Bio Saga Blog - A Chronicle of Life Sciences & Informatics

It is pretty sure now, that web 2.0, the new generation of web services, will (and already is playing) play an important role in the future of medicine. These web tools, expert-based community sites, medical blogs and wikis can ease the work of physicians, scientists, medical students or medical librarians. Let us being to believe that the new generation of web services will change the way medicine is practiced and healthcare is delivered. 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 the ability to create his own database for a set of Key terms. Also t...

The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper , dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”. Be a part of ...

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 proliferation of these cells to form a distal blastema which undergoes patterning and growth to restore the missing limb structures. Some of the processes that are relatively little known and most of scientists are keen in understanding are: Processes involving cell recruitment of progenitor cells to the site of disease or injury and tissue-specific differentiation Growth factors and cytokines responsible for activating the body's own native cells to initiate regen...

Previous blogging on the topic of GINA GINA Aftermath - Consumers Still Wary of Genetic Tests and in the series of blogs closing following the personal genomics industry scene . Now here is some thing very interesting and very vital that is about education the common man about GINA. Johns Hopkins University’s Genetics and Public Policy Center has launched an educational effort aimed at informing the public of how their genetic data can and cannot be used under the recently enacted Genetic Information Nondiscrimination Act. As part of its so-called “Project GINA,” the GPPC plans “to disseminate information” about the legislation to healthcare stakeholders and the general public, GPPC Law and Policy Director Susannah Baruch told last week. As part of its plan, the GPPC will launch a web site describing and explaining the federal law that bars health insurers and employers from discriminating based on genetic data. The website, slated to launch in September, will outline what protection...

The last time i blogged on this issue Reading Between Lines and now California will allow two of the fourteen consumer genomics companies it slapped with cease and desist letters two months ago to again market their genotyping services in the state, the state’s Department of Public Health confirmed Thursday. The CDPH inspected both companies, and on Aug. 7 it granted a license to operate in the state to Navigenics and a week later it gave one to 23andMe. Both of these companies were among the group that CDPH in June said were operating outside of state regulations. “State law requires these laboratories to have a license, obtain a physician's order from the consumer and demonstrate how they validate the results of their tests,” “several” other of the companies that received the cease-and-desist notification have now applied for licenses in the state, but noted that the state is not currently disclosing further information about how it is investigating the other laboratories. N...

Provision to change keywords with user’s changing research preferences in PUBMED data 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.xt...

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...

XTractor now has over Over 150 registered users from FDA , NIH , NCI , Astra Zeneca , Wyeth , MD Anderson Cancer Institute , Washington university , Scripps institute , Max Planck , Harvard Medical school and many more in less than 3 weeks !!! More than 600 annotated facts added everyday. A total of 25,000 facts added till date!!! 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 the...

The story begins (as the story ends for Ranbaxy Laboratories, India’s largest drug manufacturer) the curtains roll down... When the Singh family sold Ranbaxy Laboratories to Daiichi Sankyo it took everyone by surprise. This deal may well have opened the door for other such transactions in the future. Indian promo ters, who were considered to be sentimentally attached to their businesses, are now analysing their business portfolio and may be willing to cash out at right values. Times they are a-changin’ Never a dull moment these days at Ranbaxy Laboratories, India’s largest drug manufacturer. In the course of the summer, it has resolved its longstanding, much-publicized patent dispute with Pfizer over its generic version of Lipitor, agreed to an imminent buyout by Japanese drugmaker Daiichi Sankyo, and been sued by the U.S. government for alleged data fraud. As Ranbaxy’s World Turns, So Does Generics Model The Japanese company had agreed in June to pick up 34.8 per cent stake in Ranbaxy...

Add BioSaga to your page 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 .

We all understand that even the tiniest changes in the environment can create big opportunities and challenges for plants, animals and humans, but rarely do we consider what's happening on a microscopic level and what those changes could mean for the infinite varieties of life on Earth or how mankind's day-to-day experiences could be affected. But University of Houston researchers Yuriy Fofanov and Lennart Johnsson understand that what we don't see often carries big-picture implications. They've recently garnered international recognition for applying such vision while creating technologies to help monitor the sizes and genomic diversity of microbial communities. "The computational tools will pave the way to less expensive and more reliable tests that can be used across the globe. The sheer number of microbial communities presents great commercial potential," said Johnsson, Cullen distinguished professor of computer science, mathematics, and electrical and c...

XTractor - Discovering Newer Scientific Relations Across Abstracts http://www.xtractor.in/ 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. This has been added to Biological Informatics Subject Tracer Information Blog. This has been added to the tools section of Research Resources Subjec...

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...

Scientists at the University of Sheffield have shown how bacteria could be used as a future fuel. The research, published in the journal Bioinformatics, could have significant implications for the environment and the way we produce sustainable fuels in the future. Like all living creatures, bacteria sustain themselves through their metabolism, a huge sequence of chemical reactions that transform nutrients into energy and waste. Using mathematical computer models, the Sheffield team have mapped the metabolism of a type of bacteria called Nostoc. Nostoc fixes nitrogen and, in doing so, releases hydrogen that can then potentially be used as fuel. Fixing nitrogen is an energy intensive process and it wasn´t entirely clear exactly how the bacterium produces the energy it needs in order to perform. Now the new computer system has been used to map out how this happens. Until now, scientists have had difficulties identifying bacteria metabolic pathways. The bacterial metabolism is a huge netwo...

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...

The malaria parasite has waged a successful guerrilla war against the human immune system for eons, but a study in this week's Journal of Biological Chemistry has exposed one of the tricks malaria uses to hide from the immune proteins, which may aid in future drug development. Malaria parasites (plasmodia) are transmitted to people via infected mosquitoes. Once inside their human hosts the parasites first set up shop in liver cells, then move into red blood cells (RBCs) to replicate and wait for the next mosquito to help continue the cycle. After plasmodia infect a blood cell, they send out clusters of sticky proteins to the cell surface, enabling them to attach to blood vessels and escape destruction by the host's spleen while they replicate. This tactic can be especially problematic during pregnancy as malaria-infected RBCs congregate in the vessel-rich placenta (the source of food and oxygen for the growing fetus), creating health problems such as anemia, low birth-weight, f...

180 jobs are to go in Cork after pharmaceutical giant Pfizer announced it had failed to find a buyer for one of its five manufacturing facilities in Ireland. For the past 18 months, the company had been actively trying to sell the facility at Little Island as a going concern and retain employment there. However the sale fell through last month and the company says the facility will now closed by the end of 2009. 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 the ability to create his own database for a set of Key terms. Also the user could change the Ke...

Atrium Research has published the 2008 Electronic Laboratory Notebook Survey . This study contains the results and analysis of a survey of information technology, management, and scientific personnel in the life sciences, chemical, academic, government and food markets. Comprehensive data and analysis are reported on dozens of questions answered by 527 professionals from more than 20 countries. The report highlights user and prospective user opinions on data management challenges, technology interest, motivations, project goals, purchase timing, integration needs, and supplier product and brand perception. According to the report, the market for ELNs is exploding, with more than 30 suppliers offering commercial solutions. One of the fastest growing informatics markets with a growth rate of nearly 20 per cent per year, ELNs are radically improving the effectiveness of laboratory operations. ELNs enable new approaches to knowledge management, collaboration, and data integration. 'We ...

Switzerland's Roche Holding AG is set to become the world's biggest drugmaker by sales in 2014, as current market leader Pfizer Inc skids down the rankings to sixth place, according to a study on Monday. The realignment of the global drugs industry reflects the looming "cliff" of patent expiries, which will see many of the world's top-selling medicines cannibalized by cheap generics over the next five years. Forecasting company EvaluatePharma, which uses consensus analysts' sales estimates for its calculations, expects Roche to emerge as top dog in this tough new environment, reflecting its strength in fast-growing biotech drugs and its lack of near-term patent risks. Roche moved to consolidate its position in biotech-based cancer medicines last month by offering $43.7 billion to buy out the 44 percent of California-based Genentech Inc it does not already own. But even before that deal, which many investors expect to go through, albeit at a slightly swe...

Here a very noble thought "Science programs often pretend to be career oriented but they should be knowledge oriented. The main goal should be to teach students how to think and not how to work at a bench. Thus, students who graduate from an undergraduate—or graduate—program will have valuable skills that they can use in any career they choose." Brought out really well in this blog article check it out What will you be? The problem is not that a science undergraduate degree is not a career-oriented degree. It shouldn’t be. History, English, Philosophy, and some of the social sciences aren’t career paths either. But for those fields people seem to know that, and yet people associate science with something that leads to a job. They picture a scientist in a lab somewhere, and don’t realize that the people at the bench are either lab techs with a degree from a technical college or university students or -graduates at some point in their training . It’s all training, it never...

This one is extremely interesting, an awesome discussion, more so it attracted my interested as it sort of looked very relevant to my previous blogs Dawn of the GATTACA era! and the series of blogs on personal genomics . Nature News has an intriguing article on the next three decades of reproductive medicine: essentially a series of short musings from scientists working in the field about the issues we will be facing in 30 year's time. Thanks to Genetic Future another favorite blog of mine for having covered it. I totally agree with the author 'Daniel MacArthur' its in deed worth reading through in full. Which baby do you want? A dilemma for the 21st century parent-to-be Also read: The future of neo-eugenics Height and hypertension genes in Nature Genetics Making babies: the next 30 years 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 pr...

New preclinical research shows that cannabinoid cell surface receptor CB1 plays a tumor-suppressing role in human colorectal cancer, scientists report in the Aug. 1 edition of the journal Cancer Research. Endocannabinoid signaling is important to the normal functioning of the digestive system and has been shown to protect the colon against inflammation. Since chronic inflammation is a known risk factor for colorectal cancer, the researchers decided to look into the role of cannabinoid receptors in a mouse model of colon cancer. Cannabinoids previously had been shown to kill cancer cells in lab experiments by inducing apoptosis - programmed cell death. The team confirmed the role of CB1 in apoptosis, showing that tumor cells with high CB1 expression were sensitive to apoptosis when treated by a cannabinoid agonist. Cell lines with silenced CB1 resisted cell death. A series of experiments showed that CB1 increases cancer cell death by stifling a protein called survivin. Survivin is ov...

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...

Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the release of XTractor™, a first of its kind manually curated literature alert service. XTractor™ can be accessed free of charge by the scientific community world wide. XTractor™ acts as a literature alert service, which provides scientists with manually annotated scientific facts from literature. It enables researchers to be up-to-date with the latest scientific publications in the STM arena, as and when they are published. Once registered the scientists have the freedom to choose their keywords of choice and also set the frequency at which they wish to receive these alerts. Mining scientific literature to retrieve accurate hits or extract entity relationship has always been a long-standing problem in research. It is a daunting task to identify the right gene name or the right drug name and extract relations/association with diseases, processes; pathways etc accurately fo...

How many of us really use our multi-core processors to the fullest extent? here is a blog article which gives some cool tips using PERL to exploit the power of your multi-core. I found this very interesting, Check it out 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 accur...