Patents Examined by Robert Mondesi
  • Single step liquefaction and saccharification of corn starch using an acidophilic, calcium independent and hyperthermophilic pullulanase
    Patent number: 9340778
    Abstract: A novel thermoacidophilic pullulanase (Tk-PUL) from hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 is described here that efficiently hydrolyzes starch under industrial conditions in the absence of any additional metal ions. The gene encoding Tk-PUL was cloned and expressed in E. coli cells. The purified recombinant enzyme possesses the following properties: shows both pullulanase and ?-amylase activities, displays highest activity at 95-100° C., active over a broad pH range (3.0-8.5) with optimum working pH 3.5, stable for several hours at 90° C. and displays a half-life of 45 minutes at 100° C., activity and stability are independent of calcium and other metal ions, and hydrolyzes maltotriose. Moreover, recombinant Tk-PUL can be used for single step liquefaction and saccharification of corn starch (without any ?-amylase or ?-amylase) at pH 4.2 in the absence of calcium.
    Type: Grant
    Filed: February 18, 2014
    Date of Patent: May 17, 2016
    Inventors: Nasir Ahmed, Naeem Rashid, Muhammad Saleem Haider, Muhammad Akhtar
  • Cas9-FokI fusion proteins and uses thereof
    Patent number: 9322037
    Abstract: Some aspects of this disclosure provide compositions, methods, and kits for improving the specificity of RNA-programmable endonucleases, such as Cas9. Also provided are variants of Cas9, e.g., Cas9 dimers and fusion proteins, engineered to have improved specificity for cleaving nucleic acid targets. Also provided are compositions, methods, and kits for site-specific nucleic acid modification using Cas9 fusion proteins (e.g., nuclease-inactivated Cas9 fused to a nuclease catalytic domain). Such Cas9 variants are useful in clinical and research settings involving site-specific modification of DNA, for example, genomic modifications.
    Type: Grant
    Filed: June 30, 2014
    Date of Patent: April 26, 2016
    Assignee: President and Fellows of Harvard College
    Inventors: David R. Liu, John Paul Guilinger, David B. Thompson
  • Direct starch to fermentable sugar as feedstock for the production of isoprene, isoprenoid precursor molecules, and/or isoprenoids
    Patent number: 9315831
    Abstract: Provided herein are compositions and methods related to the direct conversion of the starch in a ground or fractionated grain into a fermentable sugar feedstock capable of serving as a carbon source for the industrial production of one or more products by a fermenting organism, such as isoprene, isoprenoid precursor molecules, and/or isoprenoids. Such conversions may be performed at temperatures at or below the initial gelatinization temperature of the starch present in the grain and may utilize one or more isolatable endogenous enzymes present in certain unrefined grains.
    Type: Grant
    Filed: March 13, 2013
    Date of Patent: April 19, 2016
    Assignees: DANISCO US INC., THE GOODYEAR TIRE & RUBBER COMPANY
    Inventors: Collette M. Blake, Gopal K. Chotani, Gang Duan, Douglas Ko, Floor Kooy, Sung Ho Lee, Michael J. Pepsin, Ying Qian, Matt Reboli, Vivek Sharma, Jayarama K. Shetty, Bruce A. Strohm, Pauline Johanna Maria Teunissen, Hongxian Xu
  • Biological production of organic compounds
    Patent number: 9309541
    Abstract: Strains of cyanobacteria that produce high levels of alpha ketoglutarate (AKG) and pyruvate are disclosed herein. Methods of culturing these cyanobacteria to produce AKG or pyruvate and recover AKG or pyruvate from the culture are also described herein. Nucleic acid sequences encoding polypeptides that function as ethylene-forming enzymes and their use in the production of ethylene are further disclosed herein. These nucleic acids may be expressed in hosts such as cyanobacteria, which in turn may be cultured to produce ethylene.
    Type: Grant
    Filed: March 10, 2015
    Date of Patent: April 12, 2016
    Assignee: Alliance for Sustainable Energy, LLC
    Inventors: Jianping Yu, Troy Paddock, Damian Carrieri, Pin-Ching Maness, Michael Seibert
  • Modified beta-lactamases and methods and uses related thereto
    Patent number: 9301995
    Abstract: The present invention relates to pharmaceuticals and modified beta-lactamases. Specifically, the invention relates to novel recombinant beta-lactamases and pharmaceutical compositions comprising the beta-lactamases. Also, the present invention relates to methods for modifying a beta-lactamase, producing the beta-lactamase and treating or preventing beta-lactam antibiotic induced adverse effects. Furthermore, the present invention relates to the beta-lactamase for use as a medicament and to the use of the beta-lactamase in the manufacture of a medicament for treating or preventing beta-lactam antibiotics induced adverse effects. Still further, the invention relates to a polynucleotide and a host cell comprising the polynucleotide.
    Type: Grant
    Filed: October 17, 2014
    Date of Patent: April 5, 2016
    Assignee: Synthetic Biologics, Inc.
    Inventors: Pertti Koski, Ulla Airaksinen, Katja Valimaki
  • Modified beta-lactamases and methods and uses related thereto
    Patent number: 9301996
    Abstract: The present invention relates to pharmaceuticals and modified beta-lactamases. Specifically, the invention relates to novel recombinant beta-lactamases and pharmaceutical compositions comprising the beta-lactamases. Also, the present invention relates to methods for modifying a beta-lactamase, producing the beta-lactamase and treating or preventing beta-lactam antibiotic induced adverse effects. Furthermore, the present invention relates to the beta-lactamase for use as a medicament and to the use of the beta-lactamase in the manufacture of a medicament for treating or preventing beta-lactam antibiotics induced adverse effects. Still further, the invention relates to a polynucleotide and a host cell comprising the polynucleotide.
    Type: Grant
    Filed: April 1, 2015
    Date of Patent: April 5, 2016
    Assignee: Synthetic Biologics, Inc.
    Inventors: Pertti Koski, Ulla Airaksinen, Katja Valimaki
  • Methods of producing triacylglyceride compositions comprising tailored oils
    Patent number: 9279136
    Abstract: Methods and compositions for the production of food compositions, oils, fuels, oleochemicals, and other compounds in recombinant microorganisms are provided, including oil-bearing microorganisms and methods of low cost cultivation of such microorganisms. Microalgal cells containing exogenous genes encoding, for example, a lipase, a sucrose transporter, a sucrose invertase, a fructokinase, a polysaccharide-degrading enzyme, a keto acyl-ACP synthase enzyme, a fatty acyl-ACP thioesterase, a fatty acyl-CoA/aldehyde reductase, a fatty acyl-CoA reductase, a fatty aldehyde reductase, a fatty aldehyde decarbonylase, and/or an acyl carrier protein are useful in manufacturing food compositions, and transportation fuels such as renewable diesel, biodiesel, and renewable jet fuel, as well as oleochemicals such as functional fluids, surfactants, soaps and lubricants.
    Type: Grant
    Filed: September 28, 2012
    Date of Patent: March 8, 2016
    Assignee: Solazyme, Inc.
    Inventors: Scott Franklin, Aravind Somanchi, Janice Wee, George Rudenko, Jeffrey L. Moseley, Walt Rakitsky
  • Compositions comprising a polypeptide having cellulolytic enhancing activity and a quinone compound and uses thereof
    Patent number: 9273335
    Abstract: The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a quinone compound. The present invention also relates to methods of using the compositions.
    Type: Grant
    Filed: August 5, 2011
    Date of Patent: March 1, 2016
    Assignee: NOVOZYMES, INC.
    Inventors: Jason Quinlan, Feng Xu, Matthew Sweeney
  • Evolution of bond-forming enzymes
    Patent number: 9267127
    Abstract: Strategies, systems, methods, reagents, and kits for the directed evolution of bond-forming enzymes are provided herein. Evolution products, for example, evolved sortases exhibiting enhanced reaction kinetics and/or altered substrate preferences are also provided herein, as are methods for using such evolved bond-forming enzymes. Kits comprising materials, reagents, and cells for carrying out the directed evolution methods described herein are also provided.
    Type: Grant
    Filed: June 20, 2013
    Date of Patent: February 23, 2016
    Assignee: President and Fellows of Harvard College
    Inventors: David R. Liu, Irwin Chen, Brent M. Dorr
  • Methods and compositions for gene correction
    Patent number: 9267123
    Abstract: Disclosed herein are methods and compositions for correction and/or mutation of genes associated with Parkinson's Disease as well as clones and animals derived therefrom.
    Type: Grant
    Filed: December 15, 2011
    Date of Patent: February 23, 2016
    Assignees: Sangamo BioSciences, Inc., Whitehead Institute for Biomedical Research
    Inventors: Rudolf Jaenisch, Josee Laganiere, Frank Soldner, Lei Zhang
  • Glucose dehydrogenase
    Patent number: 9260699
    Abstract: An object of the present invention is to provide a novel glucose dehydrogenase, a method for producing the glucose dehydrogenase, and applications of the glucose dehydrogenase. An isolated flavin-binding glucose dehydrogenase comprising a polypeptide having an amino acid sequence with 80% or more identity to the amino acid sequence of SEQ ID NO: 1, and having glucose dehydrogenase activity is provided.
    Type: Grant
    Filed: April 30, 2014
    Date of Patent: February 16, 2016
    Assignee: Toyobo Co., Ltd.
    Inventors: Yosuke Sumida, Hiroshi Aiba, Hiroshi Kawaminami, Rie Hirao, Yuu Utashima, Takahide Kishimoto, Shusaku Yanagidani
  • Malodour standards and inhibitors
    Patent number: 9249448
    Abstract: The invention pertains to the field of reaction systems generating malodor, particularly from constituents of human sweat. Specifically, the invention pertains to proteins for generating malodors, substrates for generating such malodor, inhibitors of such malodor generation and test and screening systems for measuring their malodor inhibition efficacy and finding substances previously not known to inhibit malodor generation. Thus, the invention also pertains to the field of deodorants.
    Type: Grant
    Filed: December 19, 2011
    Date of Patent: February 2, 2016
    Assignee: BASF SE
    Inventor: Markus Pompejus
  • Isobutanol production using yeasts with modified transporter expression
    Patent number: 9249420
    Abstract: The present invention relates to recombinant microorganisms comprising an isobutanol producing metabolic pathway and methods of using said recombinant microorganisms to produce isobutanol. In various aspects of the invention, the recombinant microorganisms may comprise one or more modifications resulting in the reduction in the expression and/or activity of an endogenous transporter protein. In various embodiments described herein, the recombinant microorganisms may be microorganisms of the Saccharomyces clade, Crabtree-negative yeast microorganisms, Crabtree-positive yeast microorganisms, post-WGD (whole genome duplication) yeast microorganisms, pre-WGD (whole genome duplication) yeast microorganisms, and non-fermenting yeast microorganisms.
    Type: Grant
    Filed: May 31, 2011
    Date of Patent: February 2, 2016
    Assignees: VIB VZW, KATHOLIEKE UNIVERSITEIT LEUVEN, K.U. LEUVEN R&D
    Inventors: Catherine Asleson Dundon, Christopher Smith, Piruz Nahreini, Johan Thevelein, Sofie Saerens
  • Probe reagent for measurement of proteolytic activity
    Patent number: 9249449
    Abstract: This invention relates to a probe reagent comprising, in order from the N-terminus to the C-terminus, the amino acid sequences of a fluorescent protein I, a peptide capable of terminating protein degradation (i.e., a degradation-terminating peptide), a spacer peptide, a fluorescent protein II, and a protein to be degraded, wherein the protein to be degraded is a protein degraded by the ubiquitin-proteasome system, and the probe reagent is degraded from the C-terminus, but that the degradation of the probe reagent is terminated at the degradation-terminating peptide, a nucleic acid encoding the probe reagent, and use of the probe reagent or the nucleic acid.
    Type: Grant
    Filed: January 21, 2011
    Date of Patent: February 2, 2016
    Assignees: Japan Science and Technology Agency, Riken
    Inventors: Atsushi Miyawaki, Masahiko Hirano
  • Methods and materials for treatment of pompe's disease
    Patent number: 9249399
    Abstract: This document relates to molecular complexes having acid alpha glucosidase activity and at least one modification that results in enhanced ability of the molecular complex to be transported to the interior of a mammalian cell.
    Type: Grant
    Filed: March 14, 2013
    Date of Patent: February 2, 2016
    Assignee: Oxyrane UK Limited
    Inventors: Wouter Vervecken, Kathleen Camilla Telesphore Alida Maria Piens, Jan Robert Ludo Stout, Gwenda Noëlla Pynaert
  • Methods and compositions for production of blue pigment indigoidine
    Patent number: 9243269
    Abstract: The present disclosure provides for an expression system for the production of blue pigment indigoidine. The system comprises a heterologous host cell, a DNA sequence encoding a Sc-IndB protein, and a DNA sequence encoding a Sc-IndC protein. The system may be configured for the co-expression of the Sc-IndB and Sc-IndC. DNA sequences encoding the Sc-IndB and Sc-IndC may be provided on at least one vector. Alternatively, the DNA sequences encoding the Sc-IndB and Sc-IndC may optionally be integrated into the genome of the heterologous host genome. The expression system may further comprise a sfp gene or a PPTase.
    Type: Grant
    Filed: November 14, 2013
    Date of Patent: January 26, 2016
    Assignee: Utah State University
    Inventor: Jixun Zhan
  • Restriction endonucleases and their uses
    Patent number: 9243233
    Abstract: A restriction endonuclease with a recognition sequence 5?-TCGA-3?. The restriction endonuclease is sensitive to the presence of a modified cytosine residue in the recognition sequence. Methods and kits using the restriction endonuclease with a recongition sequence 5?-TCGA-3? are also disclosed.
    Type: Grant
    Filed: July 1, 2013
    Date of Patent: January 26, 2016
    Assignee: Thermo Fisher Scientific UAB
    Inventors: Renata Rim{hacek over (s)}elienė, Remigijus Skirgaila, Arvydas Lubys
  • Method of production of 2,4-dihydroxybutyric acid
    Patent number: 9238829
    Abstract: A method of producing 2,4-dihydroxybutyric acid (2,4-DHB) by a synthetic pathway that includes the transforming malate in 4-phospho-malate using a malate kinase, said 4-phospho-malate being transformed in malate-4-semialdehyde using a malate semialdehyde dehydrogenase and said malate-4-semialdehyde being transformed in 2,4-DHB using a DHB dehydrogenase.
    Type: Grant
    Filed: October 27, 2011
    Date of Patent: January 19, 2016
    Assignee: ADISSEO FRANCE S.A.S.
    Inventors: Thomas Walther, Helene Cordier, Christopher Topham, Isabelle Andre, Magali Remaud-Simeon, Robert Huet, Jean-Marie Francois
  • Method for producing L-cysteine
    Patent number: 9234223
    Abstract: A method for producing L-cysteine and the like is provided by developing a novel technique for improving bacterial L-cysteine-producing ability. The method includes the steps of culturing a bacterium belonging to the genus Escherichia which has L-cysteine-producing ability, and in which expression of a gene involved in sulfite reduction is enhanced, in a medium containing thiosulfate, and collecting L-cysteine, a related substance thereof, or a mixture thereof which accumulate in the medium.
    Type: Grant
    Filed: March 27, 2012
    Date of Patent: January 12, 2016
    Assignee: AJINOMOTO CO., INC.
    Inventors: Shunsuke Yamazaki, Gen Nonaka, Kazuhiro Takumi
  • Star-worm luciferase
    Patent number: 9234186
    Abstract: The present invention relates to a luciferase derived from a star-worm belonging to genus Diplocladon, the luciferase inducing luminescence such that a maximum luminous wavelength falls within a range of 557 to 562 nm over the entire pH range of 5.5 to 8.0, or the luciferase inducing luminescence having 1.5 times the luminous intensity of luminescence induced by Photinus pyralis firefly luciferase.
    Type: Grant
    Filed: September 13, 2013
    Date of Patent: January 12, 2016
    Assignees: OLYMPUS CORPORATION, NIMURA GENETIC SOLUTIONS CO., LTD., PERAK STATE DEVELOPMENT CORPORATION
    Inventors: Ryutaro Akiyoshi, Katsunori Ogo, Hirobumi Suzuki