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Rudolf Rigler, Aperio Technologies, Applera, Eppendorf Array Technologies, Agilent Technologies, Affymetrix, BioMicro Systems, GE Healthcare

Rudolf Rigler of St. Sulpice, Switzerland, has received European Patent No. 1786928, "Parallel high throughput single molecule sequencing process using an enzyme array." The patent claims a process and an apparatus for parallel, high-throughput sequencing of nucleic acid molecules, as well as the study of enzyme-substrate interactions, in a single molecule format. The claimed process works by providing nucleic acid molecules carrying fluorescent labeling groups immobilized on a surface. The base sequence of the molecules is determined on the basis of time-dependent change, which is measured by fluorescence as nucleotide building blocks are cleaved off by immobilized enzyme molecules. A separate support with nucleic acid-degrading enzyme molecules affixed is used to measure the fluorescence of degradation in parallel.

Aperio Technologies of Vista, Calif., has received European Patent No. 1784763, "System and method for data management in a linear-array-based microscope slide scanner." The patent claims a data management system and method for processing, storing, and viewing imagery data produced by a linear-array-based microscope slide scanner. According to the patent's abstract, the system can receive, process, and store data from a scanner at 3 gigabytes per minute. The data is received as a series of overlapping stripes and combined into a seamless and contiguous baseline image. The baseline image is then mapped into a series of regions that can be addressed to facilitate viewing and manipulation of the baseline image, the abstract states. The system also enables imagery data compression while capturing new image stripes. Additionally, the system employs standard file formats and supports the analysis of high value specimens, such as tissue arrays.

Applera has received European Patent No. 1786552, "Method of making polymer monolith composite substrate and resulting substrate as well as beads and bead array." The patent describes a composite substrate comprised of a porous copolymer-monolith, formed by inverse phase photo-copolymerization, attached covalently to the substrate, which can be polymer or glass. According to the patent, features can also be arrayed on the substrate, including bead arrays positioned in an addressable arrangement.

Eppendorf Array Technologies of Namur, Belgium, has received European Patent No. 1788097, "Identification and quantification of a plurality of nucleic acids in a homogeneous assay combining real–time PCR and hybridization to an array." The patent claims a system and method of conducting real-time PCR, where unlabeled capture molecules of a specific design are immobilized on a solid support and contacted with amplicons produced in one or more PCR cycles. The detection of the amplicons may then take place during or between the PCR cycles while the solid support is in fluidic contact with the PCR solution. According to the patent's abstract, the method is suitable for the simultaneous detection and quantification of closely homologous target molecules.

Agilent Technologies has received US Patent No. 7,221,785, "Method and system for measuring a molecular array background signal from a continuous background region of specified size." The patent claims a method and system for estimating background signal over an arbitrarily sized region of a scanned image of a molecular array, including a background region surrounding the region of interest corresponding to the feature. The method works by generating a bit mask, based on a molecular array, a feature-based data set that includes pixel-based intensities, and a list of features. The list includes feature coordinates and feature region-of-interest radii, to indicate those pixels in the scanned image of the molecular array corresponding to background, and those pixels in the scanned image of the molecular array corresponding to features and regions of interest. An integrated intensity for a background region of arbitrary size and shape can then be determined by selecting pixels within the background region that are indicated to be background pixels in the bit mask. By selecting background anuli of sufficient size to overlap with the background anuli of neighboring features, a continuous function of background-signal-versus-position can then be obtained across the surface of a molecular array in order to examine non-local, background-signal-related phenomena.

Agilent has also received US Patent No. 7,223,592, "Devices and methods for performing array based assays." The patent claims devices and methods for assaying a sample for the presence of at least one analyte. The claimed compression devices include a base and a cover configured to apply a compression force to a structure comprising a first substrate separated from a second substrate by a separator. The methods include contacting a sample with a first surface of a first substrate to produce a substrate supported sample and placing the substrate supported sample in contact with a second substrate to form a structure that includes the first and second substrates spaced-apart from each other by a separator. Compression force is then applied to compress the structure together using the compression device. The arrays are then read to obtain a result.

Affymetrix has received US Patent No. 7,222,025, "System, method, and product for dynamic noise reduction in scanning of biological material." The patent describes systems and methods for processing an emission signal, such as a fluorescent signal, to compensate for noise in an excitation beam. Furthermore, a scanning system is described that includes an excitation signal generator that provides: a) an excitation signal having excitation values representative of an excitation beam; b) an excitation reference provider that provides at least one excitation reference value; c) a normalization factor generator that compares the excitation reference value to at least one representative excitation value; and d) a comparison processor that adjusts at least one emission value corresponding to the at least one representative excitation value based, at least in part, on the normalization factor.

BioMicro Systems of Salt Lake City has received US Patent No. 7,223,363, "Method and system for microfluidic interfacing to arrays." The patent claims a method and system for providing a fluidic interface to slides bearing microarrays of biomolecules or other samples. According to the patent's abstract, an interface device seals against the slide to form a chamber or chambers containing all or a portion of the microarray, providing selective access to portions of the slide. The interface device includes inlet and outlet ports permitting liquid sample and reagents to be introduced to and removed from the chamber accessing the slide surface. Pre- and post-array microfluidic circuitry may be included in the interface device or in attachable modules. The system may include one or more compartments for collecting and storing waste fluids, as well, the abstract states.

GE Healthcare has received US Patent No. 7,223,538, "Post-synthesis labeling of nucleic acids, assays using nucleic acids that are labeled post-synthetically, single nucleotide polymorphism detection, and associated compounds and microarrays." The patent claims a nucleic acid expression assay, that works by: a) performing in vitro transcription of target nucleic acid template to generate cRNA; b) contacting the cRNA with a probe immobilized on a microarray under conditions that allow hybridization between the cRNA and the probe; and c) detecting the hybridized cRNA to assay expression of the target nucleic acid template. According to the patent, during this final step at least one phosphorothioate moiety is incorporated in the cRNA. The cRNA is then labeled by conjugating a reporter molecule to the phosphorothioate moiety, followed by reaction with a labeling moiety that specifically reacts with the conjugating moiety.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

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.