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Pioneering Study Analyzes Community Proteome

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University of California Berkeley researchers have used mass spectrometry and bioinformatics techniques to study the proteome of an entire community of microorganisms for the first time.

The researchers, led by Rachna Ram, a postdoctoral scientist, and Jillian Banfield, a professor in the department of environmental science, policy and management at UC Berkeley, say they decided to study the proteins within all the organisms collected from an acid mine drainage environment, rather than study the proteomes of individual organisms, because data from a multi-organism community collected from its natural environment is more representative of what is happening in nature than individual organisms cultured in laboratories.

The research, which is believed to be the first of its kind, potentially adds broader significance to the proteomic community because it paves the road for the proteomes of other types of communities to be studied as well.

“It makes sense, because in the microbial ecology world you should be thinking about how microorganisms interact with each other in mixed communities in nature,” says Ram, the lead author of a paper describing the study, which appeared in the June 24 issue of Science. “If you study each individual organism, you might be missing some of the picture by taking them out of the context of where they were in nature.”

The research stemmed from a genomic study also done by Banfield’s research group on the same acid mine drainage community, located at a Superfund site outside Redding in northern California. By matching protein sequences with genomic sequences from the earlier study, Ram and her colleagues were able not only to look at proteins within the whole community, but also to separate out which proteins came from which organisms.

— Tien-Shun Lee

Cellzome expanded a proteomics-based collaboration with Novartis that the companies initially formed last September. Novartis has made a “substantial equity investment” in Cellzome and will also contribute an undisclosed amount of research funding for two years with the option of extending the collaboration for a further two years.

 

Caprion Pharmaceuticals joined up with Boehringer Ingelheim to track down metabolic and inflammatory disease biomarkers. If all goes as planned, Caprion will identify pharmacodynamic markers in plasma resulting from the administration of pre-clinical pharmaceutical compounds.

 

Kirkegaard and Perry Laboratories won exclusive rights to market protein immunodetection products based on Expression Pathology’s Liquid Tissue technology in the life-science research market. The products will allow customers to create reverse-phase arrays and dot blots and to characterize and validate protein biomarkers.

 

Agilix granted Protana a non-exclusive license to its protein labeling technology.

 

The Max Planck Institute brought in protein crystallization automation technology from Formulatrix for its department of biophysical chemistry.

 

In a collaboration with Imperial College, Prolexys Pharmaceuticals will create a comprehensive protein-protein interaction map of Mycobacterium tuberculosis.

 

 

PATENT WATCH

US Patent 6,921,642. Protein expression profiling. Inventors: Stephen Kingsmore; Girish Nallur; Barry Schweitzer. Assignee: Qiagen. Issued: July 26, 2005.

This patent covers “methods for detecting small quantities of analytes such as proteins and peptides,” according to the abstract. “Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized.” The method relies on amplified DNA to provide a signal for those proteins.

 

US Patent 6,914,239. System for analyzing mass spectrometric data. Inventors: Kiyomi Yoshinari; Kinya Kobayashi; Atsushi Otake; Toyoharu Okumoto. Issued: July 5, 2005.

“The system analyzes one of the structure of precursor ion at each stage of dissociation and the structure of parent ion based on the characteristics and spectrometric data,” according to the abstract. The patent also covers “an analytical means for providing characteristics of a candidate for estimated structure of a precursor ion that is representative of pre-dissociation structure at each stage of dissociation.”

 

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By percentage, stake that Quest Diagnostics has purchased in Ciphergen Biosystems as part of a strategic alliance to develop and commercialize proteomic diagnostic tests based on Ciphergen’s SELDI ProteinChip technology. The news drove Ciphergen shares up nearly 15 percent.

 

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