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February 19, 2009 | Another Harvard Research Star Changes Constellations
Arizona State University's Biodesign Institute has landed a Harvard Medical School scientist – Joshua LaBaer - to launch a cutting-edge research lab that aims to pursue more accurate ways to diagnose and treat diseases such as breast cancer and diabetes, according to a report in The Arizona Republic.

Joshua LaBaer, a Phoenix native who now serves as director of Harvard Medical School's Institute of Proteomics, will relocate his lab to the Biodesign Institute as director of the new Virginia G. Piper Center for Personalized Diagnostics, according a report in The Arizona Republic. Recently, D. Gary Gilliland left Harvard to lead Merck’s cancer research. The report quotes LaBaer, “"I get to move in a direction that would have been hard to do at a place as rich and crowded as Harvard," LaBaer said. "One thing that is appealing about Arizona is that it is relatively new in this particular biomedical space, and people have not really built these institutional silos here." Read article.

Millipore Uses GeneGo Data in New Pathway Tool
Millipore licensed 250 manually curated pathway maps from GeneGo for use in Millipore’s new Interactive Biological Pathway Tool. Available at
 www.millipore.com/pathways, the tool links Millipore’s antibodies, proteins, and assays as well as relevant bioinformatics content to related biological pathways. These maps have been categorized by diseases and cellular processes to make it easier to find relevant information.

“This tool provides a relevant new interface to assist scientists in planning and executing their research within the context of the biological systems in which they are interested,” said Siamak Baharloo, director of eBusiness at Millipore When a researcher accesses a pathway map, they see a detailed description of the pathway and supporting literature reference.

Separately, GeneGo announced today that Becker Medical Library at Washington University in St. Louis has licensed MetaCore. The Becker Medical Library Bioinformatics@Beckerprogram is a university wide resource which provides bioinformatics support for researchers and students. MetaCore is an easy to use data mining tool that provides users with fast easy access to up to date pertinent pathway information. “Becker Medical Library at Washington University in St. Louis is an important customer for GeneGo as we build up the number of libraries using GeneGo products,” said Julie Bryant, GeneGo’s VP of business development. Read releases.

ISB Develop Automated, High Throughput Microfluidic Platform 
Researchers at the Institute for Systems Biology and the University of British Columbia report developing a new fully automated microfluidic experiment platform for conducting live-cell experimentation that enables high throughput imaging and on-chip microenvironment manipulation.

A paper describing the platform was published recently in the Proceedings of the National Academy of Sciences. "This is a very exciting advance that will have significant applications any time researchers are trying to understand how cells collect, process and respond to information about their environment,” said Tim Galitski, PhD, associate professor at the Institute for Systems Biology (ISB). "In a single run, we can preprogram on-chip dynamic changes in microenvironment and chemical stimuli for hundreds of separate experiments on live cells, gather dynamic image data reporting morphological and gene-expression responses to those changes, and make it all happen at the push of a button.” 

As proof of principle, researchers used the platform to conduct 3,000 live-cell experiments examining the response of a prototypical molecular pathway, the mating pheromone response of yeast, to genetic and environmental changes. The objective was to identify whether the pathway exhibits "memory” of previous stimulatory episodes and to identify genes that affect how long that memory lasts. The paper describing the new platform can be viewed at http://www.pnas.org/content/early/2009/02/13/0813416106.full.pdf+html.

Euro Consortium Targets Plasma Biomarker Platfrom
A consortium of European companies and universities has been awarded €3 ($3.8 million) under the European Commission's 7th Framework Program to develop a plasma biomarker discovery platform, according to a GenomeWeb report. The three-year project, called Proactive, will be coordinated by Olink Bioscience of Uppsala, Sweden. Other partners include Innova Biosciences, Copenhagen University, Fujirebio Diagnostics, Uppsala University, and Integromics.

The goal of the initiative is to develop methods and reagents for multiplexed proximity ligation assays for detecting low-abundance proteins in plasma, along with statistical methods and data-management tools. The participants plan to carry out a series of pilot biomarker projects focused on colorectal cancer detection in blood samples. The participants plan to develop a platform that can analyze 100 samples per week. The platform will be able to detect 180 putative protein biomarkers using four microliters of plasma, the participants said. Read article.

BioImagene Receives FDA Clearance for PATHIAM
BioImagene, a leading provider of digital pathology solutions, has received FDA 510(K) clearance for PATHIAM System with iScan for assessment of HER2/neu immunohistochemistry tests. The scanner and associated software are used to detect and provide a quantitative measurement of HER2/neu, a protein that is measured in breast cancer patients in order to determine if they are candidates for treatment with the breast cancer drug Herceptin.

“Many pathology workflow innovations are possible only by going digital. This clearance will help increase adoption of digital pathology and accelerate the progress toward personalized medicine,” said Ajit Singh, CEO of BioImagene, in a release. Read release.

HHMI Scientists Developed New Approach to Protein Profiling
Microarray technology, generally used to quantify protein production, can identify messenger RNA, does not measure the payoff – the actual assembly of proteins. In contrast, Jonathan Weissman’s new technology, called ribosome profiling, is more precise and reliable in identifying which proteins a cell produces in response to changing conditions. It also provides a way to measure how much of any given protein is produced.

“We recognized that ribosome profiling could provide a powerfulcomplement to microarray technology, taking the next step beyond identifying messenger RNA to measure actual protein synthesis – the ultimate payoff of gene expression,” says Weissman, who is a Howard Hughes Medical investigator at UCSF. Read article.

Drew Endy Calls for National Synthetic Biology Initiative
Stanford University bioengineering researcher Drew Endy argued the US needs a national initiative to support and encourage synthetic biologyat the American Association for the Advancement of Science meeting last. Speaking at a session on synthetic life, Endy highlighted a slew of recent developments in genetic engineering — from bacteria programmed to take photos to synthetic bacterial genomes created in a single step. Even so, Endy and others believe the field is poised to enjoy even greater success, particularly if there is sufficient investment in areas such as appropriate tools, standardization, and DNA construction.

Drawing parallels to the stone age and the technology age, Endy predicted that it will be new tools — not particular applications — that will fuel progress in genetic engineering. For instance, he said, asking what synthetic biology will produce in the future is akin to asking early computer developers about the applications of their technology. Read GenomeWeb report.

Metabolon Work on Prostrate Cancer Progression Biomarkers
Metabolon’s global biochemical profiling technology has been used to identify biomarkers indicative of prostate cancer progression, reports the company. The results of the study, conducted with researchers at the University of Michigan, were published in the February 12 issue of Nature in a paper, “Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression.”

The study described in the Nature paper was undertaken to better understand and profile the metabolic changes associated with prostate cancer progression. Using Metabolon’s biochemical profiling to generate global, non-targeted metabolic analysis of tissue, urine and plasma samples, the researchers were able to identify a series of metabolites (including sarcosine) that are key potential predictors of cancer aggressiveness. The complete publication detailing the results of this study can be accessed online at http://www.nature.com/nature/index.htmland in the February 12, 2009 print edition of Nature. Read release.

SciQuest Partrners with Ceiba
The companies say partnership will enable life sciences organizations to enhance their investment in enterprise resource planning (ERP) systems by quickly and seamlessly integrating with leading strategic procurement solutions delivered by SciQuest. Read release.

Thomson Reuters Launches Liquent PublishPerfect
Thomson Reuters introduced Liquent PublishPerfect, an enterprise publishing product that enables the efficient, integrated, and compliant publishing of reports. The seamless document management system integration provides an uninterrupted user experience from compilation to approval. "In a market where time is of the essence, Liquent PublishPerfect allows users to remain in one program instead of going between several," said Jeff Huntsman, Vice President Global Sales, Services & Software Solutions at Thomson Reuters.  "The resulting reports are generated to the PDF specification as required by regulatory authorities, saving time and money." Read release.

Organisms Are More Than the Sum of Their Genes
John Yin, a professor of chemical and biological engineering at University of Wisconsin-Madison College of Engineering, developed computer models a simple virus to show that genes alone do not make an organism. As shown in a new paper, simply shuffling the order of the five genes in the virus’s genome has a huge impact on how well the virus grows and how it interacts with its simulated host cell. The results are reported Friday, Feb. 6, in the journal PLoS Computational Biology at
 http://dx.doi.org/10.1371/journal.pcbi.1000283.

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This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription.

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