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IP Roundup: Oct 6, 2009

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Nanogen of San Diego has received US Patent No. 7,597,932, "Mesoporous permeation layers for use on active electronic matrix devices." The patent describes synthetic polymer hydrogel permeation layers for use on active electronic matrix devices for biological assays. It also claims methods for forming a permeation layer on an array of microelectrodes including the steps of attaching a linker to the surface of the array and providing a polymerization solution that includes a porogen. The surface of the array is then contacted with the polymerization solution and the polymerization solution is then polymerized on the surface of the array to form a permeation layer that is attached o the surface of the array through the linker. The porogen is then removed from the permeation layer, creating void spaces in the permeation layer.


Universitat Konstanz of Constance, Germany, has received US Patent No. 7,598,019, "Method for cleavage of labile functional groups from chemical compounds." The patent provides a method for cleavage of labile functional groups from molecules by the action of electromagnetic radiation, where the molecules are contacted with a chemical compound whose triplet state is energetically higher than the triplet state of the labile functional group, and are subsequently exposed to electromagnetic radiation. The patent also provides a method for preparing DNA chips by spatially addressed, light-controlled nucleotide synthesis on solid substrates.


The University of Chicago has received US Patent No. 7,598,037, "Method for implementing non-destructive quality control of substrates and printed biological microarrays." The patent claims a method and apparatus for implementing non-destructive quality control of gel-based microarrays prepared by dispensing a gel-forming composition on a solid substrate. The method relies on the difference between the properties of a supporting substrate and a gel, where the gel is hydrophilic. The condensation of vapor of a chemically inert water-soluble liquid, such as water or glycerol, on the surface of a substrate under inspection creates a layer of tiny droplets that affect both transmission and scattering of light on the surface. A pattern of condensation, characterized by spatial distribution, average size of the droplets, and spacing between the droplets, reflects variation in the wetting properties of the substrate. The pattern of condensation circumscribes printed microarray features to be non-destructively imaged and analyzed.


PerkinElmer has received US Patent No. 7,599,090, "Method and apparatus for automatically segmenting a microarray image." The patent claims a method where a microarray image is segmented into discrete segments for respective spots in the microarray image. The method is based on locating microarray image rows and columns by maximizing scores associated with vertical and horizontal image projections. The scores are calculated by stepping windows containing nominally spaced spot-sized row or column boundaries, over the horizontal projection curves. At each step, a total row or column score is calculated that represents the areas of the projection curves that fall within the row boundaries. The system then selects the window positions that correspond to the maximum total row score and total column score, and uses the locations of the boundaries as the locations of row and column stripes that are sized to the spot diameters. The intersections of the row and column stripes define the segments for the respective spots, and the centers of the intersections are the locations for the spot location, or grid, markers. The system may also determine the best spot size, column and row gap sizes and sub-array gap sizes by changing the boundaries accordingly and determining corresponding maximum scores, according to the inventors.


Microsoft has received US Patent No. 7,599,799, "Methods for using co-regulated genesets to enhance detection and classification of gene expression patterns." The patent claims methods for the enhanced detection of biological response patterns. According to the methods, genes are grouped into basis gene sets according to the co-regulation of their expression. Expression of individual genes within a gene set is indicated with a single gene expression value for the gene set by a projection process. The expression values of gene sets, rather than the expression of individual genes, are then used as the basis for comparison and detection of biological response.


Yeda Research and Development of Rehovot, Israel, has received US Patent No. 7,599,933, "Coupled two-way clustering analysis of data." The patent describes a coupled two-way clustering approach to gene microarray data analysis. The approach can be used for identifying subsets of the genes and samples, so that when one of these items is used to cluster the other, stable and significant partitions emerge, according to the inventors.

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