/i> Optimization; Microarray Analysis: It's a GAAS!

GADGET WATCH | Ultrafast Gel Loading Courtesy of Andre Marziali Technicians at the British Columbia Genome Sequence Centre in Vancouver spend hours loading agarose gels for high-throughput, bacterial artificial chromosome fingerprinting. Such repetition cries out for automation, and Andre Marziali, platform director for technology development at GenomeBC, was asked to design a fix. His solution--a "capillary comb loader"--can apply an entire microplate-worth of samples in one shot, reducing gel-loading time from about 10 minutes per gel to two (BioTechniques, 34:814-8, April 2003). In a typical day, the center's staff manually loads 20 to 30 gels, each containing 242 lanes--that's about 5,000 to 7,000 samples--using 8- or 12-channel pipettes. The process is laborious, error-prone, and can potentially induce repetitive stress injuries. Marziali set out to design a loader that was inexpensive, easy to use, compatible with standard gel combs, and that could measure a specified sample volume. The loader contains an array of fixed-length capillaries configured to match the well-to-well spacing of a microtiter plate on one side and of the gel on the other. Sample volume (currently 1.5 µl per lane) is invariant, a function of capillary length. Samples are aspirated pneumatically using a squeeze bulb and ejected into the wells by the hydrostatic pressure created by a column of buffer. The approach eliminates air bubbles in the wells. According to Marziali, the University of British Columbia has filed a provisional patent on this device and is in negotiations to license it. He adds that he would be willing to produce copies for other labs interested in testing it. --Jeffrey M. Perkel PATENT WATCH | Multiplexed TaqMan, sans Optimization The TaqMan® (fluorogenic 5' nuclease) technique is a real-time quantitative PCR method that detects amplification by release of a reporter fluorescent signal from a sequence-specific probe. When running multiple reactions in one tube, it's usually necessary to determine limiting primer concentrations for each assay. However, Royston, UK-based Pharmagene (www.pharmagene.com) was recently awarded a patent1 for a method of quantifying two target genes in a simultaneous PCR reaction using different fluorescent reporter signals, thereby "negating the need for lengthy assay optimization protocols," Pharmagene product specialist Jae Carey told The Scientist. "The method allows assays to detect two transcripts simultaneously to be run under standard conditions irrespective of the relative abundance of the targets in the starting material." Pharmagene is now using the method for a number of applications, including mRNA expression profiling in human tissue, to understand the gene expression changes underlying drug interactions and to quantify physiological responses to clinical treatments. The company has not granted any licenses on the technology, but would give appropriate consideration to any who apply, Carey says. --Ivan Oransky 1. J. Carey, "Quantitative analysis of gene expression using PCR," US patent 6,551,783, issued April 22, 2003. SOFTWARE WATCH | Microarray Analysis: It's a GAAS! Courtesy of Marco Masseroli A team of Italian programmers and molecular oncologists has released a free microarray data management and analysis package for Microsoft Windows, called GAAS (www.medinfopoli.polimi.it/GAAS). The suite allows users to transform disparate microarray data formats into a unified structure, process multiple experimental replicates, and apply statistical preprocessing and analysis algorithms. "The main problem is trying to clean the data from noise and values that are not really true," explains lead programmer Marco Masseroli, Politecnico di Milano, Italy. The team's goal, he says, was to present researchers with a clean view of their data that would enable them to identify "useful information from the biological point of view." GAAS consists of two programs. Users can import Microsoft Excel or ASCII data--the output from a slide scanner, for instance--into the Assembler program, which transforms the data for storage in a Microsoft Access database. They can then process that data with the Analyzer software and view it in either tabular (histogram) or graphical (scatter plot) form. They can also output the data for further analysis using external tools, such as Michael Eisen's popular Cluster and TreeView applications (rana.lbl.gov). Each user can personalize import, export, viewing, and analysis configurations. GAAS is specifically designed for cDNA microarray and macroarray data and can be configured to support oligonucleotide arrays. Masseroli says his team is working on new data loading and management features and analysis algorithms. The GAAS Web site includes sample data sets, a tutorial, and a user's guide. --Jeffrey M. Perkel function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (document.frm.score[1].checked) result = true; if (document.frm.score[2].checked) result = true; if (document.frm.score[3].checked) result = true; if (document.frm.score[4].checked) result = true; if (!result) alert("Please select") return result; } sans Optimization; Microarray Analysis: It's a GAAS!"> .myradio{background-color : #94bee5} Please indicate on a 1 - 5 scale how strongly you would recommend this article to your colleagues? Not recommended 1 2 3 4 5 Highly recommended Please register your vote

/i> Optimization; Microarray Analysis: It's a GAAS!

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