Patents Issued in April 14, 2016
  • STRESS TOLERANT PLANTS
    Publication number: 20160102316
    Abstract: The invention relates to transgenic plants and methods for modulating abscisic acid (ABA) perception and signal transduction in plants. The plants fmd use in increasing yield in plants, particularly under abiotic stress.
    Type: Application
    Filed: May 29, 2014
    Publication date: April 14, 2016
    Inventors: Vicente Rubio Munoz, Elisa Iniesto Sanchez, Maria Luisa Irigoyen Miguel
  • PLANTS HAVING INCREASED TOLERANCE TO HERBICIDES
    Publication number: 20160102317
    Abstract: The present invention refers to a method for controlling undesired vegetation at a plant cultivation site, the method comprising the steps of providing, at said site, a plant that comprises at least one nucleic acid comprising a nucleotide sequence encoding a wild-type hydroxyphenyl pyruvate dioxygenase or a mutated hydroxyphenyl pyruvate dioxygenase (mut-HPPD) which is resistant or tolerant to a HPPD-inhibiting herbicide and/or a nucleotide sequence encoding a wild-type homogentisate solanesyl transferase or a mutated homogentisate solanesyl transferase (mut-HST) which is resistant or tolerant to a HPPD-inhibiting herbicide, preferably a bicycloarylcarboxamide, applying to said site an effective amount of said herbicide. The invention further refers to plants comprising mut-HPPD, and methods of obtaining such plants.
    Type: Application
    Filed: April 28, 2014
    Publication date: April 14, 2016
    Applicant: BASF SE
    Inventors: Maciej Pasternak, Stefan Tresch, Helmut Kraus, Johannes Hutzler, Jens Lerchl, Thomas Mietzner, Liliana Parra Rapado, Jill Marie Paulik
  • MELON PLANTS WITH IMPROVED DISEASE TOLERANCE
    Publication number: 20160102318
    Abstract: The present disclosure provides melon plants exhibiting tolerance to cucurbit yellow stunt disorder virus (CYSDV) and lacking negative traits associated with CYSDV tolerance such as increased fruit size and reduced fruit set. Such plants may comprise novel introgressed genomic regions associated with disease tolerance. In certain aspects, compositions, including novel polymorphic markers and methods for producing, breeding, identifying, and selecting plants or germplasm with a disease tolerance phenotype are provided.
    Type: Application
    Filed: October 9, 2015
    Publication date: April 14, 2016
    Inventors: Susana Garcia-Andres, Eleni Bachlava, Eva King-Fan Chan, Tarek Joobeur, Joseph J. King, Petrus J. Kraakman, Subash Krishnamurthy, Jeffrey M. Mills, Jeroen de Vries
  • CMP-ACETYLNEURAMINIC ACID HYDROXYLASE TARGETING VECTOR, TRANSGENIC ANIMAL FOR XENOTRANSPLANTATION INTRODUCED WITH THE VECTOR, AND METHOD OF MANUFACTURING THE SAME
    Publication number: 20160102319
    Abstract: There is provided a CMP-acetylneuraminic acid hydroxylase targeting vector, a transgenic animal for xenotransplantation introduced with the vector, and a method of manufacturing the same. The targeting vector and the cell line for transformation prepared by the present invention can be used for the efficient production of cloned pigs for xenotransplantation by the complex regulation of the expression of the genes involved in the immunological rejection responses.
    Type: Application
    Filed: August 23, 2013
    Publication date: April 14, 2016
    Inventors: Jin Hoi KIM, Deug Nam Kwon, Jong Yi Park, Kiho Lee, Randall S. Prather, Jae Hwan Kim, Man Jong Kang
  • ADENOVIRAL VECTOR ENCODING HUMAN ATONAL HOMOLOG-1 (HATH1)
    Publication number: 20160102320
    Abstract: The invention is directed to a replication-deficient adenoviral vector comprising a nucleic acid sequence encoding a human atonal homolog-1 (Hath1) protein operably linked to a human glial fibrillary acidic protein (GFAP) promoter. The invention also is directed to a composition and method utilizing the adenoviral vector to generate sensory cells in the inner ear of a human.
    Type: Application
    Filed: October 9, 2015
    Publication date: April 14, 2016
    Applicant: GENVEC, INC.
    Inventors: Douglas E. Brough, Damodar R. Ettyreddy
  • HAIRPIN mRNA ELEMENTS AND METHODS FOR THE REGULATION OF PROTEIN TRANSLATION
    Publication number: 20160102321
    Abstract: The present invention provides novel mRNA elements capable of forming hairpin, double-stranded RNA structures independent of other non-coding RNAs. These mRNAs are stably expressed, lack polyadenylation tails, and allow minimal protein translation except when in the presence of specific proteins. Also provided, are compositions and kits comprising the mRNA element, as well as methods for its use in the regulation of protein translation. Advantageously, the disclosed elements represent a novel tool useful in regulating the expression of a wide variety of proteins of interest.
    Type: Application
    Filed: May 16, 2014
    Publication date: April 14, 2016
    Applicant: University of Florida Research Foundation, Inc.
    Inventors: Ling Chen, Arun Srivastava
  • CRISPR OLIGONUCLEOTIDES AND GENE EDITING
    Publication number: 20160102322
    Abstract: The present disclosure generally relates to compositions and methods for the genetic modification of cells. In particular, the disclosure relates to CRISPR reagents and the use of such reagents.
    Type: Application
    Filed: October 9, 2015
    Publication date: April 14, 2016
    Inventors: Namritha Ravinder, Korbinian Heil, Yizhu Guo, Xiquan Liang, Robert Potter
  • A LAGLIDADG HOMING ENDONUCLEASE CLEAVING THE C-C CHEMOKINE RECEPTOR TYPE-5 (CCR5) GENE AND USES THEREOF
    Publication number: 20160102323
    Abstract: Disclosed herein are compositions for inactivating the human CCR5 gene comprising engineered LAGLIDADG homing endonucleases (LHEs) and their derivatives, particularly derived from members of the \-OnuI subfamily of LHE. Polynucleotides encoding such endonucleases, vectors comprising said polynucleotides, cells comprising or having been treated with such endonucleases, and therapeutic compositions deriving therefrom are also provided.
    Type: Application
    Filed: May 28, 2014
    Publication date: April 14, 2016
    Inventors: Jordan JARJOUR, Alexander ASTRAKHAN
  • NEW COMPACT SCAFFOLD OF CAS9 IN THE TYPE II CRISPR SYSTEM
    Publication number: 20160102324
    Abstract: The present invention is in the field of CRISPR-Cas system for genome targeting. The present invention relates to new engineered Cas9 scaffolds and uses thereof. More particularly, the present invention relates to methods for genome targeting, cell engineering and therapeutic application. The present invention also relates to vectors, compositions and kits in which the new Cas9 scaffolds of the present invention are used.
    Type: Application
    Filed: May 28, 2014
    Publication date: April 14, 2016
    Inventors: Philippe DUCHATEAU, Claudia BERTONATI
  • Method for Storing Gaseous Hydrogen Through Producing Methanoate (Formate)
    Publication number: 20160102325
    Abstract: The present invention relates to a method for storing gaseous hydrogen, comprising the steps of producing methanoate (formate) through contacting gaseous hydrogen with carbon dioxide in the presence of a hydrogen dependent carbondioxide reductase (HDCR), and thereby storing of said gaseous hydrogen. The HDCR and/or its complex is preferably derived from Acetobacterium woodii.
    Type: Application
    Filed: June 18, 2014
    Publication date: April 14, 2016
    Applicant: JOHANN WOLFGANG GOETHE-UNIVERSITÄT
    Inventors: Volker MÜLLER, Kai SCHUCHMANN
  • METHOD FOR PRODUCING POLY-3-HYDROXYALKANOIC ACID AND AGGLOMERATES THEREOF
    Publication number: 20160102326
    Abstract: When industrially separating and purifying poly-3-hydroxyalkanoic acid produced by a microorganism, to obtain poly-3-hydroxyalkanoic acid agglomerates having an arbitrary volume mean particle diameter with favorable productivity and with decreased amount of an organic solvent used is enabled while decreasing contaminants derived from constitutive components of cellular bodies. According to the present invention, agglomerates of poly-3-hydroxyalkanoic acid are obtained by adjusting the pH of an aqueous poly-3-hydroxyalkanoic acid suspension to fall within an acidic region.
    Type: Application
    Filed: December 18, 2015
    Publication date: April 14, 2016
    Inventors: Masaki Takita, Yoshifumi Yanagita
  • METHODS AND COMPOSITIONS FOR PRODUCING FATTY ALCOHOLS
    Publication number: 20160102327
    Abstract: Methods and compositions, including nucleotide sequences, amino acid sequences, and host cells, for producing fatty alcohols are described.
    Type: Application
    Filed: May 22, 2015
    Publication date: April 14, 2016
    Applicant: REG LIFE SCIENCES, LLC
    Inventors: Zhihao HU, Vikranth ARLAGADDA
  • Microalgae Aurantiochytrium sp. LA3 (KCTC12685BP) and Method for Preparing Bio-Oil Using the Same
    Publication number: 20160102328
    Abstract: Provided herein are microalgae of a Thraustochytrid and a method for preparing bio-oil using the same, and more particularly, Aurantiochytrium sp. LA3 (KCTC12685BP) having bio-oil producibility, and a method of preparing bio-oil, particularly bio-oil having a content of omega-3 unsaturated fatty acids of 30% by weight or more based on total fatty acids, characterized by culturing the microalgae. The microalgae Aurantiochytrium sp. LA3 (KCTC12685BP) described herein has a rapid sugar consumption rate when being cultured using glucose as a carbon source, has a high oil content, allows cells to be cultured at a high concentration, and allows oil to be obtained in high productivity and a high yield, and thus, may produce bio-oil more economically and environmentally friendly.
    Type: Application
    Filed: July 30, 2015
    Publication date: April 14, 2016
    Inventors: Joong Min Park, Chang Kuk Kim, Yeon Hwa La, Young Bin Seo
  • ACOUSTIC ENERGY MEDIATION OF GENETIC FRAGMENTATION
    Publication number: 20160102329
    Abstract: Method and apparatus for controlling acoustic treatment of a sample to mediate a tagmentation process used on double stranded DNA.
    Type: Application
    Filed: October 13, 2015
    Publication date: April 14, 2016
    Applicant: Covaris, Inc.
    Inventors: James A. Laugharn, JR., Hamid Khoja
  • PRODUCTION OF DIRHAMNOSE-LIPID IN RECOMBINANT NONPATHOGENIC BACTERIUM PSEUDOMONAS CHLORORAPHIS
    Publication number: 20160102330
    Abstract: Pseudomonas chlororaphis NRRL B-30761 produces monorhamnolipids with predominantly 3-hydroxydodecenoyl-3-hydroxydecanoate (C12:1-C10) or 3-hydroxydodecanoyl-3-hydroxydecanoate (C12-C10) as the lipid moiety under static growth conditions. The cloning and sequencing of three genes and proteins involved in the biosynthesis of monorhamnose-lipid (R1L) is described. Expression of two of these genes, i.e., rhlA and rhlB, together in P. chlororaphis NRRL B-30761 increases R1L production by at least 10-fold. Also the generation of a recombinant P. chlororaphis NRRL B-30761 capable of synthesizing dirhamnose-lipid (R2L) is described. Characterization of R1L and R2L produced by the recombinant P. chlororaphis NRRL B-30761 is also described.
    Type: Application
    Filed: June 3, 2014
    Publication date: April 14, 2016
    Inventors: Daniel Solaiman, Richard D. ASHBY, Jonathan A. ZERKOWSKI, Nereus W. GUNTHER
  • EXTRACELLULAR DITERPENE PRODUCTION
    Publication number: 20160102331
    Abstract: The present invention relates to a method for the production of a diterpene or a glycosylated diterpene, which method comprises: a. fermenting a recombinant microorganism in a suitable fermentation medium, wherein the microorganism comprises one or more nucleotide sequence(s) encoding: a polypeptide having ent-copalyl pyrophosphate synthase activity; a polypeptide having ent-Kaurene synthase activity; a polypeptide having ent-Kaurene oxidase activity; and a polypeptide having kaurenoic acid 13-hydroxylase activity and whereby expression of the nucleotide sequence(s) confer(s) on the microorganism the ability to produce at least steviol, whereby a diterpene or glycosylated diterpene is produced extracellularly in the fermentation medium; and b. recovering the diterpene or glycosylated diterpene from the fermentation medium.
    Type: Application
    Filed: June 2, 2014
    Publication date: April 14, 2016
    Inventors: Viktor Marius BOER, Nicolette Jasmijn BROERS, Adam G. LAWRENCE
  • METHODS FOR MAKING TARGETED PROTEIN TOXINS BY SORTASE-MEDIATED PROTEIN LIGATION
    Publication number: 20160102332
    Abstract: We described novel methods for making targeted protein toxins by sortase-mediated protein ligation. The methods allow for a toxin and receptor-binding ligand to be ligated under mild conditions in vitro, following their expression and purification as single entities. The methods also provide a much more efficient way of making functional targeted fusion toxins compared to recombinant or chemical production of these structures.
    Type: Application
    Filed: June 1, 2015
    Publication date: April 14, 2016
    Inventors: R. John Collier, Andrew J. McCluskey, Bradley L. Pentelute
  • QUANTITATIVE CONTROL OF SIALYLATION AND SPECIFIC MONO-SIALYLATION
    Publication number: 20160102333
    Abstract: The present disclosure is directed to the use of certain glycosyltransferase variants having N-terminal truncation deletions. It was found that the combination of two different truncation variants of human ?-galactoside-?-2,6-sialyltransferase I (hST6Gal-I) exhibited different specific sialyltransferase enzymatic activities. In one example, under conditions wherein the first variant ?89 hST6Gal-I catalyzed formation of bi-sialylated target molecules the second variant ?108 hST6Gal-I catalyzed formation of mono-sialylated target molecules. Thus, disclosed are variants of mammalian glycosyltransferase, nucleic acids encoding the same, methods and means for recombinantly producing the variants of mammalian glycosyltransferase and use thereof, particularly for sialylating in a quantitatively controlled manner terminal acceptor groups of glycan moieties being part of glycoproteins such as immunoglobulins.
    Type: Application
    Filed: December 16, 2015
    Publication date: April 14, 2016
    Inventors: Tibor Czabany, Alfred Engel, Michael Greif, Christine Jung, Christiane Luley, Sebastian Malik, Rainer Mueller, Bernd Nidetzky, Doris Ribitsch, Katharina Schmoelzer, Helmut Schwab, Harald Sobek, Bernhard Suppmann, Marco Thomann, Sabine Zitzenbacher
  • RAPID ANTIMICROBIAL SUSCEPTIBILITY TEST, BASED ON AN ANALYSIS OF CHANGES IN MORPHOLOGY AND GROWTH PATTERN OF A MICROBIAL CELL UNDER DIFFERENT CONCENTRATIONS OF VARIOUS ANTIMICROBIAL AGENTS, AND AUTOMATED CELL IMAGE ANALYSIS SYSTEM THEREFOR
    Publication number: 20160102334
    Abstract: Provided are a rapid antimicrobial susceptibility test, based on an analysis of changes in morphology and growth pattern of a microbial cell under different concentrations of various antimicrobial agents, and an automated cell image analysis system therefor. The antimicrobial susceptibility test is rapidly performed based on an analysis of changes in morphology and growth pattern of a microbial cell under different concentrations of various antimicrobial agents, and this makes it possible to obtain highly reliable test results faster by six to seven times than the standard method recommended by Clinical and Laboratory Standards Institute (CLSI).
    Type: Application
    Filed: October 14, 2015
    Publication date: April 14, 2016
    Inventors: Yong-Gyun Jung, Eun-Geun Kim, Jung Heon Yoo, Sunghoon Kwon, Jungil Choi, Hee Chan Kim, Jung Chan Lee, Eui Jong Kim, Sang Hoon Song, Sei Ick Joo, Ji Soo Lee
  • BIOLOGICAL INDICATOR
    Publication number: 20160102335
    Abstract: This invention relates to a biological indicator derived from a composition comprising: a host organism comprising a spore forming bacteria; a reporter gene for producing an indicator enzyme; a regulatory gene; and a vehicle for inserting the reporter gene and the regulatory gene in the host organism; the host organism bearing a transposable genetic element in its genome for inserting an insertion sequence in the regulatory gene; the insertion sequence comprising a transposase, a pair of terminal inverted repeat sequences, and at least one open reading frame for expressing the transposase. The vehicle may be taken up by the host organism. The insertion sequence may be inserted in the regulatory gene. The host organism may undergo sporulation to form the biological indicator. A process and an apparatus for using the biological indicator are disclosed.
    Type: Application
    Filed: October 13, 2014
    Publication date: April 14, 2016
    Inventors: Phillip P. Franciskovich, Tricia A. Cregger, William A. Yirava, Peter A. Burke
  • FLUORESCENT PROBE FOR DETECTING ACTIVITY OF CALPAIN
    Publication number: 20160102336
    Abstract: [Problem] To provide a novel fluorescent probe for detecting the activity of calpain. [Solution] A compound represented by general formula (I) or a salt thereof.
    Type: Application
    Filed: March 4, 2014
    Publication date: April 14, 2016
    Applicant: THE UNIVERSITY OF TOKYO
    Inventors: Tetsuo NAGANO, Kenjiro HANAOKA, Yu KUSHIDA
  • GLUTAMATE OXIDASE MUTAGENESIS FOR DIAGNOSTIC TESTING
    Publication number: 20160102337
    Abstract: The described invention provides a method for detecting a target analyte that exhibits protease enzyme activity. The described method includes contacting a sample with a hybrid oxidase enzyme engineered to exhibit increased catalytic activity over that of a starting oxidase enzyme upon cleavage of a mutated protease cleavage recognition sequence. The mutated protease cleavage recognition sequence is a recognition sequence specific for the target analyte. The described method further includes contacting a substrate with the engineered hybrid oxidase enzyme. The substrate comprises a cognate composition of matter to the engineered hybrid oxidase enzyme, and the engineered hybrid oxidase enzyme is configured to catalyze conversion of the cognate composition of matter into a detectable product upon proteolytic cleavage of the mutated protease cleavage recognition sequence by the target analyte.
    Type: Application
    Filed: December 18, 2015
    Publication date: April 14, 2016
    Inventors: Dan Wang, G. Bruce Collier
  • BIOLUMINESCENT SUCCINATE DETECTION ASSAY
    Publication number: 20160102338
    Abstract: Provided herein are methods for detecting and quantifying succinate in a sample. Also provided are methods for detecting and quantifying 2-oxoglutarate oxygenase enzyme and/or 2-oxoglutarate oxygenase activity in a sample and methods for screening for modulators of 2-oxoglutarate oxygenase activity.
    Type: Application
    Filed: May 18, 2015
    Publication date: April 14, 2016
    Inventors: Juliano Alves, Said A. Goueli, Hicham Zegzouti
  • Sequence Conversion and Signal Amplifier DNA Having Locked Nucleic Acids and Detection Methods Using Same
    Publication number: 20160102339
    Abstract: Disclosed are methods for detecting a target nucleic acid in a sample. The methods include contacting said sample, in the presence of a polymerase and an endonuclease, with a sequence conversion oligonucleotide having locked nucleic acids at select positions sufficient to decrease non-specific background signal amplification. Also disclosed are methods for detecting a target nucleic acid in a sample in which said sample is contacted, in the presence of a polymerase and an endonuclease, with a sequence conversion oligonucleotide and a signal amplifier oligonucleotide, both having locked nucleic acids at select positions sufficient to decrease non-specific background signal amplification. The disclosure also provides compositions and kits comprising such sequence conversion and signal amplifier oligonucleotides.
    Type: Application
    Filed: October 13, 2015
    Publication date: April 14, 2016
    Inventors: Ken KOMIYA, Makoto KOMORI, Toru YOSHIMURA
  • METHODS FOR PREPARATION OF NUCLEIC ACID-CONTAINING SAMPLES USING CLAY MINERALS AND ALKALINE SOLUTIONS
    Publication number: 20160102340
    Abstract: The present invention provides a rapid and highly effective method for the preparation of biological samples for detection of both DNA and RNA target molecules. The method comprises treatment of the sample with a clay mineral followed by lysis of the sample with an alkaline solution. The method is particularly suited for preparing complex biological samples, such as blood or plasma, for the simultaneous detection of DNA and RNA targets. Samples prepared by the method of the invention may be directly used as targets in PCR amplification. The method of the invention may conveniently be coupled with further steps and devices to perform molecular analyses for diagnostic and other applications.
    Type: Application
    Filed: May 7, 2014
    Publication date: April 14, 2016
    Inventor: Heather K. BOUZEK
  • BIOMOLECULE ISOLATION AND THERMAL PROCESSING
    Publication number: 20160102341
    Abstract: Methods, devices and systems for hand-tag sample liquids, encapsulating liquids and magnetic particles are disclosed.
    Type: Application
    Filed: June 18, 2014
    Publication date: April 14, 2016
    Inventors: Kieran Curran, Robert Roeven
  • System and Method for Rapid Detection and Identification of Nucleic Acid Labeled Tags
    Publication number: 20160102342
    Abstract: A system for identifying which of a plurality of nucleic acid tag varieties are present on an item of interest. The system includes nucleic acid tag varieties each including a nucleotide-support platform attached to a nucleic acid molecule, the nucleic acid molecule including a first and a second universal primer region common to all nucleic acid tag varieties, and a first and a second unique primer region unique to each nucleic acid tag variety. The system also includes a first primer set with a first primer complementary to the first universal primer region and a second primer complementary to the second universal primer region, as well as a second primer set with a first primer complementary to the first unique primer region of one of the nucleic acid tag varieties and a second primer complementary to the second unique primer region of the same nucleic acid tag variety.
    Type: Application
    Filed: December 21, 2015
    Publication date: April 14, 2016
    Applicant: SRC, Inc.
    Inventors: Mary F. Swartz, William McKay
  • STRAND-INVASION BASED DNA AMPLIFICATION METHOD
    Publication number: 20160102343
    Abstract: A method for detecting toxigenic Clostridium difficile (C. difficile) by strand-invasion based DNA amplification is provided, together with oligonucleotides, compositions and kits suitable for use in this method.
    Type: Application
    Filed: April 23, 2014
    Publication date: April 14, 2016
    Applicant: ORION DIAGNOSTICA OY
    Inventor: Sanna FILÉN
  • Site-Specific Immobilization of DNA Origami Structures on Solid Substrates
    Publication number: 20160102344
    Abstract: The present invention relates to methods for the site-specific immobilization of DNA origami structures on solid substrates, as well as to respective assemblies comprising DNA origami structures immobilized on a solid substrate and uses thereof.
    Type: Application
    Filed: October 13, 2015
    Publication date: April 14, 2016
    Inventors: Christof Niemeyer, Rebecca Meyer, Alessandro Angelin, Nicholas S. Foulkes, Olivier Kassel, Simone Weigel, Jens Bauer, Tim Scharnweber
  • Sequence Conversion and Signal Amplifier DNA Having Poly DNA Spacer Sequences and Detection Methods Using Same
    Publication number: 20160102345
    Abstract: Disclosed are methods for detecting a target nucleic acid in a sample. The methods include contacting said sample, in the presence of a polymerase and an endonuclease, with a sequence conversion oligonucleotide. Also disclosed are methods for detecting a target nucleic acid in a sample in which said sample is contacted, in the presence of a polymerase and an endonuclease, with a sequence conversion oligonucleotide and a signal amplifier oligonucleotide. The disclosure also provides compositions and kits comprising such sequence conversion and signal amplifier oligonucleotides.
    Type: Application
    Filed: October 13, 2015
    Publication date: April 14, 2016
    Inventors: Ken KOMIYA, Makoto KOMORI, Toru YOSHIMURA
  • MULTIPLEXED DIGITAL ASSAY WITH SPECIFIC AND GENERIC REPORTERS
    Publication number: 20160102346
    Abstract: Digital assay system, including methods, apparatus, and compositions, for performing target assays in partitions each containing a generic reporter and a specific reporter for target amplification.
    Type: Application
    Filed: December 21, 2015
    Publication date: April 14, 2016
    Inventors: John F. Regan, Svilen S. Tzonev, Yann Jouvenot, Claudia Litterst, Dianna Maar, Geoff McDermott
  • METHODS FOR HIGH LEVEL MULTIPLEXED POLYMERASE CHAIN REACTIONS AND HOMOGENEOUS MASS EXTENSION REACTIONS
    Publication number: 20160102347
    Abstract: Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid.
    Type: Application
    Filed: May 22, 2015
    Publication date: April 14, 2016
    Inventors: Martin Beaulieu, Dirk Johannes van den Boom
  • METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR ACCELERATED BASE CALLING
    Publication number: 20160102348
    Abstract: Embodiments disclose methods, systems, and computer-readable media for accelerated base calling of sequencing data. These methods may be adapted to accelerate sequence determination for data arising from a variety of different nucleic acid sequencing platforms. In various embodiments, configurable logic circuits such as FPGAs and GPUs may be adapted to perform raw signal processing, basecalling, and/or sequence determination operations providing further enhancements to the sequence analysis methods.
    Type: Application
    Filed: October 12, 2015
    Publication date: April 14, 2016
    Inventor: Benjamin DONNET
  • METHODS FOR SEQUENCING POLYNUCLEOTIDES
    Publication number: 20160102349
    Abstract: The invention relates to methods and systems for sequencing and constructing a high resolution physical map of a polynucleotide. In accordance with the invention, nucleotide sequences are determined at the ends of restriction fragments produced by a plurality of digestions with a plurality of combinations of restriction endonucleases so that a pair of nucleotide sequences is obtained for each restriction fragment. A physical map of the polynucleotide is constructed by ordering the pairs of sequences by matching the identical sequences among the pairs.
    Type: Application
    Filed: January 29, 2015
    Publication date: April 14, 2016
    Inventor: Stephen C. Macevicz
  • Flow Cell Array and Uses Thereof
    Publication number: 20160102350
    Abstract: Apparatus and methods for using a flow cell array are provided herein. A method includes determining placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connecting the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and providing a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.
    Type: Application
    Filed: December 17, 2015
    Publication date: April 14, 2016
    Inventors: Evan C. Colgan, Alexey Y. Lvov, Stanislav Polonsky
  • Flow Cell Array and Uses Thereof
    Publication number: 20160102351
    Abstract: Apparatus and methods for using a flow cell array are provided herein. A method includes delivering multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; imaging multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and recording an emission from each of the multiple chemical reactions site.
    Type: Application
    Filed: December 17, 2015
    Publication date: April 14, 2016
    Inventors: Evan C. Colgan, Alexey Y. Lvov, Stanislav Polonsky
  • COMPOSITIONS CONTAINING IDENTIFIER SEQUENCES ON SOLID SUPPORTS FOR NUCLEIC ACID SEQUENCE ANALYSIS
    Publication number: 20160102352
    Abstract: Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.
    Type: Application
    Filed: December 17, 2015
    Publication date: April 14, 2016
    Inventor: Charles R. CANTOR
  • Polymorphisms Associated With Age-Related Macular Degeneration and Methods for Evaluating Patient Risk
    Publication number: 20160102353
    Abstract: The present invention provides for certain polynucleotide sequences that have been correlated to AMD. These polynucleotides are useful as diagnostics, and are preferably used to fabricate an array, useful for screening patient samples. The array is used as part of a laboratory information management system, to store and process additional patient information in addition to the patient's genomic profile. As described herein, the system provides an assessment of the patient's risk for developing AMD, risk for disease progression, and the likelihood of disease prevention based on patient controllable factors.
    Type: Application
    Filed: May 26, 2015
    Publication date: April 14, 2016
    Inventors: Johanna M. Seddon, Mark J. Daly
  • Systems For Biomarker Detection
    Publication number: 20160102354
    Abstract: Biomarker associated with Alzheimer's Disease (AD) and/or Mild Cognitive Impairment (MCI), where the biomarker is an intracellular or circulating microRNA and/or target protein thereof, and use thereof in methods for determining, diagnosing, monitoring AD, mild AD, moderate Ad, severe AD, MCI, early MCI, late MCI, and the like, as well as in methods for selecting candidate therapeutic compounds for treating same.
    Type: Application
    Filed: September 28, 2015
    Publication date: April 14, 2016
    Inventor: Eugenia Wang
  • THROMBOEMBOLIC DISEASE MARKERS
    Publication number: 20160102355
    Abstract: The invention relates to a method for a more appropriate thromboembolic event risk assessment based on the presence of different genetic variant. The invention also relates to a method for determining the risk of suffering a thromboembolism disease by combining the absence or presence of one or more polymorphic markers in a sample from the subject with conventional risk factors for thromboembolism as well as computer-implemented means for carrying out said method.
    Type: Application
    Filed: October 19, 2015
    Publication date: April 14, 2016
    Applicant: Gendiag.exe, S.L.
    Inventors: Eduardo Salas, José Manuel Soria, Miroslava Ogorelkova, Roberto Elosua Llanos, Joan Vila, Sergio Castillo Fernandez
  • ALLELIC DISORDERS CAUSED BY MUTATIONS IN TRPV4
    Publication number: 20160102356
    Abstract: The present invention provides methods, kits, and compositions for detecting mutations in transient receptor potential cation channel, subfamily V, member 4 (TRPV4). In particular, mutations are detected in TRPV4 to detect diseases such as scapuloperoneal spinal muscular atrophy (SPSMA) and hereditary motor and sensory neuropathy type IIC (HMSN IIC) or Charcot-Marie-Tooth disease type 2C (CMT2C).
    Type: Application
    Filed: December 17, 2015
    Publication date: April 14, 2016
    Applicant: Northwestern University
    Inventors: Teepu Siddique, Han-Xiang Deng, Jianhua Yan
  • NOVEL RUTHENIUM (II) COMPLEXES, PREPARATION AND USES THEREOF
    Publication number: 20160102357
    Abstract: The present invention discloses novel Ruthenium (II) polypyridyl complexes, preparation and its application as DNA imaging agents.
    Type: Application
    Filed: October 8, 2015
    Publication date: April 14, 2016
    Inventors: Amitava Das, Samit Chattopadhyay, Vadde Ramu, Nandaraj Taye
  • METHODS AND COMPOSITIONS FOR CORRELATING GENETIC MARKERS WITH CANCER RISK
    Publication number: 20160102358
    Abstract: The present invention provides methods of assessing an individual subject's risk of developing different types of cancer, comprising calculating a genetic risk score (GRS) for the subject.
    Type: Application
    Filed: October 14, 2015
    Publication date: April 14, 2016
    Inventors: Jianfeng Xu, Jielin Sun, Siqun Lilly Zheng, Zhuo Chen, Li Wang, Zheng Zhang
  • GENETIC MARKER FOR EARLY BREAST CANCER PROGNOSIS PREDICTION AND DIAGNOSIS, AND USE THEREOF
    Publication number: 20160102359
    Abstract: A gene for predicting or diagnosing the prognosis of early-stage breast cancer and to a use thereof is disclosed, and more specifically a genetic marker for predicting or diagnosing the prognosis of breast cancer, including TRBC1 (T cell receptor beta constant 1), BTN3A2 (butyrophilin, subfamily 3 member A2) or HLA-DPA1 (major histocompatibility complex, class II, DP alpha 1) for providing information necessary for predicting or diagnosing the prognosis of a breast cancer patient. The genetic marker allows the prediction or diagnosis of the prognosis of a breast cancer patient, and can therefore advantageously be used for the purpose of providing a direction as to the future course of breast cancer treatment, including a decision on whether anticancer therapy is necessary.
    Type: Application
    Filed: October 19, 2015
    Publication date: April 14, 2016
    Inventors: Young Kee SHIN, Young-Deug Kim, En Sel Oh, Jun Young Choi, Sang Rea Cho
  • GENETIC SIGNATURE OF VULNERABILITY TO INHIBITORS OF BASE EXCISION REPAIR (BER) IN CANCER
    Publication number: 20160102360
    Abstract: The invention relates to the identification of genetic signatures and expression profiles that are a part of the Base Excision Repair (BER) pathway, a major DNA repair pathway that modifies base lesions. In one embodiment, the present invention provides a method of determining responsiveness of treatment by BER inhibitors for malignant glioma by determining the presence of a low level of expression of Apex 1, a low level of expression of Apex 2, and a high level of expression of MPG.
    Type: Application
    Filed: May 21, 2014
    Publication date: April 14, 2016
    Applicants: The Translational Genomics Research Institute, Dignity Health
    Inventors: Shwetal V. Mehta, Michael E. Berens, Harshil Dineshkumar Dhruv
  • NEUROTENSIN-INDUCED TUMOR FORMATION IS REGULATED BY MICRO RNA 133A-AFTIPHILIN-DEPENDENT RECEPTOR RECYCLING
    Publication number: 20160102361
    Abstract: This application discloses methods of treating, preventing, and diagnosing colorectal cancer and IBD in a subject comprising administering an effective dose of antisense miR-133? or AFTPH to the subject or detecting expression levels of miR-133? and AFTPH.
    Type: Application
    Filed: May 19, 2014
    Publication date: April 14, 2016
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Charalabos POTHOULAKIS, Dimitrios ILIOPOULOS, Ka Man LAW
  • GEP5 MODEL FOR MULTIPLE MYELOMA
    Publication number: 20160102362
    Abstract: The invention provides, inter alia, methods of prognosing a subject with, or suspected of having, multiple myeloma. In certain embodiments, the methods entail testing the gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP 13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a biological sample isolated from the subject. The invention also provides methods of treatment for multiple myeloma, as well as kits, oligonucleotides, and systems for performing the methods provided by the invention.
    Type: Application
    Filed: May 19, 2014
    Publication date: April 14, 2016
    Inventors: Bart BARLOGIE, Pingping QU, Christoph HEUCK, Joshua EPSTEIN
  • METHODS AND COMPOSITIONS FOR PREDICTING THERAPEUTIC EFFICACY OF KINASE INHIBITORS IN PATIENTS WITH MYELODYSPLASTIC SYNDROME OR RELATED DISORDERS
    Publication number: 20160102363
    Abstract: The invention discloses a diagnostic method for predicting the therapeutic efficacy of a broad specificity kinase inhibitor in a subject with refractory cancer comprising determining the locus-specific DNA methylation profile of the subject, wherein the locus-specific DNA methylation profile predicts the therapeutic efficacy of a broad specificity kinase inhibitor for treatment of a subject with refractory cancer.
    Type: Application
    Filed: May 28, 2014
    Publication date: April 14, 2016
    Applicants: ONCONOVA THERAPEUTICS, INC., THE TRUSTEES OF COLUMBIA UNVIERSITY IN THE CITY OF NEW YORK
    Inventors: BENJAMIN TYCKO, AZRA RAZA, FRANCOIS WILHELM
  • Neuroglioma Molecular Subtyping Gene Group and Use Thereof
    Publication number: 20160102364
    Abstract: A set of gene groups for predicting or for the auxiliary prediction of the survival time prognosis of patients with neuroglioma consists of a PM gene group and an EM gene group with a total of 68 genes. A subtype marking gene group consisting of two major gene groups co-expressed with PDGFRA and EGFR can stably divide neuroglioma samples from different database sources into three specific subtypes, and can be applied to clinical diagnosis for neuroglioma and judging the survival time prognosis of patients with neuroglioma.
    Type: Application
    Filed: May 27, 2014
    Publication date: April 14, 2016
    Inventors: Xiaolong FAN, Yingyu SUN, Tao JIANG
  • ASSAYS, METHODS AND KITS FOR ANALYZING SENSITIVITY AND RESISTANCE TO ANTI-CANCER DRUGS, PREDICTING A CANCER PATIENT'S PROGNOSIS, AND PERSONALIZED TREATMENT STRATEGIES
    Publication number: 20160102365
    Abstract: Described herein are assays, methods and kits for analyzing sensitivity of a subject's cancerous tumor to a drug, predicting responses of cancerous tumors to drugs, determining the prognosis of a subject having a cancerous tumor, and developing a personalized therapy or treatment strategy for the subject. The assays, methods and kits involve analyzing gene and protein expression signatures or profiles of a subject's cancerous tumor, testing candidate drugs in cancerous cells from the subject's cancerous tumor, and classifying a subject's cancerous tumor based on ovarian cell and fallopian tube cell cell-of-origin gene expression signatures. Using these methods, a suitable drug (or drugs) is identified, the subject can be treated with that drug, and a personalized therapy can be developed for the subject.
    Type: Application
    Filed: June 4, 2014
    Publication date: April 14, 2016
    Inventor: Tan A. Ince