Patents Examined by Jennifer Dunston
  • Patent number: 11993772
    Abstract: Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids.
    Type: Grant
    Filed: March 25, 2019
    Date of Patent: May 28, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Frank J. Steemers, Kevin L Gunderson, Thomas Royce, Natasha Pignatelli, Igor Goryshin, Nicholas Caruccio
  • Patent number: 11993784
    Abstract: Gene therapy compositions and methods are provided that make use of novel transposases and/or chimeric transposases for targeted transposition.
    Type: Grant
    Filed: March 29, 2023
    Date of Patent: May 28, 2024
    Assignee: Saliogen Therapeutics, Inc.
    Inventors: Joseph J. Higgins, Scott McMillan, Ray Tabibiazar
  • Patent number: 11987605
    Abstract: The present disclosure provides technologies for MYC inhibition, including, e.g. MYC fusion polypeptides and compositions comprising the same as well as methods of using the same. In particular, the present disclosure, among others, provides fusion polypeptides comprising a mutant MYC polypeptide and a repressor domain. In some embodiments, such fusion polypeptides and compositions comprising the same can be useful for inducing cancer cell apoptosis. Accordingly, in some embodiments, such fusion polypeptides and compositions comprising the same can be useful for cancer treatment.
    Type: Grant
    Filed: September 18, 2020
    Date of Patent: May 21, 2024
    Assignee: Helix Nanotechnologies Inc
    Inventors: Taylor Gill, Hannu Rajaniemi, Nikolai Eroshenko
  • Patent number: 11898141
    Abstract: Disclosed is a method of generating a set of sequence-verified nucleic acid elements for the combinatorial construction of genetic elements. The method includes: providing a plurality of nucleic acid parts; assembling nucleic acid parts to form a one or more nucleic acid elements, wherein the nucleic acid elements include at least two sequences selected from the plurality of parts; and determining the sequence of the nucleic acid elements. Further disclosed is a pool of higher-order nucleic acid constructs or amplification products thereof, comprising one or more nucleic acid elements as well as kits including a pool of sequence-verified nucleic acid elements of claims and/or a pool of higher-order nucleic acid constructs; and a plurality of primers for retrieving one or more sequence-verified nucleic acid elements and/or higher-order nucleic acid constructs.
    Type: Grant
    Filed: May 27, 2015
    Date of Patent: February 13, 2024
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventors: Robert Nicol, Lauren Andrews, Tarjei Mikkelsen, Christopher Voigt
  • Patent number: 11896651
    Abstract: Provided herein are compositions, methods, kits, and viral particles for treating a disease or disorder associated with a deep intronic mutation using an engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system. In some aspects, provided herein is a self-limiting CRISPER-Cas system.
    Type: Grant
    Filed: April 15, 2016
    Date of Patent: February 13, 2024
    Assignee: GENZYME CORPORATION
    Inventors: Guoxiang Ruan, Abraham Scaria
  • Patent number: 11898160
    Abstract: The present application describes a method for inducing or maintaining pluripotency in a cell by contacting the cell with a biological or chemical species that increases MUC1* activity.
    Type: Grant
    Filed: October 9, 2009
    Date of Patent: February 13, 2024
    Assignee: MINERVA BIOTECHNOLOGIES CORPORATION
    Inventors: Cynthia C. Bamdad, Shawn P. Fessler
  • Patent number: 11891631
    Abstract: Fusion proteins comprising a DNA binding domain, e.g., a TAL effector repeat array (TALE) or zinc finger array, and a catalytic domain comprising a sequence that catalyzes histone demethylation, and methods of use thereof.
    Type: Grant
    Filed: April 5, 2019
    Date of Patent: February 6, 2024
    Assignee: The General Hospital Corporation
    Inventors: Jae Keith Joung, Eric M. Mendenhall, Bradley E. Bernstein, Deepak Reyon
  • Patent number: 11884925
    Abstract: Provided herein are CRISPR-based synthetic repression systems as well as methods and compositions using the synthetic repression systems to treat septicemia, an adverse immune response in a subject and Waldenström macroglobulinemia.
    Type: Grant
    Filed: November 7, 2019
    Date of Patent: January 30, 2024
    Assignee: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY
    Inventors: Samira Kiani, Mo Reza Ebrahimkhani, Farzaneh Moghadam
  • Patent number: 11884917
    Abstract: An expression cassette for conditional expression of a single guide RNA (sgRNA) of a CRISPR/Cas9 system, the cassette includes a promoter, an sgRNA sequence, and a sequence flanked by at least a pair of recombinase recognition sites, wherein recombinase activated re-combination at the pair of recombinase recognition sites is capable of excising said flanked sequence, whereby either i) at least one of said recombinase recognition sites is located within the sgRNA sequence and said flanked sequence contains an transcription disruption sequence or ii) said flanked sequence is at least a part of the promoter or of the sgRNA sequence; methods of conditional expression of sgRNA and a reaction product of the conditional expression, i.e. sgRNA with a recombination site remnant.
    Type: Grant
    Filed: March 17, 2017
    Date of Patent: January 30, 2024
    Assignees: IMBA—INSTITUT FÜR MOLEKULARE BIOTECHNOLOGIE GMBH, CAMPUS SCIENCE SUPPORT FACILITIES GMBH
    Inventors: Ulrich Elling, Krzysztof Chylinski, Maria Hubmann, Monika Borowska, Ivana Bilusic-Vilagos
  • Patent number: 11834699
    Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.
    Type: Grant
    Filed: April 1, 2019
    Date of Patent: December 5, 2023
    Assignee: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Patent number: 11827879
    Abstract: RNA molecules comprising a guide sequence portion having 17-20 nucleotides in the sequence of 17-20 contiguous nucleotides set forth in any one of SEQ ID NOs: 1-3010 and compositions, methods, and uses thereof.
    Type: Grant
    Filed: November 28, 2018
    Date of Patent: November 28, 2023
    Assignee: EmendoBio, Inc.
    Inventors: Lior Izhar, David Baram, Joseph Georgeson, Michal Golan-Mashiach, Asael Herman, Rafi Emmanuel
  • Patent number: 11827919
    Abstract: The present disclosure provides methods for detecting a single-stranded target RNA. The present disclosure provides methods of cleaving a precursor C2c2 guide RNA array into two or more C2c2 guide RNAs. The present disclosure provides a kit for detecting a target RNA in a sample.
    Type: Grant
    Filed: March 13, 2018
    Date of Patent: November 28, 2023
    Assignee: The Regents of the University of California
    Inventors: Jennifer A Doudna, Mitchell Ray O'Connell, Alexandra East-Seletsky, Spencer Charles Knight, James Harrison Doudna Cate
  • Patent number: 11795452
    Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named a PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.
    Type: Grant
    Filed: May 23, 2022
    Date of Patent: October 24, 2023
    Assignees: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone
  • Patent number: 11767534
    Abstract: The invention provides methods for determining the activity of a plurality of nucleic acid regulatory elements. These methods may facilitate, e.g., the systematic reverse engineering, and optimization of mammalian cis-regulatory elements at high resolution and at a large scale. The method may include integration of multiplexed DNA synthesis and sequencing technologies to generate and quantify the transcriptional regulatory activity of e.g., thousands of arbitrary DNA sequences in parallel in cell-based as says (e.g., mammalian cell based assays).
    Type: Grant
    Filed: May 4, 2012
    Date of Patent: September 26, 2023
    Assignee: THE BROAD INSTITUTE, INC.
    Inventors: Tarjei Mikkelsen, Andreas Gnirke, Alexandre Melnikov, Eric S. Lander, Li Wang, Xiaolan Zhang
  • Patent number: 11761001
    Abstract: Mbp_Argonaute proteins from prokaryotes and application thereof are provided. The Mbp_Argonaute protein consists of an amino acid sequence as shown in SEQ ID NO: 1 or a sequence with at least 50% or at least 80% of homology with the amino acid sequence as shown in SEQ ID NO: 1. An Argonaute protein gene derived from a cold-resistant prokaryote Mucilaginibacter paaluis is synthesized and named as MbpAgo, which has binding activity to single-stranded guide DNA and has nuclease activity to target RNA and/or target DNA complementarily paired with the single-stranded guide DNA, the MbpAgo can be used for the target RNA editing in vivo and in vitro to achieve site-specific modification of genetic material. The MbpAgo can modify highly-structured RNAs and not affect an endogenous RNAi pathway of animal and plant cells, provides a new and powerful tool for RNA editing with high cleavage activity and good specificity.
    Type: Grant
    Filed: June 30, 2022
    Date of Patent: September 19, 2023
    Assignee: HUBEI UNIVERSITY
    Inventors: Lixin Ma, Wenqiang Li, Fei Wang, Ruyi He, Yang Liu
  • Patent number: 11739309
    Abstract: The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA. The present disclosure provides methods of modulating transcription of a target nucleic acid.
    Type: Grant
    Filed: August 16, 2021
    Date of Patent: August 29, 2023
    Assignee: The Regents of the University of California
    Inventors: Jennifer A. Doudna, Basem Al-Shayeb, Jillian F. Banfield, Patrick Pausch
  • Patent number: 11702707
    Abstract: A method of determining water quality of a water sample, comprising exposing the water sample to a test cell system; generating at least one profile of ensuing changes in activities of transcription factors in the test cell system in response to such exposing; and determining from the generated at least one profile the water quality of the water sample. Computer systems and kits for carrying out the water quality determination of water specimens are also described, in which water quality can be readily and accurately determined by transcription factor activity analysis.
    Type: Grant
    Filed: September 8, 2012
    Date of Patent: July 18, 2023
    Assignee: ATTAGENE, INC.
    Inventors: Sergei S. Makarov, Alexander Vladimirovich Medvedev
  • Patent number: 11680254
    Abstract: The present invention encompasses engineered meganucleases which recognize and cleave a recognition sequence within the human PCSK9 gene. The present invention also encompasses methods for using such engineered meganucleases in a pharmaceutical composition and in methods for treating or reducing the symptoms of cholesterol-related disorders, such as hypercholesterolemia. Further, the invention encompasses pharmaceutical compositions comprising engineered meganuclease proteins, nucleic acids encoding engineered meganucleases, and the use of such compositions for treating cholesterol-related disorders, such as hypercholesterolemia.
    Type: Grant
    Filed: April 20, 2018
    Date of Patent: June 20, 2023
    Assignee: PRECISION BIOSCIENCES, INC.
    Inventors: Victor Bartsevich, Derek Jantz, James Jefferson Smith, Janel Lape
  • Patent number: 11680267
    Abstract: The present disclosure provides a nucleic acid sequence for regulating the transcription of a nucleic acid fragment of interest, wherein the nucleic acid sequence comprises at least 2 copies of TetO-operator sequences capable of binding to a transactivator rtTA regulatable by tetracycline or a derivative thereof, and 1 copy of minimal promoter sequence containing a TATA box sequence, and at least 1 copy of a CuO-operator sequence capable of binding to a transcription repressor CymR regulatable by cumate. The present disclosure also provides a vector and a host cell containing the nucleic acid sequence, and a method for inducing the expression of a nucleic acid fragment of interest in a host cell.
    Type: Grant
    Filed: September 16, 2020
    Date of Patent: June 20, 2023
    Assignee: Shenzhen Eureka Biotechnology Co., Ltd.
    Inventors: Bofu Xue, Yinhui Yang, Ke Liu, Mo Ma
  • Patent number: 11674154
    Abstract: In some aspects, the disclosure relates to compositions and methods for treating fibrodysplasia ossificans progressiva (FOP) in a subject. In some aspects, the disclosure provides isolated nucleic acids, and vectors such as rAAV vectors, configured to express transgenes that inhibit (e.g., decrease) expression of mutated AVCR1 gene in muscle cells or connective tissues.
    Type: Grant
    Filed: December 2, 2021
    Date of Patent: June 13, 2023
    Assignee: University of Massachusetts
    Inventors: Jae-Hyuck Shim, Guangping Gao, Jun Xie, Yeon-Suk Yang, Jung min Kim, Sachin Chaugule