Bio Saga Blog - A Chronicle of Life Sciences & Informatics

This one is not so recent article, nevertheless very interesting and path breaking, Scientists have successfully used "next generation sequencing" to identify mutations that may cause a rare and mysterious genetic disorder. The research, published by Cell Press on July 29th in the  American Journal of Human Genetics,  demonstrates that sequencing an affected individual's entire "exome"; that is, all of the genes that carry instructions for producing proteins, can reveal critical genes that when mutant, cause inherited disorders. Perrault syndrome is a recessive disorder that is associated with hearing loss in both boys and girls, and failure of ovarian function in girls. Some individuals with Perrault syndrome also have neurological symptoms. Prior to the current study, no genes for Perrault syndrome had been identified. A research group led by Mary-Claire King, PhD, from the University of Washington in Seattle studied the genetics of Perrault syndrome in a s...

Through a complex analysis of protein interactions, researchers from IRB Barcelona and the Joint Programme IRB-BSC have discovered new molecular mechanisms that may be involved in the development of Alzheimer’s disease. The study, a collaboration between bioinformaticians and cell biologists, was led by IRB Barcelona group leader and ICREA researcher Patrick Aloy and appears today in the Genome Research, a reference journal in the field of genomics. Alzheimer’s disease is an age-related neurodegenerative disease. Despite the considerable efforts made in recent years to understand the mechanisms that trigger this disease, an effective treatment is not yet available. This study reveals new molecular and functional data that could help researchers gain a better understanding of the disease and potentially to develop new therapies.  From the computer to the lab  Proteins are the molecular instruments that cells use to carry out their functions. Proteins don’t normally act alone,...

First the genome; now the proteome. China has already established a leading position in DNA sequencing through the work of the  BGI  in Shenzhen (formerly the Beijing Genomics Institute), which has been generating eye-catching genomics discoveries for the past few years (see  Nature  464,  22–24; 2010 ). This week, Chinese researchers are set to announce initiatives that could put them at the forefront of international efforts to catalogue and characterize all proteins in the human body. Inspired by the Human Genome Project, protein researchers worldwide have been seeking funds to build a full catalogue of human proteins — a proteome — which, they say, will explain how the information encoded in our genomes can give rise to normal and diseased states. his January, the  Human Proteome Organization  (HUPO) in Montreal, Canada, took the first steps towards an international effort. It set up the Human Proteome Project (HPP) working group to coordinat...

A team of researchers led by investigators at the Department of Energy's Joint Genome Institute reported online today in Science that they have sequenced the first amphibian genome : that of the Western clawed frog Xenopus tropicalis . The international research team used shotgun sequencing to generate a draft version of the X. tropicalis genome, which they then compared with the human and chicken genomes. In the process, they found more than 20,000 protein-coding genes in the frog genome, as well as regions of synteny with humans and chickens, and a slew of transposable element sequences. And because amphibians diverged from the amniote lineage leading to mammals, birds, and reptiles some 360 million years ago, senior author Daniel Rokhsar, a researcher affiliated with JGI and the University of California at Berkeley, and his co-authors explained, information in the X. tropicalis genome is helping to reconstruct features found in the shared ancestor of these anima...

Mutations in the protein tyrosine kinase gene ERBB4 contribute to — and may provide hints about treating — a subset of melanoma, according to a paper by researchers from the National Institutes of Health and Johns Hopkins University that appeared in the advanced, online edition of Nature Genetics this week. The team sequenced protein tyrosine kinase or PTK genes in 29 individuals with melanoma. Their search uncovered dozens of somatic mutations affecting the kinase domain of 19 different PTK genes. When they looked at the same 19 genes in another 79 melanoma patients, the researchers found that almost a fifth of those tested harbored mutations in ERBB4 . And, they reported, knocking down the mutated form of ERBB4 or using a drug that targeted the gene slowed the growth of melanoma cell lines, suggesting it might be useful to evaluate ERBB4 status in melanoma patients. Researchers at the NIH Intramural Sequencing Center sequenced all 86 PTK family genes in tumor samples from 29 ...

This Pathways Compendium provides an index of Alzheimer disease pathway models contributed by researchers and companies. Probable Interaction Networks Involved in Pathology of Alzheimer Disease: Predicting Targets and Therapeutic Agents - NetPro™ based Study . Developed by researchers at Molecular Connections Private Limited, an in silico discovery services company. Users can click on a specific node (molecule) to get information on all interactions of the molecule in the given network. Click on the interaction arrows for information on the specific interaction. The Alzheimer Research Forum is a Pioneering Biomedical Web Community . Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world. XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manu...

Mayo Clinic is extending its brand across the country. This time, it is offering a free personal health record on the Microsoft HealthVault platform. The Mayo Clinical Health Manager , as the PHR is known, will provide not only a secure place to store medical records online, but also guidance from Mayo experts that will be tailored to the information contained in that PHR. If you are a 50-year-old man with diabetes and hypertension, for example, you will receive information about how you should take care of those conditions and the tests you should receive. Initially, Mayo Clinic Health Manager will include tools and features that help consumers manage pediatric and adult wellness, immunizations, pregnancy and asthma. Forthcoming features will help users with type 2 diabetes, high cholesterol, and/or high blood pressure. According to Mayo’s press kit , PHR users will be able to “transfer data directly into [a] Mayo Clinic Health Manager profile from a wide range of providers, devices...

BANGALORE, Indian Researchers have achieved a breakthrough, identifying a protein pathway that triggers cancer in the human body owing to its erratic behaviour. Researchers at Bangalore’s National Centre for Biological Sciences (NCBS) led by Satyajit Mayor and Neha Vyas have identified what is known as the Hedgehog pathway and the ways in which it forms and leads to cancer. The researchers, who have published their work in the journal, Cell, say this pathway is formed when the proteins (called hedgehog), which are separate, get drawn to each other by electrostatic interactions between amino acids present around the proteins. A small cluster of proteins then gets formed and goes on to form a mega-cluster. This travels to other cells and creates effects that are good or bad — the cluster could be normal and help organ regeneration or tissue repair, or the cluster could get hyperactive and affect other cells, which is the sign that cancer is coming. Simply put, the NCBS research indicates...

The personal genetics service firm 23andMe , the Michael J. Fox Foundation for Parkinson's Research, and the Parkinson's Institute and Clinical Center announced yesterday that they are enrolling 10,000 people to be part of a new Parkinson's disease community. The effort is aimed at establishing the resources necessary for future genome-wide association studies and other research initiatives. In an effort to entice individuals with Parkinson's disease to participate, 23andMe is slashing the price of its service from $399 to $25 for a limited time for up to 10,000 individuals with Parkinson's disease who sign up through the Parkinson's Institute or the Michael J. Fox Foundation. Google co-founder Sergey Brin, who is married to 23andMe co-founder Ann Wojcicki, will ante up an undisclosed amount of cash to subsidize the genotyping costs. To be eligible, individuals must have physician-diagnosed Parkinson's disease and agree to provide saliva samples and fill ...

Scientists report a remarkable improvement in Alzheimer's transgenic mice following treatment with a new drug. The study provides the first demonstration that an ionophore, a compound that transports metal ions across cell membranes, can elicit rapid and pronounced improvement in neuropathology and cognitive function in mouse models of Alzheimer's Disease (AD). Recent research has implicated dysregulation of metal ions in the brain, particularly copper and zinc, in the pathogenesis of AD and the damaging accumulation of amyloid beta (Aβ) protein that is characteristic of this devastating disease. The ionophore clioquinol (CQ), an 8-hydroxyquinoline, has been shown to increase intracellular copper and zinc levels and decrease Aβ levels in cultured cells and in the brains of transgenic (Tg) AD mice. However, further studies in mice and humans demonstrated that brain entry of CQ was quite limited. This research is published by Cell Press in the July 10th issue of the journal Neuro...

Scientists have unravelled the structure of a cell signalling receptor in the blood control system which when damaged is responsible for diseases such as leukaemia. Their discovery helps to explain, for the first time, how this receptor is activated and will form the springboard for the development of new treatments. The findings, published on 8 August in the prestigious science journal, Cell , are the result of an interstate collaboration between a team of scientists led by Professor Michael Parker, St Vincent’s Institute (SVI), Melbourne and Professor Angel Lopez, Hanson Institute at the Institute of Medical and Veterinary Science, Adelaide. Using leading edge technology that allows scientists to view minute parts of cells, the scientists have developed the first 3D image of the receptor’s structure and will use the unique knowledge it provides to find drugs to modify its action and control diseases such as Leukaemia and asthma. Professor Lopez said: “Leukaemia is a...

A virus that commonly infects potatoes bears a striking resemblance to one of the key proteins implicated in Alzheimer's disease (AD), and researchers have used that to develop antibodies that may slow or prevent the onset of AD. Studies in mice have demonstrated that vaccinations with the amyloid beta protein (believed to be a major AD contributor) to produce AD antibodies can slow disease progression and improve cognitive function, possibly by promoting the destruction of amyloid plaques. Some early human trials have likewise been promising, but had to be halted due to the risk of autoimmune encephalitis. One way to make Alzheimer's vaccinations safer would be to use a closely-related, but not human, protein as the vaccine, much like cowpox virus is used for smallpox immunizations. In the August 15 Journal of Biological Chemistry, Robert Friedland and colleagues used this concept on an amyloid-like protein found in potato virus (PVY). They injected PVY into mice follo...

A report in the August issue of Behavioral Neuroscience, published by the American Psychological Association, describes how this novel use of data mining may enable investigators to test therapies to delay or even prevent disease, starting with hereditary forms. Data mining to detect the subtle behavioral expression of mutations could conceivably allow investigators to test therapies aimed at preventing, slowing or stopping disease. By being able to predict more accurately which carriers may express the disease before they experience symptoms (the "premorbid" state), researchers could test medicines that might prevent symptoms from emerging. Methods such as data mining can be therapeutically useful even before science understands how disease begins. The authors wrote, "The discovery of reliable behavioral endpoints with predictive validity, even before a good understanding of their etiology is achieved, can significantly improve intervention research." Do you want ...

Combination antiretroviral therapy (ART) is frequently initiated in resource-limited countries when patients are being treated for tuberculosis. Co-administration of ART and anti-tubercular therapy may be complicated by shared toxicity or adverse drug interactions, according to background information in the article. Rifampicin-based anti-tubercular therapy reduces the plasma concentrations of the antiretroviral agents efavirenz and nevirapine. The virological consequences of these interactions are not well known. Do you want to know more? Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user w...

Trials of the drug, known as Rember, in 321 patients showed an 81% difference in rate of mental decline compared with those not taking the treatment. The Aberdeen University researchers said the drug targeted the build-up of a specific protein in the brain. Alzheimer's experts were optimistic about the results, but said larger trials were now needed. Presenting the results at the International Conference on Alzheimer's Disease, Professor Claude Wischik said the drug may be on the market by 2012. Do you want to know more? Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with th...

18 Ways to Improve your PubMed searches Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with the ability to create his own database for a set of Key terms. Also the user could change the Keywords of preference from time to time, with changing research needs. The categorized sentences could then be tagged and shared across multiple users. Thus XTractor proves to be a platform for getting real-time highly accurate data along with the ability to Share and collaborate. Sign up it's free, and takes less than a minute. Just click here: www.xtractor.in .

In their current study, published in the online edition of the journal Nature , Conboy and her team found that old muscle produces elevated levels of a molecule called TGF-beta, which is known to inhibit muscle growth. The researchers then showed that the muscle-deteriorating effects of TGF-beta can be reversed by blocking its pathway in old mice. In the experiments, the researchers used RNA interference, which can silence specific genes, to inhibit the molecules that act downstream of TGF-beta to prevent cells from multiplying. They then locally injured the muscles of treated mice, as well as untreated old and young mice, by injecting a small amount of snake venom, which killed muscle tissue in the immediate vicinity. After five days, the team found that the young mice were able to produce healthy cells to replace damaged tissue. The treated older mice, whose inhibitory pathways were suppressed, were able to regenerate new cells in much the same way. Not surprisingly, old untreate...

Boehringer Ingelheim will acquire Actimis Pharmaceuticals through a structured buyout in which Boehringer Ingelheim will acquire shares of Actimis depending on the achievement of several successive milestones with Actimis’ leading asthma compound AP768. If AP768, currently in Phase I development, is successfully advanced into a Phase III, Boehringer Ingelheim will own 100% of Actimis’ shares. Upon successful completion of the entire development program, the total deal will be worth $515 million. AP768 interacts with CRTH21, a target for asthma and allergic rhinitis. Previous to the currently ongoing Phase I trial, the compound was shown to have a more effective mechanism of action across multiple available animal models compared to currently marketed leukotriene receptor antagonists , according to the companies.

A protein related to heart disease and Alzheimer's is found to be a factor in HIV. The apolipoprotein (apo) E4 isoform has been implicated in neurodegeneration in Alzheimer's disease, cardiovascular disease, and stroke. Now, investigators at the Gladstone Institutes, the University of California, San Francisco, the University of Texas Health Science Center at San Antonio, and the Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, Maryland have shown that this troubling protein is a risk factor for AIDS progression rates and promotes entry of HIV into cells. Do you want to read more?

Battelle Ventures has spun out a firm from the U.S. Department of Energy’s Oak Ridge National Laboratory (ORNL), with an initial $1.5 million seed investment. The company, called NellOne Therapeutics, will develop regenerative medicines. The funding will be tranched based on key technical milestones. Towards a "holy grail" in human medicine: the ability to restore organs damaged through trauma, disease, cancer, or even the normal aging process. Tissue or organ repair has been the ultimate goal of surgery from ancient times to the present day. Clearly, there is a lot of interest in the regeneration of tissues, and tissue repair in organisms is within reach. However, we are a long way from understanding how to coax the human body into regenerating complex body parts after injury or disease. As an example, regeneration of amputated limbs in amphibians - “epimorphic” regeneration which includes cellular dedifferentiation in the injured tissues of the limb stump and proliferat...