RNA Interference without the Interferon; Simplifying Dialysis and Electroelution; Microarray Analysis, TIGR-Style

PATENT WATCH | RNA Interference without the Interferon The red-hot field of RNA interference (RNAi) could benefit from patents issued jointly to Queensland, Australia-based Benitec, and the State of Queensland (US patent 6,573,099, issued June 3, 2003, and UK patent 2353282, granted May 3, 2003). The patents describe a method Benitec calls "DNA-directed RNA interference" (ddRNAi) to differentiate it from typical double-stranded small interfering RNA (siRNA). Using this method, a DNA construct is introduced into a cell, leading to the production of a double-stranded RNA that is cleaved into siRNA, which then destroys the target mRNA. "This is the first worldwide patent to be awarded ... [to a method] that applies RNAi in humans," says Benitec chairman and CEO John McKinley. Unlike traditional RNAi, McKinley says ddRNAi does not provoke an interferon response in cells. The method also can be used to reduce (instead of knocking out) gene expression, and can produce a transient rather than permanent effect. Benitec has granted Promega of Madison, Wis., rights to produce cobranded lab materials and kits based on the technology, and is discussing licensing agreements with biotechnology and pharmaceutical companies. McKinley estimates that through improved target identification and validation, ddRNAi methods can knock one to two years off traditional drug development timelines. Ellen Prediger, a spokesperson for RNA company Ambion, says the company is aware of the Benitec patent but does not wish to comment on it. --Ivan Oransky GADGET WATCH | Simplifying Dialysis and Electroelution Courtesy of GeBA Many researchers have a love-hate relationship with dialysis bags. In the love column: simplicity. A dialysis membrane's large, porous surface area efficiently removes low-molecular-weight impurities while retaining larger biopolymers. In the hate column: unwieldiness. Dialysis membranes are slippery and prone to leakage, and sample recovery is often inefficient. Israel-based Gene Bio-Application (GeBA; www.geba.org) offers a compromise: GeBAflex tubes--microcentrifuge vials containing two diametrically opposed dialysis membranes (molecular weight cutoff from 3,500 to 14,000 Da). To use, simply rehydrate, add sample, submerge in buffer, and stir. Applications include dialysis, sample concentration, and electroelution of protein and nucleic acids. To electroelute, gel slices and buffer are placed in the tube, which is immersed in a horizontal gel box such that the membranes are oriented perpendicular to the electrical field. After about two hours, once the sample has emerged from the gel and adhered to one of the membranes, the user need only reverse the field polarity for a few seconds, and collect the liquid. The resulting samples are clean enough for mass spectrometry analysis. Maurice Muller, GeBA's vice president of marketing and sales, says users can expect sample recoveries of from 60% (for protein) to 90% (for nucleic acids) using GeBAflex. Tubes are available for up to 250, 800, or 3,000 microliters. A 30-tube kit costs $191 (US). --Jeffrey M. Perkel SOFTWARE WATCH | Microarray Analysis, TIGR-Style Click for larger version (103K) The Institute for Genomic Research in Rockville, Md., is best known for its prolific sequencing arm, but TIGR's broad mandate includes functional genomics, too. With at least five ongoing microarray projects, the institute has developed a suite of applications to help collect, manage, process, and visualize the data. Intended as a complete package for dual-color microarray analyses, TIGR's free, open-source TM4 suite (www.tigr.org/software/tm4) consists of four applications--MADAM (data management), TIGR Spotfinder (image analysis), MIDAS (data analysis and normalization), and MeV (expression analysis, clustering, and data visualization)--and an underlying MySQL database. The self-contained package lets users choose between several normalization and clustering algorithms, but as the entire collection is modular and freely extensible, says Alexander Saeed, TIGR project coordinator, researchers can easily incorporate new analysis routines to keep the application current. Three of the programs, coded in Java, are cross-platform; Spotfinder, written in Visual-C++, runs only under Windows, but a new cross-platform version is slated for release by summer's end, says Saeed. Also in development: support for MAGE-ML (microarray gene expression markup language) and a new, more flexible expression file format called MEV (though support for legacy data will continue); improved installation routines and workflows; incorporation of biological pathway and chromosome information; and data loaders for single-channel Affymetrix GeneChip® and nylon membrane arrays. The TM4 Web site includes user manuals, sample datasets, and tutorials. TIGR also offers the entire suite on compact disc. --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; } .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

RNA Interference without the Interferon; Simplifying Dialysis and Electroelution; Microarray Analysis, TIGR-Style

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