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IP Roundup: Nov 30, 2010


Fluidigm of South San Francisco, Calif., has received US Patent No. 7,837,946, "Microfluidic device and methods of using same." The patent describes a variety of elastomeric-based microfluidic devices. According to the patent, some of the devices include arrays of reaction sites to support high-throughput analyses. Some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents can become suspended once sample is introduced into the reaction site, according to the patent. The devices can be used in applications such as nucleic acid amplification reactions, genotyping, and gene expression analyses.

Expression Analytics of Espoo, Finland, has received US Patent No. 7,838,228, "Method of quantitative and/or comparative measurement of mRNA expression levels in small biological samples." According to the claimed method, reverse transcription of the mRNA contained in the sample is first carried out on an array using sequence-modifying primers for one or several genes in the same reaction to obtain a pool of sequence-modified cDNA molecules. After completion of the reverse transcription, redundant sequence-modifying primers are removed or inactivated. This step is followed by co-amplifying the sequence-modified cDNA templates with a reference DNA template in individual gene-specific amplification reactions. By quantitatively measuring the amounts and determining the relative levels of the amplification products, a gene-specific cDNA-over-DNA ratio is obtained in each of the individual amplification reactions, according to the patent. Finally, by combining the ratios obtained, a sample-specific profile can be generated, which reflects the relative amounts of mRNA transcripts originally present in the sample.

Maven Technologies of Pasadena, Calif., has received US Patent No. 7,838,285, "Imaging electrophoresis system." The patent provides a way of conducting gel electrophoresis and optical imaging techniques to measure the amount of biomaterial that attaches to specified locations on a detector slide, as well as to determine the molecular weight of the molecules at those locations. A system is also described that includes an apparatus with a light source for emitting a beam of polarized light, a light-reflection surface that contains an array of probes, and a detector positioned to detect polarization changes in the reflected light beam caused by localized binding events between probes on the array and analyte molecules of a sample. The system also includes a gel layer above the probes and a means for generating an electric field in the gel layer for moving by electrophoresis functioning molecules of a sample lateral to the array of probes.

The Van Andel Research Institute of Grand Rapids, Mich., has received US Patent No. 7,838,634, "Methods for measuring glycan levels of proteins." The patent claims methods for using a microarray to measure the glycan level of a protein. A microarray slide containing a solid support and different antibodies having carbohydrate groups is provided, where the different antibodies bind specifically to target proteins and are spotted at specific addresses on the solid support. Carbohydrate groups of the different antibodies are then oxidized and derivatized by a hydrazide-maleimide bifunctional crosslinking reagent so that recognition of the carbohydrate groups by a glycan-binding protein is reduced without eliminating the binding activities of the different antibodies to their specific target proteins.

Industrial Technology Research Institute of Hsinchu, Taiwan, has received US Patent No. 7,842,238, "Fully automated microarray processing system." An automated microarray processing system is claimed that includes a microarray housing assembly module, an incubation module, a washing module, and at least one automated transport module. When the automated transport module is mechanically moved among the microarray housing assembly module, the incubation module, and the washing module, the biochemical reaction of a reaction region of a microarray and a biological sample solution disposed between them is automatically performed, and the reacted microarray is automatically cleaned when the biochemical reaction of the microarray is completed, according to the patent.

Northwestern University of Evanston, Ill., has received US Patent No. 7,842,344, "Peptide and protein arrays and direct-write lithographic printing of peptides and proteins." The patent describes the direct-write lithographic printing of proteins and peptides onto surfaces. In particular, the patent relates to methods for creating protein and peptide arrays. Nanoscopic tips can be used to deposit the peptide or protein onto the surface to produce a pattern, and the pattern can be dots or lines having dot diameter and line width of less than 1,000 nanometers, according to the patent. The tips and the substrate surfaces can be adapted for the peptide and protein lithography.

Bio-Rad Laboratories of Hercules, Calif., has received US Patent No. 7,842,498, "Hydrophobic surface chip." A water-swellable hydrophobic hydrogel as well as analytical devices, such as biochips, that incorporate the hydrogel, are claimed. Also described are methods of using the hydrogel to prepare the analytical devices and methods of using the analytical devices to detect, quantitate and discriminate between analytes in a sample. Kits that include components of a hydrogel and instructions for making a chip with a hydrophobic surface are also provided.

Illumina of San Diego has received US Patent No. 7,843,567, "Methods of identifying an analyte and nucleic acid analysis." The patent claims a method that includes the use of microparticles containing optically detectable codes. According to the patent, the microparticles have chemical probes attached, and each of the chemical probes is associated with a corresponding one of the codes. The method also includes selectively binding target analytes to the chemical probes on the microparticles to produce labeled microparticles and distributing the labeled microparticles to random locations of a substrate. A way of determining the codes for the labeled microparticles in the random array and code positions of the codes in the random array is also described. The method further includes the detection of the label on the labeled microparticles in the random array and label positions of the labels in the random array, as well as using the code positions and the label positions to analyze the target analyte.

Aperio Technologies of Vista, Calif., has received US Patent No. 7,844,125, "Systems and methods for image pattern recognition." The patent claims methods for image pattern recognition using digital image capture and encoding using vector quantization of the image. A vocabulary of vectors is built by segmenting images into kernels and creating vectors corresponding to each kernel. Images are encoded by creating a vector index file having indices that point to the vectors stored in the vocabulary. The vector index file can be used to reconstruct an image by looking up vectors stored in the vocabulary. According to the patent, pattern recognition of candidate regions of images can be accomplished by correlating image vectors to a pre-trained vocabulary of vector sets that correlate with particular image characteristics. In virtual microscopy, the methods are suitable for rare-event finding, such as detection of micrometastasis clusters, tissue identification, such as locating regions of analysis for immunohistochemical assays, and rapid screening of tissue samples, such as histology sections arranged as tissue microarrays, the patent claims.

Samsung Electronics of Suwon, Korea, has received US Patent No. 7,844,940, "Mask set for microarray, method of fabricating mask set, and method of fabricating microarray using mask set." A mask set with a light-transmitting region of a controlled size for performing in situ synthesis on probes of a microarray is provided. According to the patent, each mask in the set includes a light-transmitting region and a light-blocking region, where the size of the light-transmitting region is equal to or greater than about 5 percent of the total size of the light-transmitting and light-blocking regions.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.