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Waters Will Add Matrix Search Engine to its Protein-ID Software

Matrix Science's Mascot interface will become part of Waters' protein informatics platform, the companies said this week.

Scientists using Waters ProteinLynx Global Server software can send queries to and display results from the Mascot search engine and the PLGS search engine in real-time, the companies said in a statement. The features are available to customers using Waters' MALDI micro MX and Q-ToF mass spectrometers, the companies added.

Matrix customers using the company's software to process mass spectrometry data will receive "enhanced support" for Waters' MassLynx data, due to the integration of its file-access libraries into Mascot Distiller, the companies said.

The companies did not disclose financial terms of the agreement.


Beckman Coulter Leases New Facility Near Los Angeles

Beckman Coulter is one of the new tenants in a newly constructed office park in southern California, according to local news reports.

The 138-acre Chino South Business Park, developed by Oltmans Construction Co. and Carson Co., comprises a 182,000-square-feet lease and a 137,000-square-foot lease.

The building that will house Beckman Coulter is located in Chino, west of Los Angeles, and is a "concrete tilt-up structure" designed by RGA Architects of Irvine, Calif., according to GlobeSt.com. Beckman is headquartered in Fullerton, located southwest of Chino.

The website quoted Matt Vanderhorst, president of the Carson Cos., as saying that Beckman Coulter leased the new facility. The size or duration of Beckman's lease was not immediately known. Calls to Beckman Coulter were not immediately returned.

When completed, the Chino South Business Park will have 2.5 million square feet of real estate, and "is designed for major distribution operations as well as companies that require extensive and sophisticated tenant improvements," the website reported. It added that Fischer Scientific is currently an occupant with a 162,000 square-foot lease.


Blueprint Initiative Spins Out New Company; Inaugural Product to Launch in May

Mount Sinai Hospital's Blueprint Initiative has spun out a new company that will soon release its first informatics product, the hospital said last week.

The company, Unleashed Informatics, was created in part with a CA$1.2 million ($970,000) grant from Sun Microsystems of Canada. Together with Blueprint it will unveil its inaugural hardware and software platform at the Bio-IT World Conference in Boston next month.

"At the same time, Blueprint's commitment to developing leading-edge, open-source standards-based, and freely available public databases like BIND remains as strong as ever," Christopher Hogue, Blueprint's principal investigator and acting CEO of Unleashed Informatics, said in a statement.


Avecia Chooses Waters' Empower Software
For Its Gas Chromatography Labs

Avecia, a Manchester, UK-based specialty chemicals company, will use Waters' Empower Software in its gas chromatography laboratories, Waters said last week.

Empower is Waters' flagship chromatography software that allows scientists to collect data and to control multiple instruments made by Waters, as well as other vendors.


Userspace to Evaluate IPFlex Processor for Proteomics Research Project

Userspace has begun an evaluation of IPFlex's DAPDNA-2, a reconfigurable processor, for use in a National Institutes of Health-sponsored proteomics research project, the companies said this week.

In October, Userspace received a two-year NIH grant worth $394,000 to research and develop instrument routers for protein processing, the companies said. Real-time tagging and data modeling of mass spectrometry data is a central theme of this project, they added.

"With protein characterization now one of the cornerstones of systems biology, real-time mass spectrometry will spearhead the understanding of disease processes. This means tagging and searching of mass spectral data in real-time," Sanjaya Joshi, co-founder and CTO of Userspace, said in a statement. "The IPFlex DAPDNA platform would be evaluated as a flow-processor for this standardization."

Tokyo-based IPFlex first launched the processor in Japan last year, and began marketing it in the US in January. Userspace is the first US customer.

Specific terms of the companies arrangement were not disclosed.


ABI Posts Weak Q3 Revenue Growth; Remains 'Concerned' About Sequencing Business

Applied Biosystems this week said that organic fiscal third-quarter revenue inched up 1 percent as sales in DNA sequencing and RT-PCR/applied genomics increased, and mass-spec and core PCR/DNA synthesis receipts declined.

Total revenues for the three months ended March 31 increased to $455 million from $440 million in the year-ago quarter. Contributing 2 percent to this increase were "favorable foreign currency affects," which gave ABI a 3-percent jump in total third-quarter revenues, the company said.

Broken down by division, ABI said year-over-year revenue from its DNA sequencing business increased 3 percent to $141 million, and receipts from RT-PCR/applied genomics swelled 20 percent to $134 million.

However, year-over-year revenue from its mass spectrometry segment declined 4 percent to $105 million, and receipts from ABI's core PCR and DNA-synthesis unit slid 1 percent to $50 million. Revenue from all other product lines fell 17 percent to $26 million.

ABI said R&D spending decreased in the third quarter to $51 million from $52 million year over year.

Net income in the period grew to $56 million, or $.28 per basic share, from $46 million, or $.23 per basic share, year over year.

Despite the strong earnings growth, CEO Tony White warned in a statement that "due to the constrained funding environment, we remain cautious." He said ABI President Cathy Burzik is "focused on new initiatives to drive long-term revenue growth."

He did not elaborate, but BioCommerce Week, ProteoMonitor's sister publication, recently reported that ABI has begun looking for additional customers for consumables, services, and software to complement its manifold instruments. ABI is looking to several components of its business, notably in its sales organization, to accomplish that task.

"We have an incredible strength in capital equipment sales," Carl Hull, vice president and general manager for ABI's RT-PCR and gene-expression business lines, told investors visiting the company's Foster City, Calif., headquarters during an April 5 junket. "Our real opportunity is to take that core competence and build a shell around it. Consumables represent a big opportunity for us and we are focused on that."

In the statement, Burzik stressed that "we remain concerned about factors that may have a negative influence on future sequencing revenue."

"While we saw in total only slight revenue growth from the prior year, we had double-digit revenue growth in the real-time PCR/applied genomics product category, driven by increased sales of our biosecurity, human identification, and TaqMan Gene Expression Assay and Low Density Array products," Burzik said. "We also saw a slight increase in DNA Sequencing revenue as a result of increased sales of low- to medium-throughput instruments.

"However, these results were largely offset by a decline in Mass Spectrometry revenue driven by lower sales of the 4000 Q TRAP LC/MS/MS System," she said. "In the prior year quarter, we filled a substantial backlog of orders for this system."

Looking ahead, ABI said revenue for fiscal 2005 will grow in the low-single-digits over fiscal 2004. The company said receipts from its RT-PCR/applied genomics and mass spectrometry segments "are expected to increase" over fiscal 2004, while revenues from DNA sequencing, core PCR and DNA synthesis, and other product lines "are expected to decline."


Waters Said Organic Q1 Revenues Grew 3 Percent; Income Up 14 Percent

Waters this week said that first-quarter revenues increased 5 percent to $268.3 million from $255.1 million year over year.

Waters said that a foreign currency translation benefit accounted for approximately 2 percent of its first-quarter revenue growth, meaning that organic growth amounted to 3 percent.

Waters spent $16.7 million on research and development during the first quarter, a slight increase over the $16.1 million spent on R&D in the same quarter last year.

The company said net income for the three months ended March 31 increased 14 to $46.6 million, or $.39 per basic share, from $40.8 million, or $.34 per basic share, in the year-ago period.

Waters said that cash and cash equivalents on hand totaled $587 million as of April 2.

On March 29, Waters revised its estimate of 2005 sales growth to between 3 and 4 percent from the 13- to 14-percent range it identified in a January conference call with investors. The company also revised its projected first-quarter per-share earnings from $.44 to between $.34 and $.37. In a statement, the firm said that the lowered earnings were the result of "weaker than expected sales growth."

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.