Fighting the Membrane Protein-Extraction Blues; Cell-Free Apoptosis System; Database Searching on Your Schedule

GADGET WATCH | Fighting the Membrane Protein-Extraction Blues Courtesy of Geno Technology Efficient extraction of membrane proteins can be a dicey business: Add too little detergent, and you fail to extract the protein; add too much, and purification procedures and downstream applications may be compromised. Geno Technology (www.genotech.com) of St. Louis offers one solution: Optimizer-blueBALLS™, which are glass beads coated with a hydrophobic blue dye that behaves like membrane-bound proteins. According to company literature, the coated beads can help researchers determine optimal detergent concentration (also called critical micelle concentration, or CMC) and extraction time for membrane proteins. The CMC value refers to the amount of detergent required to form micelles, which sequester hydrophobic proteins. Typically determined using light scattering or surface-tension analysis, the CMC is highly variable and depends on the detergent, temperature, pH, ionic strength, and buffer conditions, among other parameters. Thus, conditions that work well in one case may fail in others. To use blueBALLS, researchers need only track the solubili-zation of the beads' blue dye. They can either add the beads to an extraction, or set up mock controls to optimize conditions. Users can calculate the CMC, for instance, from a plot of absorbance versus detergent concentration. They can then optimize extraction time. Optimizer-blueBALLS cost $89 (US) for 500 beads, with each extraction using from one to three beads. --Jeffrey M. Perkel PATENT WATCH | Cell-Free Apoptosis System As the recognition grows that apoptosis plays an important role in many diseases, "there is a need ... for in vitro methods for the analysis of compounds and biological factors which trigger or accelerate apoptosis or which interfere with the induction of apoptosis," according to a patent issued recently to Xiaodong Wang and Xuesong Liu and held by Emory University, Atlanta (US patent 6,558,900, issued May 6, 2003). The patent is for a cell-free system that includes a 100,000 x g HeLa cell supernatant that is assayed--in the presence of challenge compounds, dATP, and cytochrome c--either for CPP32 proteolytic activity or for nuclease activity; both are biochemical markers of apoptosis. The method "allows the study of apoptosis and regulators thereof in a cell-free system in which the analysis is not complicated by previous induction of the apoptotic pathway in the cells used to prepare the test extracts," according to the patent. It also provides researchers with a tool to increase the apoptotic effect of chemotherapeutic agents in cancers, especially those expressing oncogenic bcl-2. Emory has granted an exclusive license for the patent's use to Idun Pharmaceuticals (www.idun.com), a San Diego-based drug discovery company. --Ivan Oransky SOFTWARE WATCH | Database Searching on Your Schedule BioQuery screenshotClick for larger version (70K) Searching biological databases has become an essential research task, but staying current is a challenge, as these resources often are updated daily. To make the results manageable, users sometimes develop highly complex searches, but with no way to store such queries, they have to key them anew each time they want to run them. Now a new program simplifies and automates this process. James Brundege, senior systems analyst at Oregon Health & Science University, Portland, developed BioQuery (www. bioquery.org) as a postdoctoral fellow at OHSU. From a single interface, users can build complex queries line by line for several different databases, save them, schedule them to run automatically at defined intervals, and E-mail the results, even filtering for records that are new or modified since the last search. The program is a free, open-source, client server-based Java application; queries are stored in a password-protected account on an OHSU server. BioQuery currently supports the National Center for Biotechnology Information's PubMed, Nucleotide, Protein, PopSet, Structure, Genome, OMIM, and Taxonomy databases, but its modular architecture supports plug-ins for new data sources, too (instructions available online). The task requires programming savvy, but Brundege says his team can help: "We're responsive to that." New features in development include a "metasearch agent," which will enable simultaneous searching of multiple databases with one query; development of data-specific viewers; and the ability to select export formats, to support EndNote users, for instance. --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

Fighting the Membrane Protein-Extraction Blues; Cell-Free Apoptosis System; Database Searching on Your Schedule

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