Patents Examined by Samuel C. Woolwine
  • Patent number: 11987841
    Abstract: Embodiments of a method and/or system (e.g., for improved single molecule sequencing, etc.) can include preparing a set of unique molecular identifier (UMI)-based molecules associated with a set of target nucleic acid sequences; facilitating generation of (e.g., generating, etc.) a set of tagged nucleic acid molecules based on the set of UMI-based molecules and a set of nucleic acid molecules corresponding to (e.g., including, etc.) the set of target nucleic acid sequences; and/or facilitating (e.g., performing, etc.) single molecule sequencing with the set of tagged nucleic acid molecules.
    Type: Grant
    Filed: October 9, 2018
    Date of Patent: May 21, 2024
    Assignee: Psomagen, Inc.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Eduardo Morales, Luis Leon, Sara W. Bird, Juan Ugalde
  • Patent number: 11981956
    Abstract: Provided herein, in some embodiments, are compositions and methods for proximity detection of molecular targets.
    Type: Grant
    Filed: January 25, 2019
    Date of Patent: May 14, 2024
    Assignee: President and Fellows of Harvard College
    Inventors: Sinem K. Saka, Jocelyn Yoshiko Kishi, Peng Yin
  • Patent number: 11981917
    Abstract: Methods of modulating expression of a target nucleic acid in a cell are provided including introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to DNA, wherein the DNA includes the target nucleic acid, introducing into the cell a second foreign nucleic acid encoding a nuclease-null Cas9 protein that binds to the DNA and is guided by the one or more RNAs, introducing into the cell a third foreign nucleic acid encoding a transcriptional regulator protein or domain, wherein the one or more RNAs, the nuclease-null Cas9 protein, and the transcriptional regulator protein or domain are expressed, wherein the one or more RNAs, the nuclease-null Cas9 protein and the transcriptional regulator protein or domain co-localize to the DNA and wherein the transcriptional regulator protein or domain regulates expression of the target nucleic acid.
    Type: Grant
    Filed: October 25, 2022
    Date of Patent: May 14, 2024
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Prashant G. Mali, Kevin M. Esvelt
  • Patent number: 11981960
    Abstract: Provided are methods of capturing an analyte from a biological sample using a hydrogel that includes capture probes to capture the analyte, identifying a region of interest of the biological sample, and isolating the region of interest from the biological sample by removing a portion of the hydrogel that corresponds to the region of interest. Compositions and kits for performing the methods are also provided.
    Type: Grant
    Filed: July 6, 2021
    Date of Patent: May 14, 2024
    Assignee: 10x Genomics, Inc.
    Inventors: Bill Kengli Lin, Jill Herschleb, Cedric Uytingco
  • Patent number: 11976306
    Abstract: Thermostable Cas9 nucleases. The present invention relates to the field of genetic engineering and more particularly to nucleic acid editing and genome modification. The present invention provides an isolated Cas protein or polypeptide fragment thereof having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 77% identity therewith. The Cas protein or polypeptide is capable of binding, cleaving, marking or modifying a double stranded target polynucleotide at a temperature in the range 20° C. and 100° C. inclusive. The invention further provides isolated nucleic acid molecules encoding said Cas9 nucleases, expression vectors and host cells. The invention also provides PAM sequences recognized by the Cas protein or polypeptide, The Cas9 nucleases disclosed herein provide novel tools for genetic engineering in general, in particular at elevated temperatures.
    Type: Grant
    Filed: August 16, 2017
    Date of Patent: May 7, 2024
    Assignees: Stichting Voor De Technische Wetenschappen, WAGENINGEN UNIVERSITEIT
    Inventors: John Van Der Oost, Richard Van Kranenburg, Elleke Fenna Bosma, Ioannis Mougiakos, Prarthana Mohanraju
  • Patent number: 11970692
    Abstract: Disclosed herein are embodiments of a fixed magnet assembly that can be implemented into automated platforms for performing polynucleotide extraction from biological samples and preparing the polynucleotides into an amplification-ready form. The fixed magnet assembly can be used to provide magnetic energy to a container containing magnetic particles and a reaction mixture of polynucleotides, in order to bring about a separation of the magnetic particles from the reaction mixture. This can prevent or reduce magnetic particle carryover in the prepared amplification-ready sample, thereby improving amplification results.
    Type: Grant
    Filed: December 10, 2020
    Date of Patent: April 30, 2024
    Assignee: Becton, Dickinson and Company
    Inventors: Edward Carrese, Alexandre Daviet, Rohini Rao, Alyssa Shedlosky, Ben Hopwood, Dwight Livingston
  • Patent number: 11965217
    Abstract: A method and a kit for detecting Mycobacterium tuberculosis are provided. The method includes a step of performing a nested qPCR assay to a specimen. The nested qPCR assay includes a first round of amplification using external primers and a second round of amplification using internal primers and a probe. The external primers have sequences of SEQ ID NOs. 1 and 2, and the internal primers and the probe have sequences of SEQ ID NOs. 3 to 5.
    Type: Grant
    Filed: May 24, 2021
    Date of Patent: April 23, 2024
    Assignee: DELTA ELECTRONICS, INC.
    Inventors: Yi-Chen Li, Chih-Cheng Tsou, Min-Hsien Wu, Hsin-Yao Wang, Chien-Ru Lin
  • Patent number: 11953495
    Abstract: Disclosed are a molecule detection unit, a chip and a preparation method. The molecule detection unit includes a single-hole liquid storage cavity, a liquid resistance flow channel, a buffer flow channel, a sensing electrode, a substrate, a first structural layer, a second structural layer and a sample flow channel. The first structural layer is arranged on the top of the substrate; the single-hole liquid storage cavity and the buffer flow channel are arranged in the first structural layer and are independent of each other; the liquid resistance flow channel is arranged in the first structural layer, and two ends of the liquid resistance flow channel are respectively communicated with the single-hole liquid storage cavity and the buffer flow channel; the second structural layer is arranged on the top of the first structural layer and covers the top of the buffer flow channel.
    Type: Grant
    Filed: September 20, 2023
    Date of Patent: April 9, 2024
    Assignee: Beijing Qitan Tech Co., Ltd.
    Inventors: Yuan Wang, Xiaoxiang Xia, Lu Song
  • Patent number: 11952622
    Abstract: Methods for analyzing DNA-containing samples are provided. The methods can comprise isolating a single genomic equivalent of DNA from the DNA-containing sample to provide a single isolated DNA molecule. The single isolated DNA molecule can be subjected to amplification conditions in the presence of one or more sets of unique molecularly tagged primers to provide one or more amplicons. Any spurious allelic sequences generated during the amplification process are tagged with an identical molecular tag. The methods can also include a step of determining the sequence of the one or more amplicons, in which the majority sequence for each code is selected as the sequence of the single original encapsulated target. The DNA-containing sample can be a forensic sample (e.g., mixed contributor sample), a fetal genetic screening sample, or a biological cell.
    Type: Grant
    Filed: July 15, 2014
    Date of Patent: April 9, 2024
    Assignee: The Johns Hopkins University
    Inventors: Andrew B. Feldman, Jeffrey S. Lin, David Weitz, Assaf Rotem
  • Patent number: 11946067
    Abstract: The present invention concerns a genetic tool comprising at least two distinct nucleic acids optimized to facilitate the transformation and modification by homologous recombination of a bacterium of the genus Clostridium, typically a solventogenic bacterium.
    Type: Grant
    Filed: May 24, 2019
    Date of Patent: April 2, 2024
    Assignee: IFP ENERGIES NOUVELLES
    Inventors: Nicolas Lopes Ferreira, François Wasels, Gwladys Chartier
  • Patent number: 11946099
    Abstract: The invention comprises a method of amplifying nucleic acids by primer extension with reduced formation of primer-primer byproducts.
    Type: Grant
    Filed: February 23, 2021
    Date of Patent: April 2, 2024
    Assignee: ROCHE SEQUENCING SOLUTIONS, INC.
    Inventor: Brian Godwin
  • Patent number: 11939604
    Abstract: A clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for adaptive antiviral defence (Cascade); the Cascade protein complex comprising at least CRISPR-associated protein subunits Cas7, Cas5 and Cash which includes at least one subunit with an additional amino acid sequence possessing nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity. The Cascade complex with additional activity is combined with an RNA molecule to produce a ribonucleoprotein complex. The RNA molecule is selected to have substantial complementarity to a target sequence. Targeted ribonucleoproteins can be used as genetic engineering tools for precise cutting of nucleic acids in homologous recombination, non-homologous end joining, gene modification, gene integration, mutation repair or for their visualisation, transcriptional activation or repression.
    Type: Grant
    Filed: February 18, 2021
    Date of Patent: March 26, 2024
    Assignee: Caribou Biosciences, Inc.
    Inventors: Stan Johan Jozef Brouns, John van der Oost
  • Patent number: 11920151
    Abstract: Provided are: a composition for DNA double-strand breaks (DSBs), comprising (1) a cytosine deaminase and an inactivated target-specific endonuclease, (2) a guide RNA, and (3) a uracil-specific excision reagent (USER); a method for producing DNA double-strand breaks by means of a cytosine deaminase using the composition; a method for analyzing a DNA nucleic acid sequence to which base editing has been introduced by means of a cytosine deaminase; and a method for identifying (or measuring or detecting) base editing, base editing efficiency at an on-target site, an off-target site, and/or target specificity by means of a cytosine deaminase.
    Type: Grant
    Filed: September 13, 2017
    Date of Patent: March 5, 2024
    Assignees: TOOLGEN INCORPORATED, SEOUL NATIONAL UNIVERSITY R&Db FOUNDATION, INSTITUTE FOR BASIC SCIENCE
    Inventor: Daesik Kim
  • Patent number: 11913081
    Abstract: A proximity dependent split T7 RNAP (RNA polymerase) sensor using continuous molecular evolution is described. The versatility of the platform is described by creating robust light and small molecule-responsive genetic sensors. The activity-responsive RNAP platform dramatically simplifies and expands genetic circuit creation, and opens new opportunities in protein engineering, synthetic biology, and bioengineering.
    Type: Grant
    Filed: June 6, 2017
    Date of Patent: February 27, 2024
    Assignee: The University of Chicago
    Inventors: Bryan C. Dickinson, Jinyue Pu, Julia Zinkus
  • Patent number: 11913017
    Abstract: A guide RNA comprising: a gRNA spacer sequence at the 5? end of the guide RNA, wherein the spacer sequence is complementary to a target gene, a scaffold sequence that binds to Cas9, and an RNA capture and sequencing domain comprising: a barcode sequence, and a primer binding sequence; nucleic acids and vectors encoding the guide RNA; cells expressing the guide RNA; and a library comprising a plurality of guide RNAs. Also disclosed are methods of introducing a genetic perturbation into a cell, methods of assessing an effect of at least one genetic perturbation on RNA expression in a cell, methods of identifying nucleic acid sequences associated with a disease state and a method of identifying candidate therapeutic agents.
    Type: Grant
    Filed: June 28, 2017
    Date of Patent: February 27, 2024
    Assignee: The Regents of the University of California
    Inventors: Kun Zhang, Prashant Mali, Yan Wu, Dongxin Zhao
  • Patent number: 11915795
    Abstract: Methods are provided for nucleic acid analysis via a platform which incorporates a digital sample partitioning platform such as a microfluidic chip or digital droplet platform and instrumentation to accomplish universal amplification, High Resolution Melting (HRM), and machine learning within reactions simultaneously.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: February 27, 2024
    Assignee: The Regents of the University of California
    Inventors: Stephanie I. Fraley, Sinead Charpentier, Daniel Ortiz Velez, Mridu Sinha, Benjamin Albert Yang
  • Patent number: 11905549
    Abstract: Provided is a method of modifying a target site in the genome of a eukaryotic cell, the method comprising: (1) a step of introducing into the cell, introduction nucleic acids comprising (a) a template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease, (b) a template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or a guide RNA, and (c) a template nucleic acid comprising a nucleic acid sequence encoding a selectable marker; and (2) a step of selecting a cell expressing the selectable marker, wherein the number of moles (C) of (c) the template nucleic acid comprising a nucleic acid sequence encoding a selectable marker, subjected to the step (1), is smaller than any of the number of moles (A) of (a) the template nucleic acid comprising a nucleic acid sequence encoding an RNA-guided nuclease and the number of moles (B) of (b) the template nucleic acid comprising a nucleic acid sequence encoding a guide RNA, or the guide RNA.
    Type: Grant
    Filed: August 9, 2017
    Date of Patent: February 20, 2024
    Assignee: GENAHEAD BIO, INC.
    Inventor: Tsukasa Sugo
  • Patent number: 11906511
    Abstract: The present invention provides compositions and methods for detecting exhausted T cells in a subject. The present invention also provides methods for treating a subject having a disease characterized by the presence of exhausted T cells or certain subpopulations thereof.
    Type: Grant
    Filed: October 26, 2018
    Date of Patent: February 20, 2024
    Assignee: The Trustees of the University of Pennsylvania
    Inventors: E. John Wherry, Bertram Bengsch, Omar Khan, Jennifer Wu, Josephine Giles
  • Patent number: 11905554
    Abstract: A sequencing primer set comprising a universal upstream primer, a universal downstream primer and a downstream primer in rich of promoter; wherein the universal upstream primer has a sequence of: 5?-TBarcodeCAAAXXXXNNN-3?; the universal downstream primer has a sequence of: 5?-GACTGCGTACGZZZZNNN-3?(SEQ ID No. 9); the downstream primer in rich of promoter has a sequence of: 5?-GACTGCGTACYYNCTATA-3?(SEQ ID No. 7).
    Type: Grant
    Filed: September 25, 2020
    Date of Patent: February 20, 2024
    Inventors: Zhiqiang Xia, Meiling Zou, Wenquan Wang
  • Patent number: 11896678
    Abstract: The present disclosure provides compositions and methods for the treatment of PPARG activated cancer. For example, the present disclosure provides PPARG signaling modulators for the treatment of bladder cancer. In particular, therapeutic and/or prophylactic compositions and uses of PPARG inverse-agonists are described.
    Type: Grant
    Filed: March 28, 2018
    Date of Patent: February 13, 2024
    Assignees: Dana-Farber Cancer Institute, Inc., The Broad Institute, Inc.
    Inventors: Jonathan Goldstein, Matthew Meyerson, Craig Strathdee