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Patent Watch: Jan 6, 2009

Ocimum Biosolutions of Indianapolis has received US Patent No. 7,469,185, “Primary rat hepatocyte toxicity modeling.” The patent claims a method for determining whether a test compound is a liver toxin by: a) exposing liver tissue or liver cells to the test compound; b) preparing a normalized gene expression profile of at least ten genes for the liver tissue or liver cells; c) comparing the gene expression profile to a hepatotoxicity model; and d) scoring the comparison to determine whether the test compound is a hepatotoxin.

The Whitehead Institute for Biomedical Research of Cambridge, Mass., has received US Patent No. 7,470,507, “Genome-wide location and function of DNA binding proteins.” The patent describes a method of identifying a region of a genome of a cell to which a protein of interest binds. In the methods described, DNA binding protein of a cell is linked to the genomic DNA of a cell. The genomic DNA to which the DNA binding protein is linked is then removed and combined or contacted with DNA comprising a sequence complementary to genomic DNA of the cell under conditions in which hybridization between the identified genomic DNA and the sequence complementary to genomic DNA occurs. Regions of hybridization are determined to be regions of the genome of the cell to which the protein binds. A method of identifying a set of genes where cell cycle regulator binding correlates with gene expression and of identifying genomic targets of cell cycle transcription activators in living cells is also claimed.

Ribomed Biotechnologies of Phoenix has received US Patent No. 7,470,511, “Methods for determining nucleic acid methylation.” The patent claims methods for detecting the presence of a target molecule by generating multiple detectable oligonucleotides through reiterative enzymatic oligonucleotide synthesis events on a defined polynucleotide sequence. The methods include: a) using a nucleoside, a mononucleotide, and oligonucleotide, or a polynucleotide to initiate synthesis of an oligonucleotide product that is complementary to a target site on the defined polynucleotide sequence; b) optionally using nucleotides or nucleotide anologs as oligonucleotide chain elongators; c) using a chain terminator to terminate the polymerization reaction; and d) detecting multiple oligonucleotide products that have been synthesized by the polymerase.

Affymetrix has received US Patent No. 7,470,783, “Photocleavable protecting groups and methods for their use.” The patent describes compounds that are said to be useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups that can be removed by photolysis to unmask a reactive group, according to the abstract. Also claimed is a method of forming, from component molecules, compounds on a support, where each compound occupies a separate, predefined region of the support, using the compounds described in the patent.

Veridex of Raritan, NJ, has received US Patent No. 7,473,526, “Breast cancer prognostic portfolio.” The patent claims a microarray-based method of prognosticating metastasis in a breast cancer patient. The method involves identifying differential modulation of each gene, relative to the expression of the same genes in a normal population, in a combination of genes, as well as kits for employing the method.

Corning of Corning, NY, has received US Patent No. 7,473,533, “Membrane arrays and methods of manufacture.” The patent claims G protein-coupled receptor microarrays on porous substrates for structural or functional analyses of GPCRs, and methods of preparing porous substrate surfaces for receiving membranes that comprise GPCRs. In one embodiment, the GPCR microarray includes a membrane adhered to an upper surface of a porous substrate, where the membrane spans across a plurality of pores on the porous substrate to form a number of cavities that have sufficient geometry to permit entry of assay reagents into each cavity, therefore allowing the access of assay reagents to both sides of GPCR in the membrane.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.