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IP Roundup: Jul 21, 2009

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The University of Missouri at Columbia has received US Patent No. 7,563,567, "Use of ECIST microarrays in an integrated method for assessing DNA methylation, gene expression and histone acetylation." The patent provides methods for the high-throughput, dual analysis of DNA methylation and gene expression, and triple analysis of DNA methylation, gene expression, and gene-associated histone acetylation in cancer cells using arrayed expressed CpG island sequence tags, or ECISTs. Also provided are high-throughput methods for either confirming methylation-dependent gene silencing, or identifying therapeutically effective demethylating agents, using the ECIST array panels to identify hypermethylated loci and measure expression levels after cellular exposure to demethylating agents.


The United States of America has received US Patent 7,563,573, "Method for detecting radiation exposure." The patent claims a method for detecting the exposure of organisms to biologically significant or hazardous amounts of ionizing radiation. The method uses nucleic acid microarray hybridization to evaluate biological effects, such as gene expression patterns after radiation exposure. According to the patent, genes found to be responsive to radiation exposure in a variety of cell lines are incorporated into probe sets, which are exposed to a labeled nucleic acid composition from a test cell. The test cell hybridizes to members of the probe set when the cell has been exposed to a biologically significant amount of ionizing radiation. The researcher can then determine whether the nucleic acid composition hybridized to the nucleic acid molecules represents genes that are differentially expressed.


The State of Oregon has received US Patent No. 7,563,581, "Methods for detecting and localizing DNA mutations by extension of differentially fragmented DNA." The patent claims methods for detecting and localizing DNA mutations by microarray. The methods include the use of restriction endonucleases and mismatch-recognition nucleases to detect and localize mutations. In one method provided, reference and target DNA are digested using restriction endonucleases, resultant DNA strands are labeled, and the labeled mixture of DNAs is hybridized to a microarray. In another provided method, the reference and target DNA are denatured and annealed to form a mixture containing heteroduplex DNA. Mismatch-recognition nucleases are then used to cleave at least a portion of the heteroduplex DNA and resultant DNA strands are labeled. The resulting labeled mixture of DNAs is then hybridized to a microarray.


GE Healthcare has received US Patent No. 7,563,587, "Method and kit for cell analyte assay." The patent claims a method for analyzing a cell sample for cell surface-bound or intracellularly bound analytes. The method provides an array of immobilized specific binding agents for a set of different ligands, where each ligand is specific to a respective cell surface-bound or intracellularly bound analyte. The array and the set of ligands are used in an inhibition-type or a direct-type assay format to determine the cell surface-bound or intracellularly bound analytes in the cell sample.


Combimatrix of Mukilteo, Wash., has received US Patent No. 7,563,600, "Microarray synthesis and assembly of gene-length polynucleotides." The patent claims a process for the in vitro synthesis and assembly of long, gene-length polynucleotides. The process is based on the assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. More specifically, a process for the in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, on-device assembly of larger polynucleotides composed of shorter oligonucleotide fragments is claimed.


The California Institute of Technology of Pasadena has received US Patent No. 7,563,615, "Apparatus and method for automated monitoring of airborne bacterial spores." The patent claims an apparatus and a method for the automated monitoring of airborne bacterial spores. The apparatus includes an air sampler, a surface for capturing airborne spores, a thermal lysis unit to release DPA from bacterial spores, a source of lanthanide ions, and a spectrometer for excitation and detection of the characteristic fluorescence of the aromatic molecules in bacterial spores complexed with lanthanide ions. Computer-programming steps are also provided to allow for automation of the apparatus for the monitoring of airborne bacterial spores.


Amic of Uppsala, Sweden, has received US Patent No. 7,564,045, "Optical assay system." The patent claims an optical reader for an optical assay arrangement. The reader includes a polymeric sample substrate with a reaction-site surface. The surface includes protruding microstructures and at least one reaction-site area; a light source for illuminating the reaction-site area; and a detector device for detecting light emitted from the reaction-site area. The light source is arranged to inject exciting light rays into the polymeric sample substrate with a controlled angle of incidence so that the protruding microstructures guide the exciting light rays in the direction of the reaction-site area, and the detector device detects light emitted from the reaction-site area, the inventors state in the patent.


Rosetta Inpharmatics of Seattle has received US Patent No. 7,565,251, "Systems and methods for evaluating the significance of differences in biological measurements." The patent claims a method for fluorophore-bias removal in microarray experiments where the fluorophores used in microarray experiment pairs are reversed. The patent also claims a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. According to the method, the error measurement is optionally coupled with rank-based methods in order to determine a probability that a cellular constituent is up- or down-regulated in response to a perturbation. The patent also claims a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

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