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IBM, ISB, Caltech, Third Wave, Agilent Technologies, ExonHit, Danish Team, Sionex

IBM, ISB Lead Effort to Start Public Grid-Computing Protein-Folding Project

The Institute for Systems Biology, IBM, United Devices, and the University of Washington have embarked on a public grid-computing project to predict the three-dimensional structure of proteins, ISB said this week.

The project, called Human Proteome Folding Project, will be the first to run on World Community Grid, an effort started by IBM and others to leverage unused computing time of participants for a variety of projects. IBM has donated hardware, software, technical services, and expertise to build the infrastructure and will host and maintain it. United Devices, a grid solutions company, plans to integrate computing power from participating PCs into its worldwide grid.

In the proteome folding project, computers will attempt to fold a single protein of unknown shape, trying millions of shapes and returning the best ones to the central server. “This database of protein structure and possible functions will let us take those next steps in understanding how diseases that involve these proteins work,” said ISB scientist Rich Bonneau in a statement.

The project is similar in concept to Google Compute, a collaboration by the Internet search engine company with [email protected], a non-profit research project of Stanford University. The Google Compute application utilizes idle processing cycles on personal computers to process mathematical problem from such fields as drug design and global climate modeling.

Another popular application of distributed computing is the [email protected] project, which applies distributed computing to the search for extraterrestrial intelligence.

Systems Biology at Caltech Will Benefit From New $25.4M Nanotechnology Grant

Caltech said last week that a portion of a recently awarded $25.4 million grant will help fund systems biology research.

The grant, awarded by the Gordon and Betty Moore Foundation, will enable Caltech faculty to create “new nanoscale technologies to aid the emerging field commonly referred to as systems biology,” the school said in a statement.

Caltech defines systems biology as a methodology that uses, among other components, “specific gene expression as well as ... proteins expressed by genes. In many cases, systems biology depends on advances in genomics, which in turn is based upon large-scale assays of biological activity at much smaller scales.

“Nanobiotechnology promises to provide new means for such studies, ultimately at the level of individual cells and molecules,” Caltech said.

Caltech said it will use the money for “architectural modification and creation of new laboratories, professional and administrative staff, facilities operations and service contracts, state-of-the-art research equipment, and a networking/communication program to link Caltech researchers with their peers worldwide.”

The Gordon and Betty Moore Foundation focuses on “environmental conservation, science, higher education, and the San Francisco Bay Area,” the school said. The gift is part of a $300 million commitment the foundation made to Caltech in 2001.

Third Wave to Trade as Part of Nasdaq Biotech Index

Third Wave has been added the Nasdaq Biotechnology Index as part of the exchange’s semi-annual listing update, the exchange said last week.

According to the exchange, all securities being added to the Index will be phased into Nasdaq’s Opening Cross on Nov. 16.

A total of 11 companies were added to the index and two were removed during the Nasdaq’s update.

Securities currently in the Index must meet the maintenance criteria of $100 million in market capitalization and 50,000 shares average daily trading volume, according to the Nasdaq.

With Third Wave, 143 companies trade as part of the Biotech Index. Among them are the life sciences tools companies Accelrys, Affymetrix, Caliper Life Sciences, Ciphergen Biosystems, DeCode Genetics, Gene Logic, Harvard Bioscience, Illumina, Invitrogen, Orchid Biosciences, and Qiagen.

“Index securities not meeting the maintenance criteria are retained in the Index provided that such security met the maintenance criteria in the previous semi-annual ranking,” the exchange said on its web site. “Securities not meeting the maintenance criteria for two consecutive rankings are removed.”

Changes occur after the close of trading on the third Friday in May and November using March and September closing price and volume data and April and October publicly available total share outstanding data, the Nasdaq said.

Agilent and ExonHit Partner to Develop Microarray for Splice Variants

Agilent Technologies will combine its microarray platform with ExonHit’s alternative RNA splicing in an attempt to develop an array technology that can monitor the expression of splice variants, the companies said.

The companies presented results from an experimental splicing array of G-protein coupled receptors, which was designed by ExonHit and produced by Agilent, at the Splicing 2004 meeting, held in September in Bethesda, Md.

That array was able to detect multiple isoforms of several genes, and “showed good reproducibility and specificity,” the companies said in a statement today. Agilent and ExonHit “are expected to work with early test sites to generate additional experimental results,” the firms said.

Financial terms of the agreement were not disclosed.

Danish Team Hopes to Use Genomic, Proteomic Tools to Make Food Tastier (Really)

Four Danish firms have presented a plan to their government to apply genomics and proteomics techniques to give a better understanding of the interactions between food molecules and humans, which may lead to the design of safer and better-tasting foods.

Per Falholt, a member of the steering committee behind the strategy and an official with Novozyme, said he hopes that plan can get at least 5 million Danish krone ($869,813) in funding for the next five years.

Sionex Joins Boston Integrative Medicine Group

Sionex, a developer of chemical and biological sensor chips and systems, has joined the Center for Integration of Medicine and Innovative Technology.

The center aligns Boston scientists, engineers, and clinicians to develop new technologies with an emphasis on minimially invasive diagnostics and therapy. CIMIT has a center at Harvard Medical School composed of experts from Massachusetts General Hospital, Brigham and Women’s Hospital, the Massachusetts Institute of Technology, among others.

Waltham, Mass.-based Sionex has developed microDMX detection sensors.


The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.