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IP Update: Affymetrix; Intel; Royal Philips Electronics; Northwestern University; and More


Affymetrix of Santa Clara, Calif., has received US Patent No. 8,084,197, "Identification of molecular sequence signatures and methods involving the same." Methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes are claimed. They involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes, according to the inventors.

Affymetrix has also received US Patent No. 8,088,555, "Multiple step printing methods for microbarcodes." A method of forming an encoded microparticle is described. It includes depositing and patterning layers on a substrate to form a microparticles, where each microparticle consists of a number of separate segments aligned along an axis and representing a code; and releasing the microparticles in order to separate the microparticles from the substrate.

Intel of Santa Clara, Calif., has received US Patent No. 8,084,202, "Optical detection for electronic microarrays." According to the patent, a nucleic acid molecule is provided that hybridizes to a second nucleic acid molecule attached to an electronic detector, where the second nucleic acid molecule consists of two regions, one that is complementary to the probe nucleic acid and a distal region that is not complementary to the first probe nucleic acid molecule. The hybridization reaction is detected electronically, and a third nucleic acid molecule having an attached optically detectable label is hybridized to the distal region of the second nucleic acid molecule and the label is detected optically.

Royal Philips Electronics of Eindhoven, the Netherlands, has received US Patent No. 8,084,270, "Device for analyzing fluids." The device relies on magnetic means to generate a magnetic field for exerting a magnetic force on the magnetic particles in the fluid to create movement of the fluid; and a membrane containing sites for binding the targets with channels extending through the membrane that transport the magnetic particles between chambers separated by the membrane in response to the movement of the fluid through the channels.

Northwestern University of Evanston, Ill., has received US Patent No. 8,084,273, "Universal matrix." A method of depositing a patterning species from a nanoscopic tip to a substrate surface is claimed. The method is carried out at a sufficiently high humidity to facilitate the deposition and the deposition of the patterning species is facilitated by a polysaccharide carrier as well as an additional additive.

Galderma Research & Development of Biot, France, has received US Patent No. 8,086,412, "Corrective methodology for processing results of transcriptome experiments obtained by differential analysis." The method includes obtaining the results of the level of expression of genes under a reference condition, and calculating the mean level of expression of each of the genes; obtaining the results of the level of expression of such genes under a treatment condition, and calculating the mean level of expression for each of the genes; calculating the modulation coefficient for the level of expression for each of the genes; calculating a p-value associated with each modulation coefficient; and calculating isobar curves of p-value as a function of the mean level of expression of each of the genes under the reference condition; and calculating and associating a median modulation coefficient on the isobar curve of each p-value observed. The processing of results of experiments carried out on DNA chips is also described.

Penn State Research Foundation of University Park, Penn., has received US Patent No. 8,086,414, "Method and system for modeling cellular metabolism." Methods for in silico or bioinformatic modeling of cellular metabolism are claimed. These include creating a flux balance analysis model, and applying constraints to the flux model, where the constraints are selected from the set consisting of: qualitative kinetic information constraints, qualitative regulatory information constraints, and differential DNA microarray experimental data constraints. In addition, the patent provides for computational procedures for solving metabolic problems.

Sumitomo Bakelite of Tokyo and Somologic of Boulder, Colo., have received US Patent No. 8,088,340, "Polymer compound for biomedical use and biochip substrate using such a polymer compound." A biochip substrate is described that is capable of restricting a nonspecific adsorption or bonding of a substance to be detected, when used for a detection or analysis of protein, nucleic acids, and other biomolecules. According to the patent, the substrate has a layer consisting of a polymer compound obtained by copolymerizing an ethylenically unsaturated polymerizable monomer having an alkylene glycol residue, an ethylenically unsaturated polymerizable monomer having a functional group for fixing a biologically active substance and an ethylenically unsaturated polymerizable monomer having a cross-linkable functional group, on the surface of the substrate.

Columbia University of New York has received US Patent No. 8,088,575, "Massive parallel method for decoding DNA and RNA." Methods are claimed for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. Nucleotide analogues that comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the --OH group at the 3'-position of the deoxyribose, are also claimed.

Advanced Liquid Logic of Research Triangle Park, NC, has received US Patent No. 8,088,578, "Method of detecting an analyte." The method includes providing in a detection window a droplet including a signal-producing substance indicative of the presence and quantity of an analyte and one or more magnetically responsive beads that may interfere with signal produced by the signal-producing substance. A magnetic field is used for removing the magnetically responsive beads from the detection window and restricting the responsive beads from entering the detection window while transporting or retaining the droplet in the detection window. The method additionally includes detecting a signal produced by the signal-producing substance.

Baylor College of Medicine and Rice University, both of Houston, Texas, have received US Patent No. 8,089,628, "Pulsed-multiline excitation for color-blind fluorescence detection." The patent described pulse-multiline excitation, or PME, a fluorescence detection approach with application for high-throughput identification of informative SNPs, which could lead to more accurate diagnosis of inherited disease, better prognosis of risk susceptibilities, or identification of sporadic mutations, according to the inventors. The PME technology has two advantages that the inventors claim increase fluorescence sensitivity: optimal excitation of all fluorophores in the genomic assay and "color-blind" detection, which collects more light than standard wavelength resolved detection.

The Scan

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Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.