Patents Examined by Richard Hutson
  • Patent number: 9714915
    Abstract: Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions.
    Type: Grant
    Filed: May 28, 2015
    Date of Patent: July 25, 2017
    Assignee: Life Technologies Corporation
    Inventors: John Davidson, Wolfgang Hinz, Jonathan Rothberg, Richard Whitaker
  • Patent number: 9708646
    Abstract: The present disclosure provides variant Csy4 endoribonucleases, nucleic acids encoding the variant Csy4 endoribonucleases, and host cells genetically modified with the nucleic acids. The variant Csy4 endoribonucleases find use in a variety of applications, which are also provided. The present disclosure also provides methods of detecting a specific sequence in a target polyribonucleotide; and methods of regulating production of a target RNA in a eukaryotic cell.
    Type: Grant
    Filed: February 10, 2017
    Date of Patent: July 18, 2017
    Assignee: The Regents of the University of California
    Inventors: Rachel E. Haurwitz, Jennifer A. Doudna, Blake Wiedenheft, Martin Jinek
  • Patent number: 9708598
    Abstract: This invention provides for methods of sequencing and performing polymerase reactions using an improved generation of nucleic acid polymerases. The improvement is the fusion of a sequence-non-specific nucleic-acid-binding domain to the enzyme in a manner that enhances the processivity of the polymerase.
    Type: Grant
    Filed: August 20, 2015
    Date of Patent: July 18, 2017
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Yan Wang, Peter Vander Horn, Lei Xi
  • Patent number: 9695471
    Abstract: Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.
    Type: Grant
    Filed: December 29, 2014
    Date of Patent: July 4, 2017
    Assignee: Life Technologies Corporation
    Inventors: Joseph Beechem, Theo Nikiforov, Vi-En Choong, Xinzhan Peng, Guobin Luo, Cheng-Yao Chen, Michael Previte
  • Patent number: 9688969
    Abstract: The invention provides novel compositions with polymerase activity and methods of using the compositions.
    Type: Grant
    Filed: September 3, 2015
    Date of Patent: June 27, 2017
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Peter B. Vander Horn, Yan Wang
  • Patent number: 9683247
    Abstract: The disclosure relates to a recombinant microorganism engineered to express an enzyme which catalyzes the conversion of a primary amine and an acyl thioester to a fatty amide. The disclosure further encompasses a method of producing a fatty amide by culturing the recombinant microorganism in the presence of a carbon source.
    Type: Grant
    Filed: March 12, 2013
    Date of Patent: June 20, 2017
    Assignee: REG LIFE SCIENCES, LLC
    Inventors: Jason J. Lutes, Stephen del Cardayre
  • Patent number: 9677059
    Abstract: The present invention relates to thermostable endoglucanases, particularly to proteins having endoglucanase activity which comprises an amino acid sequence having at least 96% identity to SEQ. ID NO.: 2, and proteins having endoglucanase activity which belongs to the GH7 class and which shows active thermostabilization.
    Type: Grant
    Filed: April 30, 2013
    Date of Patent: June 13, 2017
    Assignee: CLARIANT PRODUKTE (DEUTSCHLAND) GMBH
    Inventors: Christoph Reisinger, Joerg Claren, Isabel Unterstrasser, Aleksandra Mitrovic, Karlheinz Flicker, Gabi Gebhardt
  • Patent number: 9663769
    Abstract: The present disclosure provide novel variants of T7 RNA polymerase. Embodiments of T7 variants, according to the instant invention, include a Cysteine-Serine substitution on position 723 of the amino acid sequence of the T7 polypeptide. Embodiments of T7 variants according to the instant invention have a DNA-dependent RNA polymerase enzymatic activity and a reduced tendency to form intramolecular homodimers by way of oxidizing thiol groups. The amino acid substitutions within the T7 variants disclosed herein impact minimally, if at all, the RNA polymerase activity of the T7 polypeptide. Further, the mutations of the disclosed embodiments may optionally be combined with mutations which provide enhanced thermostability compared to the wild-type reference.
    Type: Grant
    Filed: October 1, 2015
    Date of Patent: May 30, 2017
    Assignee: Roche Diagnostics Operations, Inc.
    Inventors: Michael Greif, Christian Rudolph, Manfred Schmidt, Harald Sobek, Johann-Peter Thalhofer
  • Patent number: 9650672
    Abstract: Provided are compositions comprising modified DNA polymerases that exhibit improved photostability compared to the parental polymerases from which they were derived. Provided are methods for generating enzymes, such as DNA polymerases, with the aforementioned phenotype. Provided are methods of using polymerases with increased resistance to photodamage to make a DNA or to sequence a DNA template.
    Type: Grant
    Filed: August 5, 2015
    Date of Patent: May 16, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventor: Keith Bjornson
  • Patent number: 9650656
    Abstract: The biosynthesis of fungal bicyclo[2.2.2]diazaoctane indole alkaloids with a wide spectrum of biological activities have attracted increasing interest. Their intriguing mode of assembly has long been proposed to feature a non-ribosomal peptide synthetase, a presumed intramolecular Diels-Alderase, a variant number of prenyltransferases, and a series of oxidases responsible for the diverse tailoring modifications of their cyclodipeptide-based structural core. Until recently, the details of these biosynthetic pathways have remained largely unknown due to lack of information on the fungal derived biosynthetic gene clusters. Herein, we report a comparative analysis of four natural product metabolic systems of a select group of bicyclo[2.2.2]diazaoctane indole alkaloids including (+)/(?)-notoamide, paraherquamide and malbrancheamide, in which we propose an enzyme for each step in the biosynthetic pathway based on deep annotation and on-going biochemical studies.
    Type: Grant
    Filed: April 3, 2013
    Date of Patent: May 16, 2017
    Assignees: THE REGENTS OF THE UNIVERSITY OF MICHIGAN, COLORADO STATE UNIVERSITY RESEARCH FOUNDATION
    Inventors: Shengying Li, Krithika Anand Srinivasan, Robert M. Williams, David H. Sherman
  • Patent number: 9644009
    Abstract: An L-amino acid is produced by culturing a microorganism of the family Enterobacteriaceae which has the ability to produce an L-amino acid and which has been modified so as to increase the expression of the evgA gene, the gadE gene, and/or the ydeO gene. These genes encode a transcription factor involved in the EvgAS two-component system regulon. The culture takes place in a medium, and the L-amino acid is collected from the medium or cells.
    Type: Grant
    Filed: March 26, 2008
    Date of Patent: May 9, 2017
    Assignee: AJINOMOTO CO., INC.
    Inventors: Shintaro Iwatani, Akira Imaizumi, Yoshihiro Usuda, Kazuhiko Matsui
  • Patent number: 9637551
    Abstract: The present invention provides multi-component inhibitors of nucleic acid polymerases, methods of making, and methods of using same. One component of the multi-component inhibitor is a molecule that binds to a polymerase (i.e., a polymerase-binding molecule (PBM)), but does not thereby substantially inhibit its polymerase activity. Another component is a molecule or complex of molecules that binds to a PBM (i.e., a PBM-binding molecule). The combination of the PBM and PBM-binding molecule/complex substantially inhibits polymerase activity.
    Type: Grant
    Filed: December 11, 2009
    Date of Patent: May 2, 2017
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: John D. Bishop, Jun E. Lee
  • Patent number: 9631057
    Abstract: In one embodiment the instant invention generally pertains to a method for producing glucose for fermentation. The method comprises first treating a biomass with acid and heat under conditions sufficient to produce a composition mixture comprising cellulose suitable for enzymatic hydrolysis. Next, at least a portion of the cellulose of step (a) is enzymatically hydrolyzed under conditions sufficient to form a composition comprising glucose. The glucose is then fermented. Advantageously, one or more reaction conditions are more efficient because they are selected by first measuring an initial hydrolysis rate of said biomass and then selecting one or more appropriate reaction conditions based upon said initial hydrolysis rate.
    Type: Grant
    Filed: November 9, 2010
    Date of Patent: April 25, 2017
    Assignees: Texaco Inc., Georgia Tech Research Corporation
    Inventors: Matthew James Realff, Ronald W. Smith, Prabuddha Bansal, Andreas Sebastian Bommarius, Melanie Hall, Jay Hyung Lee
  • Patent number: 9631213
    Abstract: The present invention relates to methods for degrading or converting a cellulose-containing material, comprising: treating the cellulose-containing material with an effective amount of a cellulolytic enzyme composition comprising a polypeptide having cellulolytic enhancing activity, and one or more (several) components selected from the group consisting of a CEL7 polypeptide having endoglucanase activity, a CEL12 polypeptide having endoglucanase activity, a CEL45 polypeptide having endoglucanase activity, a CEL7 polypeptide having cellobiohydrolase activity with a cellulose binding domain, and a CEL7 polypeptide having cellobiohydrolase activity without a cellulose binding domain. The present invention also relates to such cellulolytic enzyme compositions.
    Type: Grant
    Filed: March 27, 2015
    Date of Patent: April 25, 2017
    Assignee: Novozymes, Inc.
    Inventor: Keith McFarland
  • Patent number: 9631182
    Abstract: The invention provides nucleic acids and polypeptides for nucleic acid polymerases from a thermophilic organism, Thermus brockianus. The invention also provides methods for using these nucleic acids and polypeptides.
    Type: Grant
    Filed: September 13, 2012
    Date of Patent: April 25, 2017
    Assignee: Applied Biosystems, LLC
    Inventors: Elena Bolchakova, James Rozzelle
  • Patent number: 9617588
    Abstract: Polymorphisms are present throughout an organism's genome, and understanding which alleles are present in a particular organism's genome can be advantageous. When probing the identity of these alleles, one must minimize incorrect readings due to inefficiencies in the system. In hydrolysis probe applications, these inefficiencies may be due to over-activity of an exonuclease functionality that excises nucleotides from probes that are only partially, complementary to a region of a target. The present invention provides a mixture that contains a plurality of polymerases including one that has a 5??3? exonuclease functionality and one that lacks or substantially lacks it, each in a sufficient relative amount and concentration to increase efficiencies of the system.
    Type: Grant
    Filed: October 4, 2011
    Date of Patent: April 11, 2017
    Assignee: Thermo Fisher Scientific Baltics UAB
    Inventor: Jaakko Kurkela
  • Patent number: 9605246
    Abstract: The present disclosure provides variant Csy4 endoribonucleases, nucleic acids encoding the variant Csy4 endoribonucleases, and host cells genetically modified with the nucleic acids. The variant Csy4 endoribonucleases find use in a variety of applications, which are also provided. The present disclosure also provides methods of detecting a specific sequence in a target polyribonucleotide; and methods of regulating production of a target RNA in a eukaryotic cell.
    Type: Grant
    Filed: June 10, 2015
    Date of Patent: March 28, 2017
    Assignee: The Regents of the University of California
    Inventors: Rachel E. Haurwitz, Jennifer A. Doudna, Blake Wiedenheft, Martin Jinek
  • Patent number: 9605284
    Abstract: A microorganism with improved acid-resistance. A microorganism capable of efficiently producing 3-HP, and methods for producing an organic acid.
    Type: Grant
    Filed: November 3, 2014
    Date of Patent: March 28, 2017
    Assignee: SAMSUNG ELECTRONICS CO., LTD.
    Inventors: Juyoung Lee, Hyunmin Koo, Jaechan Park, Jieun Kim, Jinha Kim, Joonsong Park, Soonchun Chung, Byungkwan Cho
  • Patent number: 9598679
    Abstract: A composition having nucleic acid polymerase activity, which comprises an active nucleic acid polymerase and an excess amount of a non-functional mutant nucleic acid polymerase protein, wherein the non-functional mutant nucleic acid polymerase protein stabilizes the active nucleic acid polymerase against loss of polymerase activity.
    Type: Grant
    Filed: September 9, 2010
    Date of Patent: March 21, 2017
    Assignee: Thermo Fisher Scientific Baltics UAB
    Inventors: Arunas Lagunavicius, Arvydas Janulaitis
  • Patent number: 9593318
    Abstract: The present invention relates to combinations of a linker bridged gene or domain fusion reverse transcriptase enzyme, and more particularly, combinations of a linker bridged gene or domain fusion reverse transcriptase enzyme and their fusion construction utilizing for more efficient and quality DNA synthesis in reverse transcription. The composition of the invention includes a polymerase domain; a linker, consisting of 3-40 amino acids; and an RNase H domain, wherein the RNase H domain is either unmodified or modified with point mutations. The composition may further include another mutated RNase H, a mutated RNase A, and an additional linker which consists of 3-40 amino acids.
    Type: Grant
    Filed: April 25, 2013
    Date of Patent: March 14, 2017
    Inventor: Jun Euihum Lee