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BIOARRAY BRIEFS: Jun 14, 2002

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Motorola to Release BioDiscovery Hybrid Microarray Software

While recent reports have indicated that Motorola Life Sciences is up for sale, the company is plowing ahead with the introduction of a new software package for its CodeLink high-density microarray system. The package integrates BioDiscovery’s ImaGene software package with Motorola’s in-house microarray software, said Motorola Life Sciences product manager Nancy Schmelkin.

This integration is the product of a partnership that Motorola Life Sciences announced last week with BioDiscovery.

Motorola chose to go with BioDiscovery as a data analysis partner because of certain “functionalities” on BioDiscovery’s software, including their automated grid system. “Overall we thought they had a very strong approach in pieces of the system that allow you to look at one particular spot on a microarray and really analyze it,” Schmelkin said.

Currently, a full system site license to the program for an entire organization costs $45,000. The system will be available July 1.

Motorola researchers have meanwhile published a proof-of-principle paper for their CodeLink sample prep system in the June issue of Genome Research, “A Highly Reproducible, Linear, and Automated Sample Preparation Method for DNA Microarrays.” (Vol. 12, Issue 6, 976-984.)

 

Phylos Teams With Upstate to Develop Protein Chip

Protein chip maker Phylos of Lexington, Mass., has joined forces with Upstate, of Waltham, Mass. and Charlottesville, Va., to develop binding proteins for a new protein chip, Phylos said last week.

Under the arrangement, Upstate will market the chip, and Phylos will receive research funding and milestone payments and royalties, if applicable. Upstate develops drug discovery reagents, kits, and services based on cell signaling. It sells kits for kinase activity screening and for Luminex’s detection system.

Phylos’ ProFusion technology, which links proteins to encoded mRNA, is designed to enable amplification of this complex to a detectable level, according to the company. The company is applying ProFusion as a means to find specific and strong binding molecules for target proteins on chips.

 

X-Mine License Gene Expression Analysis System to Mass General

Bioinformatics startup X-Mine of Brisbane, Calif., said last week it has licensed the X-Miner gene expression analysis system to the Massachusetts General Hospital Cancer Center.

“X-Miner will identify the signature genes that will be used as the indicator of exposure of cells, animals or human beings, to specific environmental estrogens,” said Toshi Shioda, director of the of hospital’s DNA core facility, in a statement. Researchers at MGH will use the software to analyze data from Affymetrix microarrays.

X-Miner is a genomic analysis system that includes clustering algorithms, supervised machine learning programs, and also uses its “reporter” engine to mine biological literature and genome databases in order to find biologically meaningful relationships.

 

Luminex Tags Tecan for Sample Prep System Project

Luminex has secured a collaboration with Swiss biotech instrument maker Tecan to develop and co-market an integrated sample preparation and assay system, the companies said last week.

The system, which will use Luminex’s xMAP bead array technology and Tecan’s bio-robotic liquid handling instruments and sample preparation systems, is expected to be available beginning in the end of 2002. At that point, the partners will co-market this system in a nonexclusive arrangement.

Luminex’ xMAP system uses microsphere-based assays with fluorescent tags and small lasers to perform up to 100 assays simultaneously on a drop of fluid. It can be used as a medium- and high-throughput assay for pharmaceutical, diagnostics, and research applications.

 

Lets Talk Standards: EBI to Hold Conference in November

The European Bioinformatics Institute is holding a Standards and Ontologies for Functional Genomics conference at Hinxton, in the UK, from November 17 to 20, 2002.

The goal of the conference “is to bring together scientists who are developing standards and ontologies for describing microarray and other high throughput functional genomics experiments,” according to the organizers. Keynote speakers include Ken Buetow from the US National Cancer Institute, Win Hide from the South African Bioinformatics Institute, and Peter Karp from SRI International. For more information, go to the website for the conference http://www.ebi.ac.uk/microarray/General/Events/SOFG/SOFG.html.

 

TIGR on the Hunt for Array Analysis Abstracts

If you have a cluster of thoughts on microarray data analysis to share, the Institute for Genomic Research wants to hear from you. TIGR, which is organizing the 14th Annual Genome Sequencing and Analysis conference to be held in Boston from the 2nd to the 5th of October, is looking for abstracts on the subject of microarray data analysis, to be submitted by July 1. A poster session on this subject “will examine some of the data mining techniques that have been developed for exploring the relationships revealed by expression data and explore the requirements for developing common data archival and interchange formats,” a TIGR solicitation said. The symposium on microarray analysis will take place Thursday, October 3rd, from 9:30 AM to 12:30 PM. For additional information, go to http://www.tigr.org/conf/gsac/.

 

Nanogen Installs System at US CDC for Pathogen Detection

Nanogen is installing a NanoChip workstation at the US Centers for Disease Control, the company said last week. The CDC will use the system for work on detection of diarrheal Escherichia coli and other pathogens.

The system, which uses individually addressable probes and electrochemical detection of hybridization, will be placed at the CDC’s Foodborne and Diarrheal Diseases Branch in Atlanta. Under a “development site agreement,” CDC researchers will have preferential access to Nanogen technology as they develop assays for particular strains of pathogenic bacteria.

Nanogen will receive licensing and commercialization rights to these assays, and may use this research to develop other diagnostic tests.

 

Trial Date Set in Ciphergen vs. LumiCyte Lawsuit

The judge in the civil suit between Ciphergen and LumiCyte has set a trial date for January 21, 2003, according to a clerk for the California State Superior court for Santa Clara County, where the case is being heard.

The suit, originally filed by Ciphergen in July 2000, concerns the right to SELDI (Surface Enhanced Laser Desorption/Ionization) protein biomarker chip technology. Ciphergen has also sued LumiCyte founder William Hutchens, a founder and former board member of Ciphergen, for breach of fiduciary duty, alleging that he misappropriated trade secrets.

Meanwhile, the parties are proceeding with discovery in the case. A settlement conference is scheduled for January 15, if the suit is not settled before then.

Neither party chose to comment on the case.

 

Better in Birmingham: DermArray Maker Integriderm Moves On

Specialized microarray startup IntegriDerm is moving to a Birmingham, Ala., incubator for biotech startups that is affiliated with the University of Alabama at Birmingham. The company had to move out of space at the Research Genetics facility of Invitrogen, where it was housed originally. Invitrogen closed the facility at the end of April and laid off 175 employees.

IntegriDerm makes the nylon DermArray, which includes 4,400 skin disease-related genes, and the Pharm -Array drug target microarray. The company also received a National Institutes of Health SBIR grant last fall to develop a specialized gastrointestinal array.

 

The Incredible Shrinking Microarray Described in Science

While the state-of-the-art in feature size is orders of magnitude smaller than microarrays from a few years ago, researchers have just published a technique that could shrink feature size so much it would make Moore’s law seem pessimistic.

The technique, which a team from Northwestern University’s Institute for Nanotechnology described in the June 7 issue of Science, could be used to create oligonucleotide arrays up to 100,000 times as dense as the current industry standard, the researchers said.

In this method, the researchers used an atomic force microscope to directly transfer oligonucleotides onto both gold and silicon oxide surfaces. The researchers called this technique “direct-write dip-pen nanolithography.” By coating the microscope tip with a solution to make it positively charged and hydrophilic, they were able to have precise control over the flow of oligonucleotides.

The technique allowed the team to create truly tiny spots — roughly 50 nanometers — of DNA. Spotting at this resolution could permit as many as 100,000 oligo spots to fit on a chip as small as 100 x 100 micrometers.

“Effectively we can take a normal spot within an Affymetrix-type chip and put an entire gene chip within the area occupied by one of those spots,” Chad Mirkin, who directs Northwestern’s Nanotechnology Institute, told BioArray’s sister publication GenomeWeb. “There are a variety of benefits — you’d be working with smaller sample sizes, volumes, and smaller absolute amounts of targets.”

With this technique, the atomic force microscope is also used to read signals. “When you make spots so small, it turns out that when those spots react with targets all the physical parameters of the spot change — the height, the stickiness, the shape,” said Mirkin. “It can be read out fairly quickly with an ordinary scanning probe microscope.”

NanoInk, a Northwestern spinoff that Mirkin founded earlier this spring, is commercializing the technology. The company plans to introduce software that will allow users to adapt atomic force microscopes to make their own arrays.

 

AVIVA Partners With Axon Instruments

Cellular screening biochip startup Aviva Biosciences of San Diego has formed a collaboration with Axon Instruments.

Under the partnership, Axon has agreed to made an equity investment in Aviva and has provided ongoing support for the co-development program of Aviva''s biochips. Axon also will obtain an exclusive technology license agreement to the design and fabrication of these biochips, and will become the exclusive supplier of Axon''s biochip-based ion channel measurement systems.

The companies said the systems will become available in late 2002.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.