set of genes.

ENCODE consortium today published one in nature and 28 papers in genome research involving 35 groups from 80 organizations around the world, which promise to reshape our understanding of how the human genome functions. The findings totally challenge the tidy collection of independent genes , but sees as a complex networking system, along with regulatory elements and other types of DNA sequences that do not code for proteins, interact in overlapping ways not yet fully understood.

“This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome,” said NHGRI Director Francis S. Collins, M.D., Ph.D. “Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome’s functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases.”

Loads to come out of this …. few days back in nature cell biology there was a article stating small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA in an eukaryote…

Plants too recognise its kin

Now wonder,  research proves that even plants recognise their kins. Researchers from McMaster University have found that plants go competitive when forced to share their own environment like pot, with strangers of the same species, but they’re accommodating when potted with their siblings.

How they do it???

When a different plant of same species is potted with a growing plant they start growing more roots, which allows them to grab water and mineral nutrients before their neighbours get them. when they share a pot with family i.e the sibiling 1st or 2 nd generation they don’t increase their root growth. Because differences between groups of strangers and groups of siblings only occurred when they shared a pot, the root interactions may provide a cue for kin recognition. The following is the paper that is being published on the same.

Dudley, S. A. and A. L. File (2007). Kin recognition in an annual plant. Biology Letters, in press.

Future of High Throughput Genome Sequencing

In Bangalore Bio 2007 LabIndia has introduced  SOLiD: Sequencing by Oligonucleotide Ligation and Detection which is the Future of High Throughput Sequencing.

“This is useful for those who want to do full genome sequencing. Whole genome projects will be more cost effective with this new instrument than they are today,” said Dr. Anupama Gaur, Team Leader Application Support, Labindia Instruments, Pvt. Ltd.

HistoGenetics has come up with Sequence Based Typing which has many advantages such as identifying many rare and new alleles. “Nearly 2000 alleles have been identified so far and it has been launched in the US and UK as of now” said Dr. Cereb Nezih, M.D., President and co-founder, Histogenetics, Inc.

Gene Expression is affected when cells are cultured in petri dish

When trying to figure out how different respond to drugs and other environemnts in the body scientists turn to cells. The cultured cells are grown in petri dishes now with the onset of tissue microarrays the process is getting more advanced

A new Brown University study shows that nerve cells grown in three-dimensional cultures use 1,766 genes differently compared to cells grown in standard two-dimensional petri dishes.

The research shows that culture techniques can significantly affect cell growth and function. cells grown in a laboratory in 3-D environments are more like cells grown in the ultimate 3-D environment – the human body.

“More and more, we’re seeing evidence that cells cultured in three dimensions look and behave more like cells in your body,” said Diane Hoffman-Kim, the University of Brown bioengineer who spearheaded the new study,

The study is published in the May edition of Tissue Engineering,

Rribozymes prevent the spread of HIV in the body

considered by some to be the ‘living fossils’ of a time when life was based on RNA -Rribozymes have been used by researchers to prevent the spread of HIV in the body

The Medical Marketing International Group (MMI) scientists have used these ancient RNA catalysts to suppress key receptors that allow HIV to enter cells

HIV enters cells using the cellular receptors CCR5 or CXCR4 and previous work has shown that preventing the expression of these receptors using the Company’s proprietary ribozymes, which target the messenger RNA (‘mRNA’) that encodes these proteins, is highly effective at preventing HIV replication in vitro. The results announced today show that the ribozyme technology can effectively deliver the ribozyme and suppress expression of these receptors in an advanced in vivo model. Moreover, a single administration of the ribozymes was able to maintain suppression of the receptors for a significant period (>35 days so far), indicating that a pool of HIV-resistant cells could be established.

Indian genetic database offers R&D advances

Imagine a diabetic patient from NewYork being put on a drug regimen distinct from a patient London. Personalized medicine allows tratement to decided on the genetic make up of the individual. Genetically europeans and asians and others have different ways of responding to same treatment genetically

FortunatelyIf Indian researchers have their way, such customised medication based on genetic differences could be a possibility for a range of illnesses.

A consortium of Indian scientists recently completed a genetic database for India, home to one of the world’s most ethnically diverse populations that will allow researchers to understand the genetic predisposition of ethnic groups to diseases. Icelanders are considered for Human genome project because of very less number such diversity

The genetic map will enable global and Indian pharma companies to enhance research on predictive medicine and targeted drugs. Research firm TCG Life Sciences is about to become the first private player to use the database.

The consortium collected data on the genetic codes of over a 1,000 genes from among 15,000 individuals belonging to Indian sub-populations

Another user of the data is the clinical diabetics’ consortium, which aims to identify if there are specific genetic reasons for a particular ethnic group to be predisposed to the disease. It is already known that some cultures are pre disposed to certain diseases so Indian are more prone to heart attack and diabetes and such

The Indian Genome Variation Consortium, a public-private partnership that networks six Council of Indian Scientific and Industrial Research labs and some private software firms, undertook the genetic variation mapping.

UK is appealing for volunteers to help worlds biggest medical experiment project- to understand impact of Genetics and life style in illness and medical treatment

 UK is appealing for volunteers to help worlds biggest medical experiment project- to understand impact of Genetics and lifestyle in health and medical treatment

The  BBC reports about a medical experiment aiming to be the biggest in the world is appealing for volunteers to help end Scotland’s reputation as the “sick man of Europe”.

The project named as  UK Biobank will be the world’s biggest resource for the study of the role of nature and nurture in health and disease.

Funded and guided under the supervision of leading scientists from the UK and around the world. Funded by the  Wellcome Trust, the UK’s largest independent medical research charity, the  Medical Research Council, the Department of Health, the Scottish Executive and the Northwest Regional Development Agency. and many other major medical research charities, including the British Heart Foundation and Cancer Research UK. The project is also supported by the National Health Service.

claiming to help not just the volunteer, but for the future generation to come the £61m UK Biobank project will track the health of thousands of people for up to 30 years.

Information and DNA gathered from volunteers will be used by researchers to help tackle serious diseases.

Volunteers will be asked to attend an assessment centre where they will fill out a lifestyle questionnaire, have body measurements such as bone density, blood pressure, height and weight recorded, and donate a small sample of blood and urine for long-term storage as a resource for researchers in the future.

Researchers will study the relationship between our genes, our lifestyles and our current health to find out why some people develop certain illnesses and others do not.

It is hoped the project will eventually include 500,000 volunteers from across Britain, making it the biggest study of its type ever undertaken.

The Biobank will run alongside the complementary Generation Scotland project, which focuses on how genes inherited from our parents affect the likelihood of developing diseases.

Data collected by the two projects will be used to help prevent and develop new treatments for cancer, heart disease, diabetes, Parkinson’s, Alzheimer’s, mental health illnesses, osteoporosis and arthritis.

12 DNA tests that Could Change Your Life-selected by Forbes

The complete list is published at forbes website

• Breast Cancer
• Adult-Onset Diabetes
• Obesity
• Drug Metabolism
• Crohn’s Disease
• Prostate Cancer
• Duchenne Muscular Dystrophy
• Rett Syndrome
• Macular Degeneration
• Alzheimer’s Disease
• Heart Attack

Gene Testing:

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Free DNA Paternity Test for Father’s Day

I am not promoting anything here but I thought it was an intersting news aswell as nothing short of odd considering the recent and ongoing news pages spend on discussing hollywood and famous fatherhood battles inside and out of court this is  one kind of an offer that Chromosomal Laboratories, Inc. a leading DNA testing laboratory, has announced that it will repeat its  offer of five free paternity tests, a $2000 value, to fathers and alleged fathers as a special promotion to celebrate the upcoming Father’s Day holiday. Interested parties should contact Chromosomal Laboratories by June 14th to be entered into the drawing. Five fathers will be chosen at random to receive a free home paternity test kit.

source webwire

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ASGT unveils new Platform for Regulating Expression of therapeutic Genes

During 10th Annual Meeting of the American Society of Gene Therapy (ASGT) in Seattle a new methid for  Regulating Expression of therapeutic Genes was introduced.

For many applications, gene transfer is being employed to engineer cells for therapeutic applications, chek the following links for article 1 IFR , 2 (Nature), 3 (NIH) , that require precise regulation in order to ensure gene expression in the correct tissue and prevent it in unwanted cell types,

Now, a team of scientists led by Dr. Luigi Naldini at the San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET) in Milan have developed a new design that enable delivered genes to become highly responsive to a cell’s identity with the helps of gene regulation mediated by small RNA molecules, known as microRNA. This is particularly relevant for the emerging field of stem cell gene therapy, in which genes are delivered into a cell that can give rise to many distinct cell types.

MicroRNAs downregulate the expression of specific genes in cells where the gene is not needed, and thereby have an important influence over the identity of the cell.

Addition of microRNA binding sites into their gene delivery vectors results in gene regulation dictated by the cell’s own microRNA. Simply put, they could engineer their gene to be turned off in cells where the microRNA is present.

Dr. Naldini’s group has already begun to successfully exploit microRNA regulation for achieving stable long-term correction of hemophilia in the mouse model and for improving the safety of hematopoietic stem cell gene therapy.