CoMet software predicts components affecting cancer

Jeffrey Skolnick, in collaboration with John McDonald, led a team from the Georgia Institute of Technology who have developed this new strategy. As Skolnick explains, “This opens up the possibility of novel therapeutics for cancer and develops our understanding of why such metabolites work. CoMet provides a deeper understanding of the molecular mechanisms of cancer”.

The small molecules that are naturally produced in cells are called metabolites. Enzymes, the biological catalysts that produce and consume these metabolites are created according to a cell’s genetic blueprints. Importantly, however, the metabolites can also affect the expression of genes. According to the authors “By comparing the gene expression levels of cancer cells relative to normal cells and converting that information into the enzymes that produce metabolites, CoMet predicts metabolites that have lower concentrations in cancer relative to normal cells”.

The research proves that by adding such putatively depleted metabolites to cancer
cells, they exhibit anticancer properties. In this case, growth of leukemia cells was slowed by all nine of the metabolites suggested by CoMet. The future for this treatment looks bright, in McDonald’s words, “While we have only performed cell proliferation assays, it is reasonable to speculate that some metabolites may also exhibit many other anticancer properties. These could be important steps on the road to a cure”.

Source: http://www.molecular-cancer.com
Web: http://www.metabolomics.net/

Agilent debuts new scanner 
The  new instrument, which Agilent claims has better resolution and dynamic range than older models, also coincides with new scanner launches from a variety companies, including Tecan, Innopsys, and MDS Analytical Technologies.
 
Agilent’s impending 1million-feature microarrays will most likely become available by the end of the year. Agilent currently sells arrays with up to 244,000 features per slide.The  decided to launch the new scanner ahead of the new arrays in order to give customers time to integrate the system into their existing workflows, and so that they are prepared to handle new chips when they hit the market.
 
“Based on the chips that are on the market today, you don’t really need the new scanner,” according to Jeffrey McMillan, the firm’s workflow product manager “But people are getting themselves prepared for what will happen a few months down the road. Our users would like to get the scanner installed and qualified before they begin running the new generation of arrays, because it would be hard to qualify all of those things at the same time.”
 
The scanner is designed to deliver data from Agilent’s current generation of 65-micron feature arrays, as well as output from the 30-micron features of the impending million-feature arrays. The tool enables users to scan images with resolutions of 10, 5, 3, and 2 microns. Agilent’s previous scanner had 5-micron level resolution capabilities. The new instrument is an open system that enables customers to scan both Agilent and non-Agilent arrays and works with a pre-existing 48-slide carousel.
 
McMillan points out that because Agilent offers arrays in multipack formats with up to eight individual arrays printed per slide, users hypothetically can scan 384 different arrays at a time using the new scanner.
 
The company has chosen to focus on its system’s resolution and workflow over its throughput. The new scanner uses SureScan high-resolution technology, which Agilent describes as a combination of the system’s autofocus and high-resolution scanning capabilities plus its internally developed feature-extraction software.
 
“We don’t just concern ourselves with producing a nice looking image,” said McMillan. “It is about creating that quality image and applying some intelligent image analysis that takes advantage of everything you know about the array. Since we manufacture our arrays, we know our arrays best.”
 
McMillan said that the dynamic range of image scans is better than previous versions of the scanner. “We have a feature that ... gives you two scans at two different detector gains and incorporates that into a result file,” he said. “With high gain and low gain, you can get entire dynamic range, and .. don’t have to worry about scanner range. You can get a 20-bit scan in a single scan.”
 
Agilent has two ways to deliver the new scanner to customers that have older versions installed. Where available, customers can request an infield upgrade in which an Agilent service technician visits their lab, breaks down the old scanner, and rebuilds it to include the new scanner capabilities. The second option is to ship the system to an Agilent repair center for the upgrade.
 
According to McMillan, list price for the upgrade is around $38,000. Customers who wish to purchase the new scanner pay $149,500. The package includes two licenses of image-analysis software that run on Windows 32-bit or 64-bit systems. McMillan added that customers can save 10% of the scanner price if they purchase the equivalent value of that discount in Agilent arrays.

 Software
Because Agilent customers typically use different software depending on the application, as comparative genomic hybridization software for CGH experiments and GeneSpring for gene expression work, McMillan says the company will integrate these packages with the feature-extraction software in coming months in anticipation of the next-generation array launch.
 
“If our software knows what the array design is, it can process the arrays more efficiently without asking the user to do anything,” McMillan explained. “For instance, there might be canned analysis for expression work that we can do without the user doing any work. It will all be as seamless as possible. That is how we position ourselves against our competitors.”

Source: http://www.bioarraynews.com/issues/8_24/features/147466-1.html
Web: http://www.agilent.com/