A new strain of virus named after Washington University

A new strain of virus has been identified by the medical school and named the “WU” virus after Washington University.

The virus, a type known as a polyomavirus, is closely related to two others, JC and BK, which attack the nervous system of HIV patients and cause kidney transplants to fail, respectively.

The virus has been reported in such geographically disparate countries as the United States, Australia, Germany and Korea, according to Gardner.

In fact, the first samples of the then-unknown WU virus came from the University of Queensland in Australia.

The samples were sent to the University because the school has ViroChip, a sophisticated pan-viral DNA microarray. This tool allows scientists to quickly screen viral samples and compare their structure to more than 22,000 known viruses. It was instrumental in distinguishing SARS from known viruses during the 2003 outbreak

David Wang, a University professor who leads the research team, states that the WU virus has unique properties unlike either of the others and he questions if it even is a human pathogen.

The scientific article is published at PLOS Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections

Transposon insertion site profiling chip (TIP-chip)

Transposon insertion site profiling chip (TIP-chip) was invented by Researchers at the Johns Hopkins’ High Throughput Biology Center. Tip-chip can be used to help identify otherwise elusive disease-causing mutations in the 97 percent of the genome long believed to be “junk.”

TIP-chip (transposable element insertion point) can locate in the genome where so-called jumping genes have landed and disrupted normal gene function. This chip is described n the Proceedings of the National Academy of Sciences. the article titled Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposon insertion site profiling chip (TIP-chip

The most commonly used gene chips are glass slides that have arrayed on them neat grids of tiny dots containing small sequences of only hand-selected non-junk DNA. TIP-chips contains all DNA sequences. Because each chip can hold thousands of these dots – even a whole genome’s worth of information – scientists in the future may be able to rapidly and efficiently identify, by comparing a DNA sample from a patient with the DNA on the chip, exactly where mutations lie.

Jef Boeke, Ph.D., Sc.D, professor of molecular biology and genetics and director of the HiT (High Throughput Biology Center), who spearheaded both studies at the Institute of Basic Biomedical Sciences at Hopkins, and his team have focused particularly on transposable elements, segments of DNA that hop around from chromosome to chromosome.

These elements can, depending on where they land, wrongly turn on or off nearby genes, interrupt a gene by lodging in the middle of it, or cause chromosomes to break. Transposable elements long have been suspected of playing a role vital to disease-causing mutations in people. Boeke hopes that the TIP-chip eventually can be used to look for such mutations in people.

The new TIP-chip contains evenly sized fragments of the yeast genome arrayed in dots left to right in the same order as they appear on the chromosome. Boeke’s team used the one-celled yeast genome as starting material because, unlike the human genome, which contains hundreds of thousands of transposable elements of which perhaps a few hundred are actively moving around, the yeast genome contains only a few dozen copies.

Like a word-find puzzle, where words are hidden in a jumbled grid of letters, the TIP-chip highlights exactly where along the DNA sequence these elements have landed. By chopping up the DNA, amplifying the DNA next to the transposable elements and then applying these amplified copies to the TIP chip, the researchers were able to map more than 94 percent of the transposable elements to their exact chromosome locations.

double-tiled DNA chip 

Standard chips contain one layer of DNA dots that read from left to right, like the across section of a crossword puzzle. Boeke’s new double-capacity chips hold two layers of dots, a bottom layer that reads across and a top layer that reads down, again using the crossword analogy. So if their experiment lights up a horizontal row of dots, the researchers learn that the data maps to the region of the genome contained in the bottom layer; likewise, if the experiment highlights a vertical row, the data correspond to the top layer.

Says Boeke, “It’s so easy to differentiate the top and bottom layers. Next we’re going to try adding another layer reading diagonally” to triple the amount of genomic information packed onto the tiny chips.

Authors of the TIP-chip and double-tiled DNA chip papers are Sarah Wheelan, a new faculty member in the Department of Oncology, Lisa Scheifele, Francisco Martinez-Murillo, Rafael Irizarry and Boeke, all of Hopkins.

Microsoft acquires health-care software company

Microsoft has acquired the assets of Global Care Solutions Ltd., a health-care software company in Bangkok, Thailand

Global Care Solutions comprises a fully integrated hospital information system and Radiology RIS/PACS complete with image archiving, patient and bed management, laboratory, pharmacy, radiology, pathology, financial accounting, materials management and HR systems

Affymetrix and Illumina in war path again as fresh patent litigation on microarray patents

Illumina and Affymetrix have been in a patent battle since 2004. In its second wave of patent infringement litigation cas against illumina filed in UK, Germany and US, Affymetrix has targeted technology offered by Solexa, the company acquired by Illumina in January 2007, as well as all of Illumina’s BeadArray(TM) products.

The new case is for patents 5,902,723, 6,403,320, 6,420,169, 6,576,42, 7,056,666, 0834575, 0853679, 0799897

Affymetrix previously sued Illumina for patent infringement in 2004 in the United States District Court for the District of Delaware. In March 2007, the jury returned a verdict in favor of Affymetrix.

Affymetrix has developed one of the industry’s strongest patent portfolios, featuring more than 400 patents granted in the U.S. and more than 40 patents granted in Europe.

More details on the case is available at Affymetrix Investor Website

Things have improved for Affymetrix this year, The company has aposted Q3 profits with the company’s revenues for the quarter increasing 12 per cent to $94.9m compared with $84.7m during the same period last year.

The results of these lawsuits could dramatically change the face of the DNA microarray market that has seen such growth due to the application of genetic information to drug discovery and ‘personalised medicine’.

 

free web-based LIMS (Laboratory Information Management) System and ELN for Science Research

Your Lab Data is a free web-based LIMS (Laboratory Information Management System), aimed at a typical small molecular biology laboratory. It allows users to manage their chemicals, fridges, freezers, boxes, strains, plasmids or glycerol’s, oligos / primers and much more.

Register

Vote now for the Best Places to Work as a Postdoc

Your thoughts about your workplace will help us rank the best postdoc institutions around the world

Participate in the survey the the- scientist Magazine – Vote Now

Medicine OnDemand

Move over the TeleMedicine and the usual chutzpah, Yesd Web2.0 is a bubble thats going to burst, but in healthcare field strangled by Insurannce companies, web2.0 is giving a whiff of relief to some people atleast , How!

 WebMD ,MayoClinic ,eMedTV are few site that offers to help you through videos, blogs and other channels

Officials at the Department of Health and Human Services have linked the Health records to the WebMD site, With companies like google and Microsoft coming into the same field it might bring some changes in the way we see medicla treatment in the next 5-10 years, that after the inital euphoria subsides and companies starts to build comercially viable services.
                                                                                         

Final week to register for 2007 Emerging Technology Awards

Final week to register for 2007 Emerging Technology Awards

Join the Silicon Valley/San Jose Business Journal as we honor the companies on the forefront of technology and celebrate those who are leading the way in innovation and entrepreneurship at the 2007 Emerging Technology Awards.

Reserve your spot now! Registration deadline is Friday, October 26, 2007. To register please click the registration link below or email sjevents@bizjournals.com. For more information, call 408-299-1871.

Individual tickets $95 or purchase Premium VIP tickets for 10 with reserved priority seating and company signage at the row for $950.

Winners will be announced in the following categories:

  • 1. Biotechnology
  • 2. Collaboration
  • 3. Entertainment
  • 4. Green/Clean Technology
  • 5. Medical Devices
  • 6. Mobile Technology
  • 7. Resource Management
  • 8. Search
  • 9. Security
  • 10. Social Networking
  • 11. Internet Telephony
  • 12. Wireless & Networking
  • 13. Judge’s Award 
  • 14. And a special Vision Award for individual venture capitalists who have championed emerging technology.

Registration & Wine Reception 5:30pm
Awards Ceremony 6:00-7:00pm
Networking Reception with heavy hors d’oeuvres, wine and dessert 7:00-8:00pm.

Event Sponsors:

When? Thursday, November 1, 2007, 17:30:00
Where? Computer History Museum 1401 N. Shoreline Blvd., Mountain View, CA 94043
Click here to register online

Online Drug Discovery Database Launch

Assay Depot is claiming to become an on-demand” drug discovery services. The company is has launched Internet marketplace for the pharmaceutical services industry. By acting as a single point of contact between drug researchers and research service providers, the Assay Depot dramatically improves the efficiency of drug discovery research and, ultimately, helps deliver better and safer drugs to market. By bringing the true benefits of outsourcing to the pharmaceutical industry

The San Diego company has raised $ 1.8M of funding from private finanical firms. CEO Kevin Lustig has also been the Co-Founder and Research Direcotr at Kalypsys

Microsoft Research, HIV, SPAM – MS anti-spam techniques help research HIV vaccines

Ever heard of the Teiresias algorithm, for spam detection developed by Chung-Kwei at IBM – the algorithm was developed in the bioinformatics group of IBM to detect patterns in DNA

This algorithm is tested for SPAM detection- discussed in my  my earlier bioinformatics post

So you may be wodering whats thats got to do with this post, OK I am coming to it- 

Microsoft is helping  David Heckerman a Physician with a PhD in computers with spam-blocking team at Microsoft Research, to find drugs for HIV, by learning from how Anti SPAM softwares works

An e-mail featuring “Viagra,” for example, was a good bet to be spam–but things got complicated in a hurry.

if spammers saw that “Viagra” messages were getting zapped, they switched to V1agra, or Vi agra. It was almost as if spam, like a living thing, were mutating

This parallel between spam and biology got the attention of David Heckerman

Bill Gates, the company chairman “got really excited,” Heckerman says. Well versed on HIV from his philanthropy work, Gates lined up Heckerman with AIDS researchers at Massachusetts General Hospital, the University of Washington, and elsewhere.

Since then, the 50-year-old Heckerman and two colleagues have created their own biology niche at Microsoft, where they build HIV-detecting software. These are research tools to spot infected cells and correlate the viral mutations with the individual’s genetic profile. Heckerman’s team runs mountains of data through enormous clusters of 320 computers, operating in parallel. Thanks to smarter algorithms and more powerful machines, they’re sifting through the data 480 times faster than a year ago. In June, the team released its first batch of tools for free on the Internet.

watch the video to learn more about the work

Affymetrix launches Affymetrix University an education effort

Affymetrix  launched Affymetrix University, a series of courses that will be held throughout Europe and North America.

from Affy website

Santa Clara-based Affymetrix  said the courses give biologists a better understanding of how to design their microarray experiments successfully with appropriate quality control, and how to apply statistical methods to interpret biological results more effectively.

for more details check the Affymetrix website  

Twine is released in Web2.0 summit – the web3.0 application funded by Microsoft founder

Radar Networks announced an invitation-only beta test of its new “semantic web” application, Twine. Today, at the Web 2.0 Summit,

Twine provides a smarter way for people to leverage and contribute to the combined brainpower of their relationships. “We call this ‘knowledge networking,'” said Radar Networks Founder and CEO Nova Spivack. “It’s the next evolution of collective intelligence on the Web. Unlike social networking and community tools, Twine is not just about who you know, it’s about what you know. Twine is the ultimate tool for gathering and sharing knowledge on the Web.

Mr. Spivack, who previously founded Earthweb, funded in part by Paul Allen, the co founder of Microsoft

Microsoft Research, Indian Institute of Science Collaborate

Microsoft Research announced a sponsored research and collaboration agreement with the Indian Institute of Science (IISc) in Bangalore, India, to accelerate the scientific discovery process by increasing computational power in scientific and engineering research. This is the first agreement Microsoft Research has signed in India as part of a global effort to collaborate with leading institutions around advanced computing for science and engineering. Under this agreement, Microsoft Research has committed to providing funding and research expertise to assist with major projects around life sciences research and advanced high-performance computing platforms based on Microsoft Windows Compute Cluster Server 2003 for scientific applications, such as modeling of the Indian Ocean in the coming two to three years.

Professor Nagasuma Chandra, on the faculty of the Bioinformatics Centre at IISc, will be the principal investigator collaborating with Microsoft Research India for the biological data mapping project. The goal of the project is to create research tools for integration of various biological data, leading to greater understanding of biological systems as well as facilitating ready applications in many stages of drug and vaccine discovery.

Prof. R. Govindarajan of Supercomputer Education and Research Centre at IISc will lead the second project on high-performance applications using commodity clusters.

Gene Logic sells in genomics division

It hardly a week I have wrote about acquisition and mergers , it seems the rain is noit going to stop any time soon, the latest one , to give away the home plate is Genelogic agreeing to sell its genomics division to India HQ Ocimum Biosolutions subject to the authorization of the transaction at a special meeting of shareholders of Gene Logic.

This is a transforming event of significant strategic proportion,” said Charles L. Dimmler, III, President and Chief Executive Officer of Gene Logic.

Genelogic bought its preclinical division from TherImmune, a Gaithersburg company, in April 2003 for $51 million which was sold to Bridge Pharmaceuticals for $15 Million,

Gene Logic Inc said it agreed to sell its Genomics assets to Ocimum Biosolutions Ltd for $10 million in cash. Under the terms of the Ocimum sale agreement, Gene Logic retains full rights in perpetuity to utilize the existing information data bases of its former Genomics business as key elements in building its emerging drug repositioning and development business. Furthermore, the Company will retain specified assets related to molecular diagnostics and will continue to explore strategic alternatives for these assets

The sale is part of the Genelogic new strategy to focus on to build drug repositioning and development business which was decided last year.

Ocium will assume certain liabilities associated with the Genomics assets and business and will pay Gene Logic $7 million at closing and $3 million payable in a promissory note due 18 months from closing.

The purchase includes Gene Logic’s Knowledge Products business including the The BioExpress® System a continually growing genomic database of gene expression data and associated clinical information from over 18,000 human and animal tissues and cell line samples. ToxExpress® a toxicogenomics reference database.

Ocimum will continue to operate the business out of the current state-of-the-art laboratory facility of Gene Logic in Gaithersburg, Maryland.

Mergers Acquisitions Consolidation-Microarray Industry bubble in making- The days are numbered

Bioinformatics promise has already had its brush with plenty of resistance, not it seems the time for microarray industry with consolidation and acqusitions and megers announced almost every week. The slow adoption and too many fragmented with disparate standards has made the industry a victim of its own success.

the new kid on the block to unload its microarray and genomics business include Nanogen with its plans to unload its loss making microarray business, While the most of the biotech IPO featured in the market in the last 6 month in US have failed to generate expected results.

But pharmaceutical firms are racing to buy up biotech firms Roche has acquired 454 Life science,and Nimblegen and now Bristol-Myers Squibb is buying Adnexus Therapeutics for $430 million. Wyeth has bought Haptogen Ltd, which emerged from Aberdeen University five years ago, pharmaceutical firm Wyeth is the fourth largest biotechnology company in the world. PerkinElmer is planning to buy the cord blood banking firm Viacell Inc

On the the report of Bradstreet Israel warning on Sunday that majority of Israel’s publicly-traded biotechnology companies will be forced to halt their research and development activities in as little as two-and-a-half years if they do not alter their business strategies immediately, research company Dun & In many cases, biotech companies are not doing sales, but only conducting research programs,” said Reuven Kuvent, director-general of D&B Israel. “They don’t focus enough on raising capital or attracting investor things they must do if they intend to continue to be operational over the next few years.”

While Asian genomics and biotech companies like Biocon which recently sold its enzu=yem business to NovoZyme and Strand Genomics which was selected as TECHNOLOGY PIONEERS 2007 by World Ecconomic Forum and smaller startups like Ocimum Biosolutions which are now pumping vast amount of funds into acquiring genomics business across US and Europe are waiting inthe wings to take off . Still there are others racing to create the cheapest microarray and sequencing methods only time will tell theeir fate,

Oracle Openworld 2007- Personalized Genomics session

Its the time -Personalized Genomics

Advances in genetic information and laboratory technologies mean new ways to diagnose disease and determine patient risk. The wealth of genetic information makes it harder to provide meaningful information. During Oracle OpenWorld 2007 Oracle is presenting how laboratory information systems principles and Oracle customer relationship management and enterprise resource planning applications weave together, using Oracle Fusion Middleware to create a unique platform for translational medicine.


Click here to register now.

Oracle OpenWorld

Experience Innovation. November 11-15, 2007, San Francisco, Moscone Center.

As the Life Sciences industry continues to grow and change, Oracle is there to help you learn, adapt, and succeed.

Please join us this fall in San Francisco as we address some of the biggest challenges facing the Life Sciences industry and how Oracle is prepared to meet those challenges.

Session highlights include:

  • Product Lifecycle Management—At this session, learn how Oracle’s Agile product lifecycle management solutions for Life Sciences improve new product introduction cycle times, reduce direct material and operating costs, and enable cost-effective compliance.
  • A Cure for Clinical Trials: From Data Capture to Submission—Approximately 80,000 clinical trials are being conducted in the United States at any given time. More than half of them are behind schedule by one to six months. Clinical trial sponsors hope to reduce this and other costly delays through the use of IT. Hear how the latest enhancements in Oracle’s industry-leading Life Sciences applications are streamlining the process of data capture, management, analysis, and reporting.
  • Enabling Personalized Medicine in Research and Development—The sequencing of the human genome is yielding exciting new tools to help physicians tailor treatments to individuals and their diseases. This powerful new capability, called personalized medicine, holds great potential to improve patient health. Learn how Oracle’s technology is enabling personalized medicine and improving efficiencies and outcomes in clinical development.

Click here for a full list of Life Sciences sessions.

Registration is now open for the most exciting technology and business conference of the year.
Registration fees go up soon So don’t wait—act now to save $900.

Click here to register now. To receive your special discount, select a registration category and enter keyword: ORF at the bottom of step 2 of the registration process.

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Copyright © 2007, Oracle Corporation and/or its affiliates. All rights reserved.  

Microsoft launches Personal Healthcare Intiative -conversation with Peter Neupert VP of Microsoft’s Health Solutions Group about HealthVault

After Google announced the personal genomics and healthcare library intitaitves it is now the turn of Microsoft offering free personal health records on the Web

Microsoft announced HealthVault, an online platform where personal electronic health records can be stored.

The company’s consumer health offering includes a personal health record, as well as Internet search tailored for health queries, under the name Microsoft HealthVault www.healthvault.com

The organizations that have signed up for HealthVault projects with Microsoft include the American Heart Association, Johnson & Johnson LifeScan, NewYork-Presbyterian Hospital, the Mayo Clinic and MedStar Health,

Take a look at the  conversation with Peter Neupert VP of Microsoft’s Health Solutions Group about HealthVault  from the Channel9 MSDN

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