Bio Saga Headlines

Bio Saga

Thursday, May 29, 2008

"Biotechnology? Oh, you need a Ph.D. to do that!"

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 of person who's in demand. When the biotech companies say there's a workforce shortage, they mean that there's a shortage of skilled technicians, particularly in a production environment. It's a bit funny and maybe a bit sad, that when reporters say that there's a shortage of scientists, some people interpret this as a shortage of Ph.D. level investigators. In industry, the word "scientist" has a broader meaning. In academics, you're only considered a scientist if you have a Ph.D., in industry, you're a scientist if science is what you're doing. Technicians with 2 year community college degrees (and sometimes a 4 year degree, too) are the people who are in demand.

"Biotechnology? Oh, you need a Ph.D. to do that!"

Still, the misconception that you need a Ph.D. to work in a scientific field might be a problem. If the general public views science as an occupation for the elite, students might be reluctant to take science courses. In biotech, nothing could be further from the truth. Some of the most successful graduates from biotech program are students who had done poorly in their large lecture weed-them-out chemistry-type courses, but had a good grounding in common sense and an ability to work with their hands. The need of the hour is to bridge the gap between the industry requirement and the knowledge that such biotech & lifescience school have to offer. The key question is, How can we educate the trained workforce that companies need?


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Wednesday, May 21, 2008

Novel Enzyme Inhibitor Paves Way for New Cancer Drug: Agent Proves Effective Against Melanoma Cells

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 senior author of the study.

PI3Ks are a family of lipid kinases – enzymes that transfer a phosphate group to an important signaling molecule in the cell called a lipid. They play a key role in a wide range of cellular functions, including cell growth, proliferation, differentiation, motility, survival and intracellular trafficking. Lipid kinases also drive cell division by modifying fatty acid molecules and directing cells to grow, change shape and move.


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Scientists characterize protein structure of environmentally friendly bacteria

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.

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De Novo Sequencing of Nonribosomal Peptides

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?

Tuesday, May 20, 2008

A brief history of the platypus!

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 widely available.

  • Platypus biology at the Australian Platypus Conservancy

Monday, May 19, 2008

A to Z list of bioinfomatics companies

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
www.biodiscovery.com
www.bioforensics.com
www.biognostik.com
www.bioinformaticist.biz
www.bioinformatics.co.uk
www.bioinformatics.csiro.au
www.bioinformaticsservices.com
www.bioinformaticssolutions.com
www.bioinformatik.de
www.bioit-il.com
www.biolateral.com.au
www.biomax.com
www.biomax.de
www.biomedcomp.com
www.biomind.com
www.bioplanet.com
www.biosentients.com
www.biosiris.com
www.biosis.org
www.biosoft.com
www.biosoftsolutions.de
www.biosolve.de
www.biospec.com
www.biotiquesystems.com
www.biotools.com
www.biowell.com.tw
www.biowisdom.com
www.bioxtal.com
www.bluespeed.net
www.bmi-heidelberg.com
www.caesar.de
www.caesarsoftware.com
www.cambridgeantibody.com
www.cambridgebluegnome.com
www.cbssci.com
www.celera.com
www.cellectis.com
www.centagenetix.com
www.ceuticalsoft.com
www.cgen.com
www.changbioscience.com
www.chemcomp.com
www.chemgenes.com
www.cimsoft.com
www.clcbio.com
www.clearlinetech.com
www.clonaid.com
www.clondiag.com
www.cmrsinc.com
www.cognia.com
www.colnow.com
www.compass.com.ph
www.compassgenomics.com
www.compudrug.com
www.compugen.co.il
www.concurrentpharma.com
www.corelims.com
www.corimbia.com
www.correlogic.com
www.cresset-bmd.com
www.crti.com
www.cybergene.se
www.cybgen.com
www.d-trends.com
www.davissequencing.com
www.decode.com
www.decodon.com
www.definiens.com
www.deltagen.com
www.deosystems.com
www.designergenesinc.com
www.discoverypartners.com
www.dna-software.com
www.dna.com
www.dnastar.com
www.dnatools.com
www.doubletwist.com
www.duii.com
www.dxsgenotyping.com
www.dynacom.co.jp
www.e-proteomics.net
www.egenetics.com
www.eidogen.com
www.elitra.com
www.elixirpharm.com
www.employstrat.com
www.entelos.com
www.epigenomics.com
www.epistasis.org
www.epitope-informatics.com
www.eragen.com
www.esearchinternational.net
www.essentialinformatics.com
www.etexxbio.com
www.evprecruit.com
www.expasy.ch
www.eyesopen.com
www.familytreedna.com
www.fqspl.com.pl
www.fractalgenomics.com
www.functional-genetics.com
www.gemini-genomics.com
www.genStruct.com
www.genaissance.com
www.genamics.com
www.gene-alliance.com
www.gene-biotech.com
www.gene-chips.com
www.gene-it.com
www.gene-quantification.de
www.gene2drug.com
www.geneart.com
www.genebio.com
www.geneco.com
www.genecodes.com
www.genedata.com
www.geneformatics.com
www.genego.com
www.genelink.com
www.genelogic.com
www.genemachines.com
www.genepilot.com
www.genesearch.com.au
www.genesifter.net
www.genestudio.com
www.genesynthesis.org
www.genetargeting.com
www.genetherapysystems.com
www.genetic-id-services.com
www.geneticXchange.com
www.geneticxchange.com
www.genetix.com
www.genfit.com
www.genmatrix.com
www.genodyssee.com
www.genologics.com
www.genolyze.com
www.genomatica.com
www.genomatix.com
www.genomatix.de
www.genometrician.com
www.genomica.com
www.genomicdiscoverytools.com
www.genomicsinc.com
www.genomicsolutions.com
www.genomictechnologies.com
www.genomining.com
www.genomix.com
www.genops.com
www.genoptix.com
www.genset.fr
www.gentech.fr
www.geospiza.com
www.glycominds.com
www.gnsbiotech.com
www.goldenhelix.com
www.gtc-bio.com
www.helixinfosystems.com
www.hessjobs.com
www.hippron.com
www.hybridon.com www.ibiomatics.com
www.idrtech.com
www.idtdna.com
www.illumina.com
www.imagingresearch.com
www.imaxia.com
www.imphasis.com
www.incellico.com
www.incogen.com
www.incyte.com
www.informagen.com
www.informaxinc.com
www.inforsense.com
www.ingenovis.com
www.ingenuity.com
www.innaphase.com
www.innomedical.com
www.inpharmatica.co.uk
www.inpharmatica.com
www.inpharmix.com
www.insightful.com
www.insilico-biotechnology.com
www.insilico.com
www.insilicolabs.com
www.insilicos.com
www.interactiva.de
www.intronn.com
www.inveniobio.com
www.invitrogen.com
www.io-informatics.com
www.iobion.com
www.iper1.com
www.it-omics.com
www.iuvita.com
www.jaexecutivesearch.com
www.jubilantbiosys.com
www.katonahgroup.com
www.kennatechnologies.com
www.kerberholtdevol.com
www.kinematik.com
www.knowledge.com
www.koada.com
www.kooprime.com
www.labbook.com
www.labdb.com
www.lablogic.com
www.labonweb.com
www.labvantage.com
www.lambdaplus.com
www.lazaron.com
www.lifesciencesworld.com
www.lionbioscience.com
www.lloydstaffing.com
www.lsbio.com
www.ludesi.com
www.lynxgen.com
www.macrogen.com
www.mag.com
www.mantik.de
www.markergene.com
www.mastl.com
www.mathecology.com
www.matrixscience.com
www.mdli.com
www.medbioworld.com
www.medicel.com
www.medigenomix.de
www.mendelbio.com
www.meta-helix.com
www.metabolic-explorer.com
www.metalife.de
www.metaphorics.com
www.microdiscovery.de
www.microrite.com
www.midilabs.com
www.miraibio.com
www.mirusbio.com
www.mol-net.de
www.molecularconnections.com
www.molecularmed.com
www.molecularmining.com
www.molecularware.com
www.molmine.com
www.molsoft.com
www.mpi-softtech.com
www.mri-boston.com
www.mutransposon.org
www.mutransposon.orgwww.worksinc.com
www.myriad.com
www.nadii.com
www.neomorphic.com
www.netgenics.com
www.netid.com
www.newportsearch.com
www.nonlinear.com
www.nuvelo.com
www.ocimumbio.com
www.od260.com
www.ogs.com
www.oligos.com
www.omnigon.com
www.omniviz.com
www.ontrackpro.com
www.origenel.com
www.ozgene.com
www.packardbiochip.com
www.pangenex.com
www.paracel.com
www.partek.com
www.peoplesgenetics.com
www.petagen.com
www.ppl-therapeutics.com
www.predictivepatterns.com
www.premierbiosoft.com
www.primegenbiotech.com
www.proceryon.com
www.proconverse.com
www.progeny2000.com
www.proglab.se
www.prolume.com
www.prosanos.com
www.proteinmechanics.com
www.proteom.com
www.proteomeconsult.com
www.proteomes.co.kr
www.pubgene.com
www.puretechventures.com
www.q-pharm.com
www.qgene.com
www.quantiom.de
www.rabbithutch.com
www.receptorscience.com
www.redasoft.com
www.redstormscientific.com
www.reeltwo.com
www.relevantsoftware.com
www.rescentris.com
www.rii.com
www.rosettabio.com
www.sas.com
www.savingsandclone.com
www.science-factory.com
www.scinovaindia.com
www.scitechint.com
www.scitegic.com
www.sdc.co.jp
www.searchfirm.com
www.seascapelearning.com
www.seattlegenetics.com
www.semantxls.com
www.seqbio.com
www.sequenom.com
www.sequiturinc.com
www.seqwright.com
www.sgi.com
www.sgxpharma.com
www.sigenetics.com
www.silicoinsights.com
www.silicongenetics.com
www.simulations-plus.com
www.softberry.com
www.softgenetics.com
www.soonersci.com
www.spotfire.com
www.spsoft.com
www.spss.com
www.sratemecula.com
www.stafftopia.com
www.starbridgesystems.com
www.stewartgroup.net
www.strandgenomics.com
www.strubix.com
www.sunflaremarketing.com
www.synamatix.com
www.syngene.com
www.syngentabiotech.com
www.teranode.com
www.textco.com
www.the-genetics.com
www.tib-molbiol.com
www.timelogic.com
www.tmdg.com
www.transgene.fr
www.transgenic-software.com
www.tripos.com
www.turbogenomics.com
www.ubi.ca
www.valentis.com
www.vglab.com
www.vialogy.com
www.virtualchemistry.com
www.visgen.com
www.visipoint.fi
www.visualizeinc.com
www.vizxlabs.com
www.wabansoftware.com
www.webgenetics.com
www.wireworkswest.com
www.wita-proteomics.com
www.x-mine.com
www.xenogen.com
www.xpogen.com

Friday, May 16, 2008

Biomarkers Predict Heart Deaths

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. Despite the wide concentration ranges and limitations of certain analytical techniques, the utility of the plasma proteome as a principle diagnostic material for biomarker analysis is on the rise (Anderson et al., 2002; Anderson et al., 2004; Adkins et al., 2002). Cardiovascular disease (CVD) is one of the leading causes of death, though preventable. Understanding of pathophysiological components and their role in diagnosis and timely prediction could become vital in this largely preventable disease. Analyzing the plasma proteome using CliPro™ has helped us to identify and validate potential biomarker-CVD disease association.

Using literature-mining efforts, we have systematically compiled a list of plasma proteins that contains concentration values reflecting alterations between normal versus various disease states. Using CliPro™, we found significant differences in the levels of some of the plasma proteins, influenced by genetics, sex, age, physiological state and various factors. Of the many protein candidates, we have prioritized a list of around 180 clinically significant plasma proteins of different types with their concentration ranges reflecting a clear-cut CVD association. By analyzing the concentration values of the plasma proteins in disease versus normal conditions, we find that more than 50% of the proteins clearly serve as biomarkers, which will enable to measure the presence/ progress of a disease or the effect of therapeutic intervention in the treatment of a disease.

Do you want to know more?


Thursday, May 15, 2008

Workforce shortages are a growing problem in the US biotech industry, may be boon to India and China

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 science and engineering degrees isn't increasing at the same rate as the number of jobs. In fact, the numbers are still about the same as they were a decade ago, with only 12 percent of college graduates entering science and engineering fields.

Do you want to know more?

23andMe and The Parkinson’s Institute Announce Initiative to Advance Parkinson’s Disease Research

23andMe, a privately-held personal genetics company, and The Parkinson's Institute and Clinical Center (Parkinsons Institute) today announced a research initiative under which Parkinsons 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 Parkinsons disease.

The new research initiative is designed to improve current methods of collecting information for Parkinsons research by leveraging the internet to dramatically expand the involvement of Parkinsons patients in clinical research and increase the frequency and quality of patient data collection. Specifically:

  • Together, 23andMe and the Parkinsons Institute will design and validate web-based clinical assessment tools that can be administered to online communities.
  • 23andMe will establish a social networking platform to facilitate the development of communities and research projects based on common traits of Parkinsons disease patients.
  • All participating Parkinsons Institute patients will be enrolled in the 23andMe Personal Genome Service and will provide a saliva sample for a comprehensive genome scan generating more than 580,000 data points per patient.
  • Parkinsons Institute patients will provide specific information and insights that will include their individual environmental exposures, family history, disease progression and treatment response.
  • Patients risk factor and clinical data collected through the newly developed and validated web-based tools will then be merged with their genetic data to conduct research on Parkinsons disease.
  • New surveys will be developed and administered to the growing cohort of patients, generating new risk factor and clinical data for comparison with the existing genetic data.
  • Through the deployment of an innovative approach to clinical research information gathering utilizing web-based tools, the initiative will help to expand the involvement of Parkinsons disease patients in clinical research and increase the frequency and uniformity of patient data collection.

Tuesday, May 13, 2008

DNA is clearly in the public consciousness

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...

Ranbaxy Laboratories Signs Drug Discovery Development Pact With Merck & Co., Inc.

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 sum and could receive more than $100 million for each drug target, depending on successful development and regulatory approval. It will also be entitled to royalties under the five-year deal.

Monday, May 12, 2008

Human-pathogen Protein Interactions Illuminated With Bioinformatics

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 towards the study of how infection by a pathogen causes disease in humans. We have to leverage the opportunity to compare protein interactions between human and pathogen proteins, from 190 different pathogens to provide important insights into the strategies used by pathogens to infect human cells."

"Previous studies have suggested that protein interaction networks have topologies that are resilient to attacks on random nodes but are susceptible to targeted attacks, for example on hubs. Our results provide a striking example of how pathogens may have evolved the ability to exploit the structure of interactions between human proteins in order to promote infection. This global study also suggests that many viruses share similar strategies to control the human cell cycle, regulate programmed cell death, and transport viral genetic material across the nuclear membrane in the human cell." said one of the investigators

The researchers paid particular attention to two networks of human proteins -- proteins that interact with at least two viral pathogens and proteins that interact with at least two bacterial pathogens. Gene Ontology (GO) terms computed for both sets of proteins provided key information on the functions of the different proteins. Some of the striking findings of the study included a clear demonstration that pathogens preferentially interact with two classes of human proteins referred to as hubs and bottlenecks. Hubs are popular proteins that interact with many other proteins in the human protein interaction network.

Bottlenecks are proteins that lie on many of the shortest paths in the network. Pathogens appear to maximize their likelihood of success by targeting these high-impact, influential proteins during infection. In many cases, human proteins that mediate pathogen effects are proteins that are known to be involved in cancer pathways, for example, the transcription factor STAT1 or the tumor suppressor protein TP53. This finding suggests interesting parallels between pathogen infection and cancer and opens up future areas for research.

Also read

Friday, May 9, 2008

What's Our Connection to the Platypus?

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, birds and reptiles evolved from a common ancestor some 315 million years ago. And researchers at Stanford University School of Medicine report in Genome Research that they linked the evolution of a gene in the old platypus to a mutated version in humans responsible for moving the testes outside of the body and into an external pouch, or scrotum.

An international team of researchers that sequenced and analyzed the genome of a wild female platypus named Glennie, which lives in southeastern Australia. Among its findings: The platypus' genome is two thirds the size of the human genome and contains 18,500 genes. (The human genome comprises 20,000 to 25,000 genes.) Eighty-two percent of the animal's genes are found in other mammals. The genome is organized into 52 chromosomes (tightly packed structures of DNA stored in a cell's nucleus), 10 of which determine the animal's sex. (In humans, there are 46 chromosomes—23 pairs—and only two (X and Y) are sex-determining.)

Genome analysis of the platypus reveals unique signatures of evolution


Thursday, May 8, 2008

Computational intelligence approaches for pattern discovery in biological systems

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 component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics.

Do you want to know more?


VisANT: an integrative framework for networks in systems biology

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 discover pathways and processes embedded in known data, but not currently recognizable. Among the tools being developed to meet this challenge is VisANT (freely available at http://visant.bu.edu) which integrates, mines and displays hierarchical information. Challenges to integrating modeling (discrete or continuous) and simulation capabilities into such visual mining software are briefly discussed.

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The Beta Workbench: a computational tool to study the dynamics of biological systems

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?

Wednesday, May 7, 2008

Biomarkers to Open the Door to Personalized Medicine and Represents a Seismic Shift for the Pharma Industry

“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 make clinical trials more efficient
  • Reduce treatment overheads by optimizing dosages and measuring a patient’s response more quickly and accurately
Molecular Connections Private Ltd. Bangalore India has announced the launch of its new Knowledgebase of Clinically Significant Proteins - CliPro.
  • Knowledgebase, is a result of manually mining thousands of papers, on proteins present in various human body fluids , with their known concentration values and biomarker information as available in literature
  • Platform to analyze protein biomarker- disease associations
  • Catalogue of clinically significant proteins in biofluids such as plasma, cerum, CSF, synovial fluid, saliva, urine, peritonial fluid, bal fluid, amniotic fluid, tears
  • includes >1000 clinically significant proteins – with ~2000 different disease/pathological correlations
  • Biomarkers with disease associations are broadly either diagnostic, prognostic, predictive or efficacy markers
Also read A price tag of around US$1 billion to map human proteome

Tuesday, May 6, 2008

East meets West, yet another story of an successful Indian entrepreneur

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'd see people actually getting healed," he says.

In 2004, Ayyadurai returned to MIT, this time to work on a Ph.D. in systems biology, a relatively new field that integrates biology, engineering and computer science. The goal of systems biology is to figure out how the layers of a biological system, from genes to cells to organs to the whole body, are linked.

Systems biologists start by figuring out how individual cellular pathways work, but deciphering just one pathway can take years. To speed up that process, Ayyadurai developed a computer model that can integrate the activities of all the different pathways in a cell--work that formed the basis of his doctoral thesis. Shiva not only provided the basic system called Cytosolve, but he used it to create a new composite model of the upregulation of interferon following viral infection.

Now, he wants to explore what Eastern and Western medical traditions can learn from each other. Ayyadurai sees the exchange as a two-way street: He plans to apply Western scientific rigor to testing the long-established traditions of the East, and to study how the Eastern "elements" can inform Western medicine.

He points out that the market for alternative therapies based on Eastern medicine is growing every year, even without scientific evidence to support their usefulness.

"Let's look at glucosamine and see if it really works. Let's look at ginkgo and see if it really works," he says.

Ayyadurai departs for India this month to begin his studies, and he also plans to start raising funds to launch an MIT-affiliated center to study Eastern medicine.

"Viruses are masters of cunning" - Imaging Of Influenza Virus Protein Opens Way To Design New Anti-viral Drugs

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 functioning of the host cell. The influenza virus steals a password from host messenger RNAs, molecules that carry the instructions for protein production, and uses it to gain access to the cell's protein-making machinery for its own purposes," says Cusack.

In the current issue of Nature Structural and Molecular Biology they publish a high-resolution image of a key protein domain whose function is to allow the virus to multiply by hijacking the host cell protein production machinery. The findings open the way for the design of new drugs to combat future influenza pandemics.

FPGA-based systems – a very specialized programming skill that many bioinformatics developers don’t have

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 generate. Facing a Tangle of Tape, Scientists Seek New Options for Storing Sequencing Data. Fact that next-gen sequencing vendors have concentrated on engineering their instruments, but may have not spent the same degree of effort thinking about where the data will go.

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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