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SciTegic, Euroscreen, Incyte Revenues, Ultraconserved Regions of Vertebrate Genomes, Model of E. coli Regulatory Network

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SciTegic Licenses Pipeline Pilot to Euroscreen

SciTegic last week said it had licensed its Pipeline Pilot analysis workflow technology to GPCR discovery firm Euroscreen for three years.

Euroscreen will use Pipeline Pilot to automate data management for its cheminformatics and high-throughput screening efforts. The company said it also plans to use the tool to create a corporate data warehouse.

Financial terms for the licensing agreement were not provided.


Elimination of Data Business Lowers Incyte’s Q1 Costs and Revenues

Incyte last week attributed a 50 percent drop in quarterly revenues and a narrowed net loss to the elimination of its genomic information business.

The company, which closed its Palo Alto, Calif., facilities on April 2, 2004, posted $6.6 million in revenues for the quarter ended March 31, 2004, compared to revenues of $12.5 million for the same period in 2003. The company’s revenues have traditionally come from its information products, so the drop-off “reflects the company’s decision to discontinue its Palo Alto-based information products line,” Incyte said in a statement.

Incyte reported a net loss for the first quarter of $37.7 million, or $0.52 per share, compared to $55.8 million, or $0.81 per share, for the same period in 2003.

The company said it expects to eliminate up to $50 million in annual costs from the closure of the Palo Alto facility.

Quarterly R&D expenses also dropped year over year, to $26.2 million in the first quarter of 2004, compared to $30.2 million for the same period of 2003. Incyte attributed this decreased expense to cost cutting associated with the Palo-Alto-based information business, as well.

As of March 31, 2004, Incyte’s cash, cash equivalents, and marketable securities totaled $501 million, compared to $294 million as of Dec. 31, 2003.


UCSC Bioinformatics Team Uncovers ‘Ultraconserved’ Regions of Vertebrate Genomes

A team of researchers at the University of California, Santa Cruz, led by David Haussler has identified 481 segments longer than 200 bp in the human genome that are 100 percent conserved (with no insertions or deletions) in the rat and mouse genomes. In addition, “nearly all” of these segments are also conserved in the chicken and dog genomes, and two-thirds were found in the fugu genome, the researchers report in the May 6 issue of Science Express.

Only 111 of the ultraconserved elements overlap coding regions of the human genome, and in most of those cases they overlap only a short span of the coding region and extend beyond it to noncoding areas. Most of the remainder of the ultraconserved regions reside near genes involved in regulation or transcription or in introns.

“There was some speculation among biologists as to whether we would find new kinds of things when we sequenced the complete genomes of animals, including our own genome, or if it would just be more of the same kinds of things that were already known. Well, it’s not just more of the same,” Haussler said in a statement.


UCSD/Caltech Team Publishes Model of E. coli Regulatory Network

Bernhard Palsson and colleagues at the University of California San Diego and the California Institute of Technology have published the first genome-scale computational model of the gene regulatory system in Escherichia coli.

Their work, published in the May 6, 2004, issue of Nature, builds on the Palsson lab’s previous model of E. coli metabolism, published in 2000.

The UCSD model includes a network for 1,010 genes, including 104 regulatory genes, whose products together with other molecules regulate the expression of 479 of the 906 genes known to be involved in metabolism.

To build the model, the team gathered experimental data on E. coli’s response to oxygen deprivation using strains of E. coli in which genes involved in oxygen regulation were knocked out. In an iterative process, they used the in silico model to simulate and predict cellular behavior and then guide additional data-gathering experiments using microarrays. When the predicted outcomes did not match the experimental outcomes, the experimental data was used to update the model.

“We went into the experiments thinking that oxygen regulation is fairly well understood. But in one fell swoop, we identified 115 previously unknown regulatory mechanisms,” said co-author Markus Covert of Caltech. In several cases, for example, the researchers found that when a protein that transcribes a gene is active, the expression level of that gene is actually reduced. “We also identified new regulatory interactions for genes that no one previously had described,” Covert said.

UCSD said it has filed a patent on the model. Palsson’s group will continue to develop the E. coli model, and is also beginning to model the regulatory network in yeast. Meanwhile, Covert said he plans to focus on modeling signaling transduction pathways in mouse.

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