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Large Scale Proteomics, Agilent Technologies, NanoBioDynamics, Brigham and Women s Hospital, Battelle Memorial Institute, Rosetta Inpharmatics


Large Scale Proteomics of Vacaville, Calif., has received US Patent No. 6,846,635, “Microarrays and their manufacture.” The patent covers microarrays that are prepared by using a separate fiber for each compound being used in the microarray. The invention relates to the preparation of microarrays, wherein elongated filaments or tubes are bundled together and cut transversely many times at short intervals to yield cross-sectional slices. A further aspect of the invention is the inclusion of markers that are either integral with the tubes or fibers or are contained in the media contained in hollow fibers, which allow the fibers to be distinguished along the entire length thereof.

Agilent Technologies of Palo Alto, Calif., has received US Patent No. 6,846,454, “Fluid exit in reaction chambers.” The patent covers apparatus and methods for controlling flow of fluid inside a chamber. A device comprises a chamber comprising at least one wall, a first opening for introducing a fluid into the interior of the chamber, and a second opening opposite the first opening. At least one wall of the chamber is designed to provide a contracting section, a section having substantially constant cross-sectional area and a diffusing section through the chamber from the first opening to the second opening. The device may be employed as a gas outlet in a reaction chamber for conducting reactions where it is desired to control the internal atmosphere of the reaction chamber. The apparatus may be employed in the manufacture of biopolymers on the surface of a support such as an array of biopolymer features on the support. Also disclosed is a holding element for a support wherein the holding element is a low drag body.

NanoBioDynamics of Berkeley, Calif., has received US Patent No. 6,846,638, “Method and system for rapid biomolecular recognition of amino acids and protein sequencing.” Methods, compositions, kits, and apparatus are provided wherein the aminoacyl-tRNA synthetase system is used to analyze amino acids. The method allows very small devices for quantitative or semi-quantitative analysis of the amino acids in samples or in sequential or complete proteolytic digestions. The methods can be readily applied to the detection and/or quantitation of one or more primary amino acids by using cognate aminoacyl-tRNA synthetase and cognate tRNA. The basis of the method is that each of the 20 synthetases and/or a tRNA specific for a different amino acid is separated spatially or differentially labeled. The reactions catalyzed by all 20 synthetases may be monitored simultaneously, or nearly simultaneously, or in parallel. Each separately positioned synthetase or tRNA will signal its cognate amino acid. The synthetase reactions can be monitored using continuous spectroscopic assays. Alternatively, since elongation factor Tu:GTP (EF-Tu:GTP) specifically binds all AA-tRNAs, the aminoacylation reactions catalyzed by the synthetases can be monitored using ligand assays. Microarrays and microsensors for amino acid analysis are provided. Additionally, amino acid analysis devices are integrated with protease digestions to produce miniaturized enzymatic sequenators capable of generating either N- or C-terminal sequence and composition data for a protein or peptide. The possibility of parallel processing of many samples in an automated manner is discussed.

Brigham and Women’s Hospital of Boston and Battelle Memorial Institute of Richland, Wash., have received US Patent No. 6,846,642, “Methods of detecting cancer based on prostasin.” The patent covers diagnostic methods based upon the expression of the protein prostasin. In particular, it is concerned with assays performed on women to determine their risk of ovarian cancer.

Rosetta Inpharmatics of Seattle has received US Patent No. 6,847,897, “Method and system for analyzing biological response signal data.” A system, method, and computer program product for enhanced computer-aided analysis of biological response data is disclosed in the patent. In a preferred embodiment, biological datasets are graphically selected by a user from a first active biological viewer window on a user computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in the destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. In another preferred embodiment, hierarchical cluster trees from biological signal profiles are presented in a hyperbolic display fashion. In another preferred embodiment, biological menu and submenu items utilized by the user computer are not stored in the user computer, but rather are stored a central biological response database. Biological menus and submenus are generated at startup time based on queries to the central biological response database, allowing for increased flexibility, changeability, and customization of the biological menus. In another preferred embodiment, correlation data between biological signal profile data is precomputed when the experiments are added to the central biological response database, eliminating the need for real time computation of correlation coefficients by the user computer.


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