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IP Roundup, Sep 14, 2010


Fujifilm of Tokyo has received US Patent No. 7,794,661, "Method and system for detecting fluorescence from microarray disk." The patent describes a fluorescence-detection method where biological specimens are irradiated with excitation light while a substrate disk is rotated. According to the patent, the biological specimens are labeled with a fluorescent material and fixed on the substrate disk. Fluorescence emitted from each of the biological specimens is then detected when a predetermined time elapses, since the biological specimen is irradiated with the excitation light.

Johns Hopkins University of Baltimore has received US Patent No. 7,794,929, "Genomic screen for epigenetically silenced genes associated with cancer." The patent claims a method of identifying at least one methylation-silenced gene associated with cancer, SFRP2. According to the patent, the array contains nucleic acid molecules corresponding to RNA expressed in cancer cells that have been treated with a demethylating agent and an inhibitor of histone deacetylase, under conditions suitable for selective hybridization. The method then calls for contacting the array with nucleic acid subtraction products, and detecting selective hybridization. According to the patent, the subpopulation of nucleotide sequences are not re-expressed in the presence of the histone deacetylase inhibitor alone and are only re-expressed in the presence of the combination of at least one demethylating agent and at least one histone deacetylase inhibitor. The detected subpopulation of nucleic acid sequences therefore represents methylation-silenced genes.

The University of Idaho of Moscow, Idaho, has received United States Patent No. 7,794,939, "Methods of DNA methylation detection." The patent provides for methods of generating and detecting specific electronic signals that report the methylation status of targeted DNA molecules in biological samples. The patent describes two methods: direct and indirect detection of methylated DNA molecules in a nanotransistor device. In direct detection, methylated target DNA molecules are captured on the sensing surface resulting in changes in the electrical properties of a nanotransistor. These changes generate detectable electronic signals. In indirect detection, antibody-DNA conjugates are used to identify methylated DNA molecules. RNA signal molecules are generated through an in vitro transcription process. These RNA molecules are captured on the sensing surface change the electrical properties of nanotransistor, generating detectable electronic signals.

Affymetrix has received US Patent No. 7,794,943, "Modified nucleic acid probes." The patent claims a method of detecting a mutation or polymorphism in a target oligonucleotide by: a) attaching a first oligonucleotide analog probe set to the array, where the probes contain a sugar moiety with a modified 2' position, an interrogation position, and are complementary to the target oligonucleotide sequence; b) attaching a second oligonucleotide analog probe set to the array, where the second probe set is identical to the first probe set, except that the second probe set contains a different nucleotide analog than the first probe set; c) hybridizing the target oligonucleotide to the array; and d) detecting which probe set is hybridized with the target oligonucleotide, revealing the mutation or polymorphism in the target oligonucleotide.

Life Technologies has received US Patent No. 7,794,946, "Microarray and uses therefor." The patent claims methods of using microarrays to simplify analysis and characterization of genes and their function. In one claimed method, arrays are used to identify and characterize antibodies having binding affinity for a specific target antigen. In a second method, arrays are used to determine gene expression at the protein level by contacting an array of characterized or uncharacterized antibodies on a solid surface with proteins and identifying the antibodies to which the proteins bind. This method can be additionally used to compare the protein expression in two different populations of cells, such as normal cells and cancer cells or resting cells and stimulated cells, the patent states. In a third method, arrays are used to determine gene expression at the protein level by contacting a microarray of nucleic acid samples derived from a variety of different sources with nucleic acid probes then identifying the sample or samples to which the probe binds.

The Institute for Systems Biology of Seattle has received US Patent No. 7,794,947, "Affinity capture of peptides by microarray and related methods." The patent provides methods of detecting polypeptides in a sample by: a) cleaving polypeptides in a test sample to generate peptides; b) adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, where the peptide standards correspond to peptides cleaved with the same reagent used to cleave the test sample; c) contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards; d) washing the array to remove unbound peptides, retaining affinity-captured sample peptides and standard peptides; e) analyzing the affinity-captured peptides using mass spectrometry; and f) determining the presence of bound test peptides and standard peptides.

The Korea Atomic Energy Research Institute of Daejeon has received US Patent No. 7,794,964, "Biochip for the detection of phosphorylation and the detection method using the same." The patent claims a biochip prepared by integrating a protein produced from the recombination of a substrate of kinase selected from a group consisting of protein kinase C, cdc2 protein kinase, DNA-dependent protein kinase, and an elevated protein such as Selenomonas ruminantium membrane protein, on a matrix surface coated with an active group. The patent also claims a kit for detecting phosphorylation composed of the biochip and a cofactor labeled with a radio-isotope, plus a method for detecting phosphorylation using the kit and chip.

Suntory of Osaka, Japan, has received US Patent No. 7,795,005, "Bacteria detecting instrument, bacteria detecting method, and bacteria detecting kit." The patent claims an array containing oligonucleotides based on species- or genus-specific nucleotide sequences of subject bacteria. By confirming whether the oligonucleotide immobilized on the substrate has hybridized with a probe prepared from a test sample, bacteria contained in the test sample can be detected and identified, according to the patent. A system for using the array is also discussed.

Luminex has received US Patent No. 7,795,040, "Methods, particles, and kits for determining activity of a kinase." The patent claims methods, particles, and kits for determining kinase activity within a sample. The method includes exposing a fluorescent particle to an assay, where the fluorescent particle includes a support substrate containing fluorescent materials and a peptide substrate coupled to the support substrate via a functional group of the support substrate. The method also includes phosphorylating the peptide substrate during exposure of the fluorescent particle to the assay and processing the fluorescent particle so that the peptide substrate is dephosphorylated and a polarized double bond is generated at a dephosphorylated site. In addition, the method includes coupling a fluorescent reporter having a nucleophilic terminal group to the fluorescent particle via the polarized double bond.

Centre National de la Recherche Scientifique of Paris, the Université de Nantes of Nantes, France, and the University of Florida of Gainesville, Fla., have received US Patent No. 7,795,182, "Method for making biochips." Biopolymers, such as DNA, proteins, oligo- or poly-saccharides, are immobilized on a solid support having a surface covered with a metal capable of coordination bonding with the phosphate groups. The phosphate groups on the surface act as anchoring functions and may be present naturally in the polymer or may be introduced by enzymatic or chemical modification, according to the patent. The anchoring is effected by ionocovalent bonding between the free phosphate group of the polymer and the metal. The inventors believe an ionocovalent bond is stronger than a hydrogen or electrostatic bond.

Illumina has received US Patent No. 7,796,333, "Encoded microparticles and a method for fabricating." The patent claims a method for fabricating microparticles. The method includes providing a removable substrate that has a photosensitive material, where the substrate has a number of inner regions. Each inner region surrounds a corresponding outer region. The method also includes providing optically detectable codes within the inner regions of the substrate and etching lines into the substrate to create microparticles containing optically detectable code. According to the patent, the microparticles have elongated bodies that extend in an axial direction. The optically detectable codes therefore extend in the axial direction within the microparticles.