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IP Update: Columbia University; Affymetrix; Cold Spring Harbor Laboratory; Merck; and More

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Columbia University of New York has received US Patent No. 8,133,492, "Pneumococcus polysaccharide-related vaccines." Nitrocellulose-based or hydrogel-based microarrays and methods of making them are claimed. The arrays can be used to detect the presence of one or more agents in a sample; to determine the amount of agents in a sample; to determine whether a subject is afflicted with a disorder; and to determine whether an agent known to specifically bind to a first compound also specifically binds to a second compound. Antibodies capable of specifically binding to a glycomer present both on the surface of a mammalian macrophage or intestinal epithelial cell, and on a bacterial cell, are also claimed, as are diagnostic methods using the antibodies.


Affymetrix of Santa Clara, Calif., has received US Patent No. 8,133,667, "Methods for genotyping with selective adaptor ligation." The patent provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. This can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has a variable position in the recognition sequence. Adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. According to the patent, this selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. Amplified fragments may be analyzed to genotype polymorphisms by hybridization to an array of probes that are complementary to target sequences.


Affymetrix has also received US Patent No. 8,133,987, "Primer array synthesis and validation." Methods are provided for releasing polymers from an array to provide oligonucleotide primers for PCR. According to the patent, linkers are attached to a substrate, each of which has an activatable cleavable moiety that, once activated, disrupts the linker to allow release of the polymer. The linkers are attached to the substrate by depositing monomers on the surface until a desired array of polymers is created.


Cold Spring Harbor Laboratory of Cold Spring Harbor, NY, and Merck of Rahway, NJ, have received US Patent No. 8,133,670, "Method for making populations of defined nucleic acid molecules." A population of nucleic acid molecules is synthesized on a substrate. Each synthesized nucleic acid molecule consists of a predetermined nucleic acid sequence and is localized to a defined area of the substrate. The molecules are subsequently harvested and introduced into vector molecules.


HandyLab of Ann Arbor, Mich., has received US Patent No. 8,133,671, "Integrated apparatus for performing nucleic acid extraction and diagnostic testing on multiple biological samples." A device is claimed that includes a module configured to extract nucleic acid from nucleic acid-containing samples. This module consists of racks, each configured to accept the samples. It also consists of a holder that includes a process chamber, a waste chamber, pipette tips, and receptacles containing reagents for carrying out extraction of nucleic acid from a sample. The device also includes a magnetic separator configured to apply a magnetic force to contents of the process chamber of each holder; a heater assembly configured to heat each of the process chambers; and a liquid dispenser configured to carry out fluid transfer operations on the holders. The device also includes a second module configured to amplify the nucleic acid extracted from the samples. This second module includes bays that consist of a heat source and are configured to receive a microfluidic cartridge. According to the patent, the cartridge is configured to separately accept and to separately amplify the nucleic acid extracted from multiple samples.


Callida Genomics of Sunnyvale, Calif., (now Complete Genomics) has received US Patent No. 8,133,719, "Methods for making single molecule arrays." The arrays described in the patent consist of concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, so that each region contains no more than a single concatemer. Different analytical chemistries can be applied to the described arrays, including sequencing-by-hybridization chemistries, sequencing-by-synthesis chemistries, SNP detection chemistries, and others, according to the patent.


Panagene of Daejeon, Korea, has received US Patent No. 8,133,985, "Peptide nucleic acids conjugated with multi-amine linkers and nucleic acid detecting device using the same." A method for preparing a peptide nucleic acid conjugated with multi-amine linkers is claimed. It includes conjugating monomers having multi-amine functionality sequentially at a PNA terminal, and immobilizing the PNA conjugated with multi-amine linkers on a solid surface. The PNA conjugated with multi-amine linkers can be used in nucleic acid detecting devices or kits for gene diagnosis such as PNA microarrays, PNA chips, PNA field-effect transistors and impedance detectors, according to the patent.


Vanderbilt University of Nashville, Tenn., has received US Patent No. 8,134,707, "On-chip polarimetry for high-throughput screening of nanoliter and smaller sample volumes." The technique relies on a substrate containing microfluidic channels. A polarized laser beam is directed onto optically active samples that are disposed in the channels and interacts with them, altering the polarization of the laser beam as it passes multiple times through the sample. Interference fringe patterns are generated by the interaction of the laser beam with the sample and the channel walls and a photodetector is positioned to receive the interference fringe patterns and generate an output signal. Methods for analyzing the signal and determining the rotation of plane polarized light by optically active material in the channel from polarization rotation calculations are also claimed.


Iverson Genetic Diagnostics of Bothell, Wash., has received US Patent No. 8,135,545, "System and method for collecting data regarding broad-based neurotoxin-related gene mutation association." The described test relies on a custom set of genetic sequences associated in peer-reviewed literature with various known genetic mutations related to exposure to toxic substances. According to the patent, these mutations include specific gene sequence alterations based on exposure to diesel fuel, aviation fuel, jet fuel, and many other toxic substances often needed in the aviation and refining industries. Custom microarrays can be used to test for the mutations and associate them with real-time phenotypic data collected from physicians as part of a service.

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.