Bio Saga Blog - A Chronicle of Life Sciences & Informatics

We are bringing out a special program, due to huge no of  enquirers  and considering a special demand by all to conduct a special batch of training on following topic Area of training/Internship Protein modeling & Drug discovery Start date - 15 th  July Emerging trend in healthcare and drug development is being appreciated and this success is being sound after a long dedicated research work on drug discovery, modeling & simulation. If you are giving a thought on finding novel drug, new molecules, we are here to help you. RASA has been very keen to give your research work a novel touch, providing few advanced skill set to you within a framed syllabus designed for you.     APPLY HERE   What will you learn? ·          Give inside how receptor binds to ligand. ·          Help to find ligand activity. ·   ...

In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools. Results: In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the secon...

Scientists have discovered a new physical form of proteins that could drastically improve treatments for cancer and other diseases, as well as overcome some of the largest challenges in therapeutics. The protein formulation strategy, developed by researchers at The University of Texas at Austin, is unprecedented and offers a new and universal approach to drug delivery one that could revolutionize treatment of cancer, arthritis and infectious disease. “We believe this discovery of a new highly concentrated form of proteins – clusters of individual protein molecules – is a disruptive innovation that could transform how we fight diseases,” Keith P. Johnston, a chemical engineering professor and member of the National Academy Engineering, said. “It required integration of challenging contributions in fundamental science and engineering from three of our chemical engineering research groups,” he said. Johnston, Chemical Engineering Professor Thomas M. Truskett and Assistant Professor Jennif...

The glycoproteins (GP) of enveloped viruses facilitate entry into the host cell by interacting with specific cellular receptors. Despite extensive study, a cellular receptor for the deadly filoviruses Ebolavirus and Marburgvirus has yet to be identified and characterized. Here, we show that T-cell Ig and mucin domain 1 (TIM-1) binds to the receptor binding domain of the Zaire Ebola virus (EBOV) glycoprotein, and ectopic TIM-1 expression in poorly permissive cells enhances EBOV infection by 10- to 30-fold. Conversely, reduction of cell-surface expression of TIM-1 by RNAi decreased infection of highly permissive Vero cells. TIM-1 expression within the human body is broader than previously appreciated, with expression on mucosal epithelia from the trachea, cornea, and conjunctiva—tissues believed to be important during in vivo transmission of filoviruses. Recognition t...

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 ...

Moxtek, a nano-photonics company, today announced that it has reached a collaboration agreement with Philips Research to develop a new wire grid microarray chip (WGM) that has been designed to offer ultra-high surface specificity and excellent suppression of background signals. The WGM is based on a wire grid pattern on a glass substrate. The WGM technology provides the potential for rapid quantitative detection with improved accuracy, of biomolecules such as proteins and nucleic acids. In addition, the technology promises to significantly simplify the work flow and improve the reproducibility for such tests by removing the washing step and performing hybridization and detection in parallel. These strengths match with the needs for advanced microarray technology in life sciences research. Rapid molecular detection for life sciences research is a fast-growing market, and could revolution...

Massachusetts Institute of Technology (MIT) researchers have demonstrated that a gel composed of small, woven protein fragments can successfully carry and release proteins of different sizes, potentially enabling the delivery of drugs such as insulin and trastuzumab (Herceptin). Researchers can control the rate of release by changing the density of the gel, allowing for continuous drug delivery over a specific period of time. The team is led by Shuguang Zhang, associate director of MIT's Center for Biomedical Engineering. The gel, known as a "nanofiber hydrogel scaffold," enables a gradual release of the proteins from the gel over hours, days or even months. The gel itself is eventually broken down into harmless amino acids - the building blocks of proteins. Peptide hydrogels are ideally suited for drug delivery as they are pure, easy to design and use, non-toxic, non-immunogenic, bio-absorbable, and can be locally applied to a particular tissue. Composed of self-assembli...

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 .

Ask XTractor - XTractor™ now turns ON its ‘Insta Search’. Get a snapshot of the XTractor data for your desired query using the Insta Search feature. Which are the biological processes involved in Leukemia? What are the drugs associated with Ovarian Neoplasm? What are the diseases modulated by FRAP? Then get a snapshot of the XTractor data from the latest published abstracts on your questions using the 'Insta Search' feature. 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...

US FDA , NIH , NCI , MD Anderson , Harvard Medical School , Novartis , Wyeth , AstraZeneca , Vertex , P&G , JNJ many more subscribe to XTractor. “XTractor™ is an intelligence that works so unconscious even for the users to perceive. It is fascinating as to how quickly XTractor transforms the most complex scientific facts into structured knowledge almost instantaneously by bringing about cross entity relationships across abstracts thereby aiding in quicker decision making through the Drug Discovery process” Bangalore, India, October 12, 2008 --( PR.com )-- Indian Life Sciences Informatics Company, Molecular Connections announced today, that its XTractor™ - The first of its kind scientific literature alert service launched in July ‘08 has built a user base of over 900 users form more than 150 premier organizations. XTractor™ has been widely accepted and received well in the scientific fraternity both the academia and the industry across the globe. Be a part of the XTractor commun...

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...

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...

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...

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length. Do you want to know more?