Patents Examined by Aaron A Priest
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Patent number: 11774449Abstract: Presented herein are methods of evaluating cellular activity by: placing a cell population on an area; assaying for a dynamic behavior of the cell population as a function of time; identifying cell(s) of interest based on the dynamic behavior; characterizing a molecular profile of the cell(s); and correlating the obtained information. The assayed dynamic behavior can include cellular activation, cellular inhibition, cellular interaction, protein expression, protein secretion, cellular proliferation, changes in cellular morphology, motility, cell death, cell cytotoxicity, cell lysis, and combinations thereof. Sensors associated with the area may be utilized to facilitate assaying. Molecular profiles of the cell(s) can then be characterized by various methods, such as DNA analysis, RNA analysis, and protein analysis.Type: GrantFiled: August 17, 2020Date of Patent: October 3, 2023Assignee: University of Houston SystemInventors: Navin Varadarajan, Gabrielle Romain, Ivan Liadi, Victor Sendra, Badrinath Roysam
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Patent number: 11767568Abstract: The invention provides a transgenic Glycine max event MON87751, plants, plant cells, seeds, plant parts, progeny plants, and commodity products comprising event MON87751. The invention also provides polynucleotides specific for event MON87751, plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides for event MON87751. The invention also provides methods related to event MON87751.Type: GrantFiled: January 4, 2022Date of Patent: September 26, 2023Assignee: MONSANTO TECHNOLOGY LLCInventors: Kim A. Beazley, Wen C. Burns, Robert H. Cole, II, Ted C. MacRae, John A. Miklos, Lisa G. Ruschke, Kairong Tian, Liping Wei, Kunsheng Wu
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Patent number: 11767553Abstract: A kit for use in assessing the status of nucleic acid degradation and/or the integrity of one or more nucleic acids in a sample by amplifying at least two overlapping regions within at least one locus and detecting the amount of the at least two amplification products. The kit includes a primer and at least two probes that bind under stringent conditions to a sequence that shares at least 80% sequence identity to a sequence selected from the group of sequences consisting of SEQ ID NO. 6 to SEQ ID NO. 47 over a stretch of 80 base pairs, or to a reverse complement thereof. One of the at least two probes binds to one of the at least two overlapping regions and the other of the at least two probes binds to a non-overlapping region.Type: GrantFiled: October 13, 2021Date of Patent: September 26, 2023Assignee: Qiagen, GmbHInventors: Miroslav Vranes, Ralf Peist, Mario Scherer, Stefan Otto Cornelius
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Patent number: 11768208Abstract: Aspects of the present invention include methods for determining a transplant category of a subject having a transplant. Common mechanisms of rejection injury are uncovered across different tissue transplants, and provide a means to understand rational drug design. Various sources of tissues are examined form the patient for understanding AR mechanism (graft biopsy), as well as monitoring by minimal invasive means (blood) or non-invasive means (urine for the kidney allograft). For biomarker discovery different categories of markers are examined such as genes, proteins, peptides and antibodies. These biomarkers can help determine the subject's transplant category (e.g., acute allograft rejection (AR), stable allograft (STA), BK viremia, BK nephritis, drug toxicity or chronic allograft injury (CAI), and the like). Also provided are compositions, systems, kits and computer program products that find use in practicing the subject methods. The methods and compositions find use in a variety of applications.Type: GrantFiled: January 29, 2021Date of Patent: September 26, 2023Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Minnie M. Sarwal, Tara Sigdel, Amit Kaushal, Li Li, Wenzhong Xiao, Atul J. Butte, Purvesh Khatri
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Patent number: 11760994Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: GrantFiled: June 25, 2021Date of Patent: September 19, 2023Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert Bacigalupo, Frank Steemers, Jeffrey Fisher, Andrew Slatter, Lewis Kraft, Niall Gormley, M. Shane Bowen
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Patent number: 11753677Abstract: The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.Type: GrantFiled: November 9, 2022Date of Patent: September 12, 2023Assignee: Encodia, Inc.Inventors: Mark S. Chee, Haibiao Gong, Kevin L. Gunderson
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Patent number: 11754552Abstract: Methods of assessing a graft recipient's predisposition to reject a transplant are provided. The risk of transplant rejection may be assessed in a subject prior to transplant, wherein subjects having a greater immune repertoire diversity prior to transplant are more susceptible to transplant rejection. Also, increases in immune repertoire diversity after transplant are indicative of transplant risk after. In another aspect, the presence or elevated abundance of immune elements comprising IGHV3-23 sequences are indicators of transplant rejection risk. In another aspect the scope of the invention encompasses methods of treating transplant rejection in a subject, by assessing transplant risk and administering immunosuppressive therapy in accordance with assessed risk.Type: GrantFiled: June 11, 2018Date of Patent: September 12, 2023Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIAInventors: Minnie Sarwal, Marina Sirota, Silvia Pineda San Juan
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Patent number: 11739389Abstract: The present invention generally relates to methods and agents for identifying and/or classifying microbes (especially bacteria), yeast organisms and filamentous fungi. In particular, the present invention concerns the discovery of unique single nucleotide polymorphisms (SNPs) in bacterial 16S ribosomal RNA (16S rRNA) and yeast organism and filamentous fungi 18S ribosomal RNA, and methods of classifying and/or identifying bacteria, yeast organisms and/or filamentous fungi in a sample based on the presence of one or more of those SNPs. The present invention also concerns probes, primers and kits that are useful in those methods.Type: GrantFiled: May 17, 2018Date of Patent: August 29, 2023Assignee: Microbio Pty LtdInventor: Flavia Huygens
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Patent number: 11739379Abstract: The invention provides a method of detecting a target polynucleotide in a sample comprising: (a) contacting the sample with a guide polynucleotide that binds to a sequence in the target polynucleotide and a polynucleotide-guided effector protein, wherein the guide polynucleotide and polynucleotide-guided effector protein form a complex with any target polynucleotide present in the sample; (b) contacting the sample with a membrane comprising a transmembrane pore; (c) applying a potential to the membrane; and (d) monitoring for the presence or absence of an effect resulting from the interaction of the complex with the transmembrane pore to determine the presence or absence of the complex, thereby detecting the target polynucleotide in the sample.Type: GrantFiled: June 29, 2021Date of Patent: August 29, 2023Assignee: Oxford Nanopore Technologies PLCInventors: Andrew John Heron, James Edward Graham, Richard Alexander Gutierrez, Rebecca Victoria Bowen, James White, Clive Gavin Brown, Daniel George Fordham
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Patent number: 11739373Abstract: Provided herein, in some embodiments, are systems, methods, compositions, and kits for detecting and quantifying analytes using a primary analyte binding molecule conjugated to a nucleic acid template.Type: GrantFiled: February 5, 2019Date of Patent: August 29, 2023Assignee: G1 Sciences, LLCInventor: Sudha Haran
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Patent number: 11732290Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.Type: GrantFiled: September 22, 2022Date of Patent: August 22, 2023Assignee: ROCHE SEQUENCING SOLUTIONS, INC.Inventor: Garry P. Nolan
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Patent number: 11732300Abstract: Disclosed herein are methods of amplifying an analyte in a biological sample using a bridging oligonucleotide that hybridizes to a captured analyte. The methods disclosed herein include steps of (a) contacting a biological sample with a substrate having capture probes comprising a capture domain and a spatial barcode; (b) hybridizing the analyte to the capture domain; and (c) contacting the analyte to a bridging oligonucleotide comprising (i) a capture-probe-binding sequence, and (ii) an analyte-binding sequence; (d) extending the bridging oligonucleotide; and (e) determining (i) all or a part of the sequence of the analyte, or a complement thereof, and (ii) the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the location of the analyte in the biological sample.Type: GrantFiled: February 4, 2021Date of Patent: August 22, 2023Assignee: 10x Genomics, Inc.Inventor: Felice Alessio Bava
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Patent number: 11725195Abstract: The present disclosure provides methods, compositions, kits and systems for nucleic acid amplification. In some embodiments, nucleic acid amplification methods include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, nucleic acid amplification methods include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the nucleic acid amplification method employs an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel and/or in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: GrantFiled: April 27, 2021Date of Patent: August 15, 2023Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Shiaw-Min Chen, Jennifer O'Neil, Rachel Kasinskas, Jonathan Rothberg, Bin Li, Kai Qin Lao
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Patent number: 11725179Abstract: An object of the present invention is to purify and concentrate differentiating cells derived from ES cells, iPS cells, or the like without damaging them.Type: GrantFiled: May 12, 2016Date of Patent: August 15, 2023Assignee: ON-CHIP BIOTECHNOLOGIES CO., LTD.Inventors: Kazuo Takeda, Yuu Fujimura, Takahide Ino, Masayuki Ishige, Jin Akagi
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Patent number: 11718848Abstract: A depleted sequencing library can be prepared by providing a composition comprising a heterogeneous mixture of linear nucleic acids having a first terminus and a second terminus. A first subset of target nucleic acids and a second subset of non-target nucleic acids can include a first adaptor region at the first terminus and a second adaptor region at the second terminus. A third subset of the target nucleic acids and a fourth subset of the non-target nucleic acids include the second adaptor region at the first terminus and at the second terminus. Removable blocker oligonucleotides can be added to the composition, non-target nucleic acids can be removed from the composition by sequence capture to bait oligonucleotides, and the composition can be treated to reduce a quantity of free blocker oligonucleotides that are not annealed to an adaptor sequence or to a sequence substantially complementary to an adaptor sequence.Type: GrantFiled: May 27, 2021Date of Patent: August 8, 2023Assignee: Color Health, Inc.Inventors: David Lee, Justin Lock
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Patent number: 11708599Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.Type: GrantFiled: December 21, 2022Date of Patent: July 25, 2023Assignee: ROCHE SEQUENCING SOLUTIONS, INC.Inventor: Garry P. Nolan
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Patent number: 11702706Abstract: The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).Type: GrantFiled: March 4, 2021Date of Patent: July 18, 2023Assignee: Becton, Dickinson and CompanyInventors: Christina Fan, Stephen P. A. Fodor, Glenn Fu, Geoffrey Richard Facer, Julie Wilhelmy
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Patent number: 11702697Abstract: The present invention provides method essentially comprising the steps of (i) providing a DNA sample, (ii) providing at least a first pair of amplification primers which is capable of generating a first amplicon from a LINE sequence that has a size of less than 80 bp, (iii) providing at least a second pair of amplification primers which is capable of generating a second amplicon from a LINE sequence that has a size of more than 160 bp, (iv) performing a qPCR and determining cq values for each of the generated amplicons, and (v) determining the relative concentrations of said amplicons.Type: GrantFiled: May 14, 2018Date of Patent: July 18, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Sophie Beckert, Bernd Hinzmann
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Patent number: 11702689Abstract: This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.Type: GrantFiled: April 24, 2020Date of Patent: July 18, 2023Assignee: MICROSOFT TECHNOLOGY LICENSING, LLCInventors: Yuan-Jyue Chen, Bichlien Nguyen
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Patent number: 11697844Abstract: The present disclose provides methods and systems for amplifying and quantifying nucleic acids and for detecting the presence or absence of a target in a sample. The methods and systems provided herein may utilize a device comprising a plurality of partitions separated from an external environment by a gas-permeable barrier. Certain methods disclosed herein involve subjecting nucleic acid molecules in the plurality of partitions to conditions sufficient to conduct nucleic acid amplification reactions. The nucleic acid molecules may be subjected to controlled heating in the plurality of partitions to generate data indicative of a melting point(s) of the nucleic acid molecules.Type: GrantFiled: October 30, 2019Date of Patent: July 11, 2023Assignee: Combinati IncorporatedInventors: Ju-Sung Hung, Megan Dueck, Andrew Zayac