Patents Examined by Gary Benzion
  • Patent number: 11459598
    Abstract: This invention is directed to a method for detecting near and distant interactions between cells, organelles and other large structures. This method can also be used for specific detection and quantification of Antibody or other binding moiety protein-protein and macro-molecular interactions, as well as quantitative analysis of multiple proteins and their modifications.
    Type: Grant
    Filed: October 20, 2016
    Date of Patent: October 4, 2022
    Assignee: Quateris LLC
    Inventors: Malcolm MacKenzie, Ilya Alexandrov, Michael Sherman
  • Patent number: 11326202
    Abstract: The present invention provides methods, compositions and kits for enriching and determining nucleotide sequences of a plurality of target loci from a sample comprising nucleic acids. The methods comprise one or more cycles of primer extension followed by PCR amplification of target sequences using nested target-specific primers.
    Type: Grant
    Filed: November 23, 2018
    Date of Patent: May 10, 2022
    Inventor: Zongli Zheng
  • Patent number: 11286522
    Abstract: The present disclosure relates to systems and methods for high efficiency electronic sequencing of nucleic acids and molecular detection.
    Type: Grant
    Filed: August 20, 2018
    Date of Patent: March 29, 2022
    Assignee: GENAPSYS, INC.
    Inventor: Hesaam Esfandyarpour
  • Patent number: 11155864
    Abstract: A method including steps of (a) providing an array of sites, wherein each site comprises a mixture of different nucleic acid templates; (b) extending primers hybridized to the different nucleic acid templates at each of the sites with different nucleotide analogs having different reversible blocking moieties, respectively, thereby producing different primer extension products at each site; (c) detecting the different primer extension products to distinguish the different nucleotide analogs at each site; and (d) removing the different reversible blocking moieties from the primer extension products at each of the sites using a first treatment that is selective for a first of the different reversible blocking moieties and a second treatment that is selective for a second of the different reversible blocking moieties.
    Type: Grant
    Filed: July 8, 2016
    Date of Patent: October 26, 2021
    Assignee: Illumina, Inc.
    Inventors: Eliane H Trepagnier, Tarun Khurana
  • Patent number: 11001882
    Abstract: Provided are methods of producing a product nucleic acid. The methods include combining a template deoxyribonucleic acid (DNA), a polymerase, a template switch oligonucleotide, and dNTPs into a reaction mixture. The components are combined into the reaction mixture under conditions sufficient to produce a product nucleic acid that includes the template DNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.
    Type: Grant
    Filed: June 27, 2016
    Date of Patent: May 11, 2021
    Assignee: Takara Bio USA, Inc.
    Inventors: Craig Betts, Andrew Alan Farmer, Nathalie Bolduc
  • Patent number: 10995361
    Abstract: The present invention relates to a method for amplifying at least one target RNA in a fixed and, optionally, expanded biological sample. In an embodiment of the invention, the method comprises incubating the fixed biological sample with a pair of polynucleotides complementary to non-overlapping and proximal sequences of a target RNA, wherein the polynucleotide pair hybridizes to the target RNA; ligating the polynucleotide pair using a ligase; and amplifying the ligation product. The invention further provides methods for detecting and optionally quantifying and/or sequencing the amplification product. As the method comprises hybridizing polynucleotide pairs to a target RNA in a fixed biological sample, the target RNA can be hybridized in situ.
    Type: Grant
    Filed: January 22, 2018
    Date of Patent: May 4, 2021
    Assignee: Massachusetts Institute of Technology
    Inventors: Fei Chen, Asmamaw T. Wassie, Shahar Alon, Adam Henry Marblestone, Anubhav Sinha, Andrew Payne, Edward Stuart Boyden
  • Patent number: 10801058
    Abstract: Disclosed is a method of quality control of nucleic acid amplification using quality control oligonucleotide. The method comprises a nucleic acid detection step and a determination step. The nucleic acid detection step comprises the steps of: preparing a nucleic acid sample containing a target nucleic acid and a quality control polynucleotide; preparing a compartment containing one molecule of the target nucleic acid and a compartment containing one molecule of the quality control polynucleotide; and carrying out nucleic acid amplification of the target nucleic acid and the quality control polynucleotide, in the compartments, and carrying out signal detection using a detection probe to detect a signal originated from the detection probe. In the determination step, it is determined as to whether or not the nucleic acid detection step is proper on the basis of the result obtained in the signal detection step.
    Type: Grant
    Filed: January 13, 2017
    Date of Patent: October 13, 2020
    Inventors: Tsuyoshi Nakano, Yuichiro Yoshida
  • Patent number: 10793922
    Abstract: The present invention provides methods for rapidly identifying an RNA viral infection using an isothermal nucleic acid amplification reaction that can be carried out extracted RNA in the context of a crude biological sample.
    Type: Grant
    Filed: October 20, 2015
    Date of Patent: October 6, 2020
    Assignee: ENVIROLOGIX INC.
    Inventors: Lars Peters, Stephen A. Judice, Daniel Shaffer, Breck Parker
  • Patent number: 10787703
    Abstract: Genomic DNA contains embedded ribonucleotides (rNMPs) that are incorporated during DNA replication and repair, or formed during DNA damage. The modifications have been linked to genome instability and disease, but no method currently exists to profile their locations genome-wide. rNMP incorporation has been extensively studied in recent years; however, locating sites of rNMP incorporation in genomic DNA has not yet been possible. Disclosed herein is a unique method for mapping rNMPs in genomic DNA that exploits the unique ligation mechanism of Arabidopsis thaliana tRNA ligase (AtRNL), normally involved in tRNA maturation. As disclosed herein AtRNL captures 2?,3?-cyclic phosphate or 2?-phosphate termini of DNA derived from alkaline cleavage of a DNA oligonucleotide (oligo) at an embedded rNMP, ligating the 2?-phosphate end to the 5?-phosphate terminus of the same DNA molecule and producing a ssDNA circle containing an embedded rNMP.
    Type: Grant
    Filed: January 9, 2017
    Date of Patent: September 29, 2020
    Assignee: Georgia Tech Research Corporation
    Inventors: Francesca Storici, Jay Hesselberth, Kyung Duk Koh
  • Patent number: 10758908
    Abstract: A self-metering reaction device has a sample reservoir, configured to accept a varying amount of fluid; a metering reservoir, configured to be a subportion of the sample reservoir and to hold a reaction amount of the fluid; a reaction chamber fluidly connected to the metering reservoir; and a plunger comprising a tip configured to make a seal with the metering reservoir so that the reaction amount of the fluid is sealed within the metering reservoir when the plunger is in contact with the metering reservoir. The plunger can be configured to plunge the sealed reaction amount of the fluid from the metering reservoir into the reaction chamber.
    Type: Grant
    Filed: September 2, 2016
    Date of Patent: September 1, 2020
    Assignee: Tetracore, Inc.
    Inventors: William M. Nelson, Aymeric Randanne de Vazeille, Kyle Armantrout
  • Patent number: 10760074
    Abstract: A composition for use in amplifying cDNA synthesized by a reverse transcription reaction and detecting RNA that serves as a template of the reverse transcription reaction, the composition containing a thermostable DNA polymerase, a thermostable ribonuclease H, and an intercalating dye. Since the composition of the present invention can suppress the influences to the nucleic acid amplification reaction by RNA that serves as a template for cDNA synthesis, the composition is useful in the detection of RNA, and more useful in quantification of RNA having a desired sequence by real-time RT-PCR.
    Type: Grant
    Filed: August 31, 2009
    Date of Patent: September 1, 2020
    Assignee: TAKARA BIO INC.
    Inventors: Kanako Usui, Takashi Uemori, Hiroyuki Mukai, Ikunoshin Kato
  • Patent number: 10745711
    Abstract: Compositions and methods related to transgenic high oleic acid/ALS inhibitor-tolerant soybean plants are provided. Specifically, the present invention provides soybean plants having a DP-305423-1 event which imparts a high oleic acid phenotype and tolerance to at least one ALS-inhibiting herbicide. The soybean plant harboring the DP-305423-1 event comprises genomic/transgene junctions having at least the polynucleotide sequence of SEQ ID NO:8, 9, 14, 15, 20, 21, 83 or 84. The characterization of the genomic insertion site of the DP-305423-1 event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the soybean DP-305423-1 events are provided.
    Type: Grant
    Filed: October 18, 2017
    Date of Patent: August 18, 2020
    Inventors: Anthony J Kinney, Kent Brink, Robert F. Cressman, Jr., Knut Meyer, Kevin L. Stecca, Natalie N. Weber, Cathy Xiaoyan Zhong
  • Patent number: 10731227
    Abstract: Provided herein include compositions comprising a primer having the nucleic acid sequence of ACeIN-F3_c, a primer having the nucleic acid sequence of ACeIN-B3_a, a primer having the nucleic acid sequence of ACeIN-B3_b, a primer having the nucleic acid sequence of ACeIN-FIP_e, a primer having the nucleic acid sequence of ACeIN-FIP_f, a primer having the nucleic acid sequence of ACeIN-BIP (or ACeIN-BIP-song), a primer having the nucleic acid sequence of ACeIN-LF; and a primer having the nucleic acid sequence of ACeIN-LB. Also provided are methods of detecting human immunodeficiency virus (HIV) nucleic acids in a sample comprising performing reverse transcription-based loop mediated isothermal amplification (RT-LAMP) on a sample using the previously disclosed compositions.
    Type: Grant
    Filed: December 11, 2015
    Date of Patent: August 4, 2020
    Assignee: The Trustees of the University of Pennsylvania
    Inventors: Changchun Liu, Scott Sherrill-Mix, Haim H. Bau, Frederic D. Bushman, Karen E. Ocwieja, Jinzhao Song
  • Patent number: 10704095
    Abstract: The purpose of the present invention is to provide a method and kit for highly precise DNA typing, in which ambiguity derived from phase ambiguity is eliminated. The present invention provides a method for the DNA typing of HLA, which is characterized by comprising: (1) a step of preparing a set of primers which can respectively anneal specifically to an upstream region and a downstream region of each of HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DPA1 and HLA-DPB1 gene in the nucleotide sequence for the human genome, and a set of primers which can respectively anneal specifically to exon-2 and a 3?-side non-translated region in HLA-DRB1; (2) a step of carrying out the PCR amplification of a sample to be tested (DNA) using the sets of primers; (3) a step of determining the nucleotide sequence for a PCR-amplified product; and (4) an optional step of carrying out the homology search in a data base.
    Type: Grant
    Filed: April 1, 2016
    Date of Patent: July 7, 2020
    Inventors: Takashi Shiina, Shingo Suzuki, Yuki Wada, Shigeki Mitsunaga, Hidetoshi Inoko
  • Patent number: 10689712
    Abstract: Compositions, reaction mixtures, kits and methods used in amplifying and detecting nucleic acids from various species of the class Mollicutes. Particular regions of the 23S rRNA or its gene have been identified as preferred targets for nucleic acid amplification reactions of a sample suspected containing at least one species of Mollicutes. Some oligomers comprise tag regions, target closing regions, promoter sequences, and/or binding moieties. Samples can be from any source suspected of containing a species of the class Mollicutes. Preferred sample sources include bioreactors, cell lines, cell culture wares and pharmaceutical manufacturing wares.
    Type: Grant
    Filed: September 8, 2017
    Date of Patent: June 23, 2020
    Inventors: Shannon K. Kaplan, Kristin W. Livezey, Michael M. Becker, James J. Hogan
  • Patent number: 10676796
    Abstract: Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of a 16S rRNA or its encoding gene from bacterial species associated with bacterial vaginosis. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.
    Type: Grant
    Filed: October 23, 2018
    Date of Patent: June 9, 2020
    Inventor: Damon K. Getman
  • Patent number: 10669594
    Abstract: Provided are compositions and methods useful to the determination of whether a microbial contaminant is present in a biological therapeutic production process. Specifically, an artificial positive amplification control plasmid and unique quantitative PCR detection probe are provided, which enables the rapid and real-time detection of a false positive result.
    Type: Grant
    Filed: March 25, 2016
    Date of Patent: June 2, 2020
    Assignee: Regeneron Pharmaceuticals, Inc.
    Inventors: Serge Monpoeho, Sheldon Mink, Paul Vescio
  • Patent number: 10633712
    Abstract: The technology described herein relates to assays and methods for the diagnosis, prognosis, and/or treatment of melanoma, e.g. relating to measuring the level of neurophilin-2 (NRP-2) mRNA expressed in melanoma cells. In some embodiments, the level of NRP-2 can be normalized to the level of Melan-A (MART) mRNA.
    Type: Grant
    Filed: December 4, 2018
    Date of Patent: April 28, 2020
    Inventors: Rhoda M. Alani, Byungwoo Ryu
  • Patent number: 10620202
    Abstract: The invention provides methods and kits for the rapid confirmation of an initial analyte test result. In a preferred embodiment, the process confirms the presence of a given microbial target in a mixed culture, or a mixed enrichment media, even when the competing organisms in the mix belong to related species, or are various biotypes of the same species.
    Type: Grant
    Filed: April 27, 2009
    Date of Patent: April 14, 2020
    Assignee: Institute for Environmental Health, Inc.
    Inventor: Mansour Samadpour
  • Patent number: 10604798
    Abstract: A heating mechanism for use in DNA applications such as DNA amplification, extraction and sterilization is provided. Nanoparticles having photo-thermal properties are put in contact with a reaction mixture and irradiated with an activation light beam to activate these photo-thermal properties, thereby releasing heat. Nanoparticles of several types may be used. Use of the same nanoparticles or of different one to monitor the reaction using a different light beam is also presented.
    Type: Grant
    Filed: August 17, 2018
    Date of Patent: March 31, 2020
    Inventors: Philip Roche, Andrew Kirk, Lenore Beitel, Miltiadis Paliouras, Mark Trifiro, Vamsy Chodavarapu, Mohamed Najih, Joachim Thiemann