Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Blogging earlier on Workforce shortages are a growing problem in the US biotech industry, may be boon to India and China , i recently read the sequel to this original article. So just thought of picking up only excerpts of it which were more relevant to the Indian scene. The scene here in India is not very different form that of the US. I very often come across companies and their CEO's complaining about the shortage in workforce. It is certainly true, although there is a slight change in the scenario, unlike US schools, schools here in India churn out huge number of students in all spheres of science. Coming to the Biotechnology and other Lifesciences there are number of good schools here in India with the IIT's and NIT's and other premier institutions offering programmes on similar lines. So now the point is the whether there's a shortage at all and the second applies to the kind of shortage. Shortage of what? The other point that needs clarification is the type o...

Previously blogging on novel anti-cancer molecules in Researchers Find that a Small Molecule Can Activate an Important Cancer Suppressor Gene. Scientists at The Wistar Institute have developed a new type of enzyme inhibitor capable of blocking a biochemical pathway that plays a key role in cancer development by combining natural organic atoms with metal complexes. Based on studies in human melanoma cells, the research paves the way for developing new ways to treat cancer by dampening the overactive enzyme activity that leads to uncontrolled tumor growth. Details of the study, to be published in the May 16 issue of the journal ACS Chemical Biology , show how small-molecule inhibitors can be designed to target a family of signaling proteins, called phosphatidyl-inositol-3-kinases, or PI3Ks. “The PI3K pathway has been called the most mutated pathway in human cancer,” says Ronen Marmorstein, Ph.D., a professor in the Gene Expression and Regulation Program at Wistar and s...

Scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory have determined the structure of a key protein domain in a bacterium that could help with bioremediation of uranium-contaminated land sites. The researchers, led by Argonne senior biophysicist Marianne Schiffer, characterized the structure of one of the principal domains in a protein responsible for certain types of movement exhibited by the bacterium Geobacter sulfurreducens. Geobacter lives in predominantly low oxygen environments and generates energy by transferring electrons to various metallic electron-accepting atoms such as iron or uranium. This ability suggests that Geobacter might be used for remediation of certain types of hazardous waste. For example, when uranium is reduced by this process to its insoluble form, it no longer leaks into groundwater and engineers can inexpensively remove the precipitated uranium. Do you want to know more?

While nonribosomal peptides (NRPs) are of tremendous pharmacological importance, there is currently no technology capable of high-throughput sequencing of NRPs. Difficulties in sequencing NRPs slow down the progress in elucidating the non-ribosomal genetic code and negatively affect various screening programs aimed at the discovery of natural compounds of medical importance. We propose to employ multi-stage mass-spectrometry (MS n ) for the data acquisition, followed by alignment-based heuristic algorithms for data analysis. Since mass spectrometry based analysis of NRPs is fast and inexpensive, this approach opens the possibility of high-throughput sequencing of many unknown NRPs accumulated in large screening programs. Do you want to know more?

Blogging earlier on the platypus What's Our Connection to the Platypus? here is some think i came across, a very interesting compilation on the history of the mystery mammal. I have always thought and fancied a platypus in the place of TUX the Linux mascot, every time i see tux i don't think of a penguin but a platypus! may be tux to me looks more like a platypus than a penguin! A nice item, a brief history of the platypus, in 5 parts that's just brilliant. Further interesting is the foot note "Further reading" don't miss it. This is a wonderful historical account and should be made more widely available. For Quick reach here : Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175-183. Abstract | Full text Relevant abstracts from Genome Research Platypus Genome Special Hall, B.K. (1999). The Paradoxical Platypus. BioScience 49(3): 211-218. JSTOR link This is a wonderful historical account and should be made more...

This is quite interesting a blog page with a list of bioinfomatics companies all over world! www-3.ibm.com www.3rdmill.com www.4-sci.com www.GenomicTechnologies.com www.PharmaDM.com www.abergc.com www.aborygen.com www.accelrys.com www.acdlabs.com www.acero.com www.aclara.com www.advancedcell.com www.affymetrix.com www.agencourt.com www.agilebio.com www.agrogene.com www.algan.com www.algonomics.com www.allometra.com www.almabioinfo.com www.alphadna.com www.amartus.com www.amaxa.com www.amebioscience.com www.amita.com www.ananomouse.com www.anedabio.com www.antivirals.com www.apocom.com www.applied-maths.com www.appliedbiosystems.com www.aptagen.com www.ariadnegenomics.com www.arraygenetics.com www.artificial-life.com www.atglabsinc.com www.autohandle.com www.axontologic.com www.base4.com www.benitec.com.au www.bforrester.com www.bio-link.org www.bioalma.com www.bioanalyticsgroup.com www.biobase.de www.biocarta.com www.biochipnet.com www.bioclon.com www.biodata.ee www.biodatabases.com ww...

Blogging previously about biomarker in, Biomarkers to Open the Door to Personalized Medicine and Represents a Seismic Shift for the Pharma Industry . Here are two interesting study on biomarkers. First one, Dr. Johan Arnlov, a researcher at Uppsala University, and lead author of a report in the May 15 issue of the New England Journal of Medicine . A bundle of four offbeat biomarkers accurately predicted the risk of death from cardiovascular disease in a study of older Swedish men, researchers report. It is just a preliminary finding in a long process that might one day lead to widespread medical use of these biomarkers in addition to well-established risk factors such as high blood pressure and cholesterol. And second one, Potential cardiovascular disease markers – CliPro™ based analysis: Introduction Quantitative analysis of proteins in body fluids for disease diagnosis has attained significant clinical relevance as it could reflect the pathophysiological state of the organism. Despi...

Workforce shortages are a growing problem in the biotech industry. Communities are concerned that a lack of trained workers will either keep companies away or cause companies to move. If companies do have to move, it's likely those jobs might be lost forever, never to return. According to Robert Reich, former U.S. secretary of labor, now a professor at UC-Berkeley, biotech companies that can't hire in the U.S. will recruit foreign workers or open research centers overseas. The reason for concern is that biotech jobs, in general, are pretty good. They pay well and people work in a nice environment. Many people working in biotech companies also enjoy the work because they know their products can help people. If the jobs are so great, why is there a shortage of employees? First, the number of students graduating with science degrees, who are ready to enter the workforce, is too small. A 2005 NSF study (cited by the Seattle PI) found that the number of students graduating with sc...

23andMe, a privately-held personal genetics company, and The Parkinson's Institute and Clinical Center ( “ Parkinson ’ s Institute ” ) today announced a research initiative under which Parkinson ’ s Institute patients, with financial support from The Michael J. Fox Foundation, will enroll in the 23andMe Personal Genome Service ™ to support the development of advanced methods for clinical and epidemiologic research for Parkinson ’ s disease. The new research initiative is designed to improve current methods of collecting information for Parkinson ’ s research by leveraging the internet to dramatically expand the involvement of Parkinson ’ s patients in clinical research and increase the frequency and quality of patient data collection. Specifically: Together, 23andMe and the Parkinson ’ s Institute will design and validate web-based clinical assessment tools ...

It is true that the DNA has become vernacular now, blogging previously on the Genome entering the drawing rooms in Dawn of the GATTACA era! found another cute, small and interesting article which relates to this interesting fact on how common a word is the "DNA" now When you care enough to send the very best DNA . After reading it i felt in days to come, well we might have MATTEL come out with a "Francis Crick DNA code-breaker toy" fighting and saving the world and a "Craig Venter" toy challenging him...

Life Sciences is the next big thing to IT and that is happening to India now, Ranbaxy to develop anti-infective drugs for Merck... India's Ranbaxy Laboratories Ltd. (Ranbaxy) is to develop new anti-infective drugs for Merck & Co Inc, (Merck) in a major deal underlining the growing use of Indian pharmaceutical research by multinational Companies. Ranbaxy and Merck announced today that they have signed a strategic Product Development Agreement (the “Agreement”) providing for a drug discovery and clinical development collaboration for new products, in the anti-infective field. Potential Payments Totaling More than $100 Million . Ranbaxy and Merck will work together to develop clinically validated anti-bacterial and anti-fungal drug candidates. Ranbaxy will carry-out drug discovery and clinical development through Phase IIa clinical trials, with Merck conducting development and commercialization of drug candidates thereafter. The Indian group will get an undisclosed upfront su...

Previously blogging on the how protein interactions play significant roles in various aspects of the structural and functional organization of the cell, and their elucidation sheds light on the molecular mechanisms of biological processes. Researchers Find that a Small Molecule Can Activate an Important Cancer Suppressor Gene . Here is another study where researchers have provided the first global analysis of human proteins interacting with viral proteins and proteins in other pathogens. The scientists examined experimental data for 190 different pathogens that comprise 10,477 interactions between human and pathogen proteins. This approach provides a highly detailed network map of human proteins interfacing with proteins in different pathogens. The network of interactions reveals possible key intervention points for the future development of therapeutics against infectious diseases. "Infectious diseases result in millions of deaths each year. Although much effort has been directed...

The platypus ( Ornithorhynchus anatinus ) is endemic to Australia and one of nature's oddest creatures, seemingly assembled from the spare parts of other animals. The semi-aquatic monotreme is a venomous, duck-billed mammal that lays eggs, nurses its young and occupies a lonely twig at the end of a sparse branch of the vertebrate evolutionary tree. The ancient, patchworked platypus is a relatively unchanged animal that may be a scientific boon for researchers, who are learning a lot from its recently decoded genome about mammalian gene regulation and immune systems, which could have huge implications for human disease susceptibility research. Professor Jenny Graves, at Australian National University (ANU), Canberra explains the findings, in an interview with Anna Buckley from BBC World Service's Science in Action programme . This mix-and-match animal is more than just an oddity, though. Researchers report in Nature that its genome provides important clues into how mammals, bird...

Natural Selection, Inc. is a very interesting find that i came across after reading through a publication in Oxford journals. This company has unique expertise in computational intelligence applied to bioinformatics problems. Led by Dr. Gary Fogel. The bioinformatics team there has developed a suite of computational tools for small molecule lead discovery and optimization. Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key...

Integrative Visual Analysis Tool for Biological Networks and Pathways Already blogging on the topic Structured Digital Abstracts - Easier Literature Searching dicussing the inportance of networks in the form of interactions, and further in several others about visualization tools, here is one more. The essence of a living cell is adaptation to a changing environment, and a central goal of modern cell biology is to understand adaptive change under normal and pathological conditions. Because the number of components is large, and processes and conditions are many, visual tools are useful in providing an overview of relations that would otherwise be far more difficult to assimilate. Historically, representations were static pictures, with genes and proteins represented as nodes, and known or inferred correlations between them (links) represented by various kinds of lines. The modern challenge is to capture functional hierarchies and adaptation to environmental change, and to di...

The Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. Show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Provide a comparison with related approaches and some hints for future extensions. Do you want to know more?

“For example, the presence of a specific protein in the blood or in any body fluid might indicate a specific infection. Once an association between a biomarker and a disease is clearly established, the one can be used to signal the other, and to a high degree of certainty. As well, changes in the prevalence of a biomarker in the organism can immediately and reliably signpost a patient’s response to treatment” Some pharmaceutical companies are already advancing their research and harnessing the power of biomarkers, which can: Be used to detect the predisposition for disease in a population, screen for its presence, confirm its diagnosis, assess its severity, predict its response to available therapies and measure its clinical course Be used as targets to discover new drugs Be a decisive factor in determining whether or not to continue research on an entity Show early in the development phase whether an entity could lead to side effects that should terminate further research Help to mak...

HCL founder and chairman and chief strategy officer of HCL Technologies Shiv Nadar was named for the Padma Bhushan honour . Here is yet an interesting and inspiring story of another Shiva, to those aspiring a career in informatics as well as all aspiring entrepreneurs. In the 26 years since he first arrived at MIT as a freshman, V.A. Shiva Ayyadurai has earned four MIT degrees and started two multimillion dollar companies. This fall, he will use his most recent degree, a Ph.D. in computational systems biology, and a Fulbright Scholarship to explore one of his lifelong interests: the intersection of Eastern and Western medicine. Ayyadurai started dreaming as a child in India, where his grandfather was a farmer and his grandmother a shaman, or traditional healer. He became interested in medicine watching his grandmother diagnose and treat patients based on a system of "elements"--earth, water, fire, metal and wood. That approach may seem strange to Westerners, but "you...

Already blogging about vital information that can be obtained form publications and scientific literature Smart tools to track, analyze and visualize research and the importance of Protein structure information in Protein structure databases with new web services for structural biology and biomedical research . Now one of the tactics used by influenza virus to take over the machinery of infected cells has been laid bare by structural biologists at the European Molecular Biology Laboratory ( EMBL ) and the joint Unit of Virus Host-Cell Interaction of EMBL, the University Joseph Fourier and National Centre for Scientific Research (CNRS), in Grenoble, France. The high-resolution image of the influenza virus' PB2 protein shows how the virus steals a 'cap' molecule from its host to take over the protein production machinery and multiply. PB2 binds the cap by sandwiching it between aromatic amino acids. "Viruses are masters of cunning when it comes to hijacking the normal f...

An “ecosystem” of partners who will use programmable hardware to create a standardized approach for analyzing data from second-generation sequencing instruments. Intel Seeks Partners to Develop FPGA-Based Solution for Next-Gen Sequencing Analysis . “Primary data analysis seems to be where Intel can play the most useful role” in the field, considering the initial analytical steps in sequencing: image processing, base calling, and alignment and assembly. One downside to this scenario, however, is that these codes would need to be written for FPGA-based systems – a very specialized programming skill that many bioinformatics developers don’t have. This challenge could present an opportunity for companies that develop FPGA-based algorithms and software-development toolkits. While the task of harvesting data from second-generation sequencing instruments has only just begun, both large and small labs are already facing some big choices over how to store the terabytes of data that these tools...