Patents Issued in December 29, 2016
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Publication number: 20160376606Abstract: The invention relates to identifying and evaluating target coding sequences for control of plant parasitic nematodes by inhibiting one or more biological functions, and their use. The invention provides methods and compositions for identification of such sequences and for the control of a plant-parasitic nematode population. By feeding one or more recombinant double stranded RNA molecules provided by the invention to the nematode, a reduction in disease may be obtained through suppression of nematode gene expression. The invention is also directed to methods for making transgenic plants that express the double stranded RNA molecules, and the plant cells and plants obtained thereby.Type: ApplicationFiled: June 27, 2016Publication date: December 29, 2016Inventors: Andrey A. Boukharov, Zijin Du, Liang Guo, Michelle C. Hresko, David K. Kovalic, Zhaolong Li, Maolong Lu, James P. McCarter, Nancy M. Miller, Mark Vaudin, Deryck J. Williams, Wei Wu
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Publication number: 20160376607Abstract: Compositions and methods for controlling pests are provided. The methods involve transforming organisms with a nucleic acid sequence encoding an insecticidal protein. In particular, the nucleic acid sequences are useful for preparing plants and microorganisms that possess insecticidal activity. Thus, transformed bacteria, plants, plant cells, plant tissues and seeds are provided. Compositions are isolated insecticidal proteins and nucleic acids. The sequences find use in the construction of expression vectors for subsequent transformation into organisms of interest, as probes for the isolation of other homologous (or partially homologous) genes. The insecticidal proteins find use in controlling or killing lepidopteran, coleopteran, dipteran, fungal, hemipteran, and nematode pest populations and for producing compositions with insecticidal activity.Type: ApplicationFiled: June 29, 2016Publication date: December 29, 2016Applicant: PIONEER HI-BRED INTERNATIONAL, INC.Inventors: ANDRE R. ABAD, ZHENGLIN HOU, LU LIU, BRAD POLAND, UTE SCHELLENBERGER, INGRID UDRANSZKY, JIMEI WANG, JUN-ZHI WEI, THOMAS C. WOLFE, WEIPING XIE, LAN ZHOU, GENHAI ZHU
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Publication number: 20160376608Abstract: The present disclosure describes improved adeno-associated virus (AAV) vectors for gene therapy applications in the treatment of glycogen storage disease, particularly glycogen storage disease type Ia (GSD-Ia). Described are recombinant nucleic acid molecules, vectors and recombinant AAV that include a G6PC promoter/enhancer, a synthetic intron, a G6PC coding sequence (such as a wild-type or codon-optimized G6PC coding sequence), and stuffer nucleic acid sequence situated between the G6PC promoter/enhancer and the intron, as well as between the intron and the G6PC coding sequence. The recombinant AAVs disclosed herein exhibit highly efficient liver transduction and are capable of correcting metabolic abnormalities in an animal model of GSD-Ia.Type: ApplicationFiled: November 25, 2014Publication date: December 29, 2016Applicants: The U.S.A., as represented by the Secretary, Department of Health and Human Services, University of Florida Research Foundation, IncorporatedInventors: Janice J. Chou, Barry J. Byrne
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Publication number: 20160376609Abstract: The present invention relates to methods and compositions for chromosome integration of nucleic acids into Deinococcus bacteria. The invention more particularly relates to IS-mediated multicopy gene insertion or chromosome engineering in Deinococcus bacteria, the resulting bacteria, and the uses thereof.Type: ApplicationFiled: December 19, 2014Publication date: December 29, 2016Inventors: RÉMI BERNARD, ESTHER GERBER, ELENA HAUSER, JEAN-PAUL LEONETTI
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Publication number: 20160376610Abstract: Fusion protein comprising a programmable DNA modification protein and a cell cycle regulated protein, and methods of using the fusion protein to modify chromosomal sequences and/or regulate gene expression in a cell cycle dependent manner.Type: ApplicationFiled: June 24, 2016Publication date: December 29, 2016Inventors: Gregory D. Davis, Qingzhou Ji, Carol A. Kreader
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Publication number: 20160376611Abstract: A method for producing ethanol, which is a method for producing ethanol from a saccharide obtained from biomass, includes a step of adding an additive solution containing at least acetic acid, formic acid, furfural, and hydroxymethylfurfural to the saccharide to prepare a mixed solution containing the saccharide and the additive solution, and a step of adding a microorganism to the mixed solution to ferment the saccharide using the microorganism, thereby producing ethanol.Type: ApplicationFiled: December 12, 2013Publication date: December 29, 2016Applicant: JGC CORPORATIONInventors: MAKOTO IKEO, SHOHEI OKINO
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Publication number: 20160376612Abstract: A method for producing ethanol using yeast is provided. The method includes a boiling process of heating a fermentation raw material, a saccharification process of saccharifying the boiled fermentation raw material with a coenzyme added thereto, and a fermentation process of inputting a mixed strain culture fluid into the saccharified fermentation raw material and fermentating the resultant product, wherein the mixed strain culture fluid is a culture fluid acquired by cultivating two or more kinds of Saccharomyces cerevisiae strains. According to the ethanol producing method, the bacterial growth is inhibited, thereby demonstrating excellent effects in improving the growth, cultivation and fermentation yields of the yeast. In addition, according to the ethanol producing method, a high yield of pure alcohol is demonstrated, thereby effectively saving the distillation cost for eliminating impurities.Type: ApplicationFiled: January 27, 2015Publication date: December 29, 2016Inventor: Heui Kyu RYU
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Publication number: 20160376613Abstract: Provided herein are glycerol-3-phosphate dehydrogenase (GPD) enzymes with increased KM for NADH and GPD enzymes with substantially the same affinity for NADH and NADPH and/or are feedback inhibited by glycerol-3-phosphate. Also provided herein are recombinant microorganisms comprising a heterologous gene encoding GPD and a deletion or disruption in an endogenous gene encoding GPD. Also provided are recombinant microorganisms comprising a heterologous gene encoding GPD and a butanol biosynthetic pathway. Further provided are methods of producing butanol comprising providing the recombinant microorganisms described herein and contacting the recombinant microorganism with at least one fermentable carbon substrate under conditions wherein butanol is produced.Type: ApplicationFiled: August 4, 2016Publication date: December 29, 2016Inventors: RITU BHALLA, GOPAL K. CHOTANI, MICHAEL DAUNER, MARK J. NELSON, DANIEL P. O'KEEFE, CAROLINE M. PERES, JAHNAVI CHANDRA PRASAD, JEAN-FRANCOIS TOMB
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Publication number: 20160376614Abstract: The invention provides non-naturally occurring microbial organisms comprising a 1,4-butanediol (BDO), 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine pathway comprising at least one exogenous nucleic acid encoding a BDO, 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine pathway enzyme expressed in a sufficient amount to produce BDO, 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine and further optimized for expression of BDO. The invention additionally provides methods of using such microbial organisms to produce BDO, 4-hydroxybutyryl-CoA, 4-hydroxybutanal or putrescine.Type: ApplicationFiled: June 3, 2016Publication date: December 29, 2016Inventors: Robert HASELBECK, John D. TRAWICK, Wei NIU, Anthony P. BURGARD
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Publication number: 20160376615Abstract: The invention provides recombinant microorganisms and methods for the production of acetone from gaseous substrates. For example, the recombinant microorganism may be modified to express an exogenous thiolase, an exogenous CoA transferase, and an exogenous decarboxylase.Type: ApplicationFiled: July 8, 2016Publication date: December 29, 2016Inventors: Michael Koepke, Sean Simpson, Fungmin Liew, Wendy Yiting Chen
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Publication number: 20160376616Abstract: The invention relates to a method for treating a solution containing a saccharide comprising a heat treatment step of heating the saccharide solution at a temperature of 100° C. or higher and 180° C. or lower and a reduction step of reacting a reducing agent with the saccharide solution heated in the heat treatment step, a method for producing a treated saccharide solution using the treatment method, a treated saccharide solution obtained through treatment by the treatment method, a method for producing an organic compound comprising an organic-matter production step of obtaining an organic compound by causing a microorganism capable of producing organic matter to act on an organic raw material containing the treated saccharide solution and a method for culturing a microorganism using the treated saccharide solution as a carbon source.Type: ApplicationFiled: September 13, 2016Publication date: December 29, 2016Applicant: MITSUBISHI CHEMICAL CORPORATIONInventors: Kiminori KAWAKAMI, Yasuyo Saito, Takanao Matsumoto, Ryusuke Aoyama, Shigeki Nitta, Masaru Utsunomiya
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Publication number: 20160376617Abstract: Methods and compositions for the production of dielectric fluids from lipids produced by 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 sucrose transporter, a sucrose invertase, a fructokinase, a polysaccharide-degrading enzyme, a lipid pathway modification enzyme, a fatty acyl-ACP thioesterase, a desaturase, a fatty acyl-CoA/aldehyde reductase, and/or an acyl carrier protein are useful in manufacturing dielectric fluids.Type: ApplicationFiled: June 10, 2016Publication date: December 29, 2016Inventors: Scott Franklin, Walter Rakitsky, George Rudenko, Xinhua Zhao, Felipe Arana Rodriguez, Wenhua Lu, Janice Wee
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Publication number: 20160376618Abstract: The present invention is directed to processes for the preparation of lisdexamfetamine and related derivatives, wherein the processes comprise coupling to racemic or enantiomerically enriched amphetamine and wherein the resulting product is advantageously enantiomerically or diastereomerically enriched in the desired stereoisomer.Type: ApplicationFiled: June 15, 2016Publication date: December 29, 2016Inventors: Pietertje Elisabeth Goudriaan, Jasper Kaiser, Hemen Ibrahim, Govert Arie Verspui, Douglas Phillip Cox
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Publication number: 20160376619Abstract: The present invention is directed to methods of modifying the plant development process comprising of exposing a seed, seedling, or plant to volatiles biosynthesized by one or more bacteria or enzymes. Specifically, the embodiment uses one or more bacteria selected from the plant growth promoting bacteria group consisting of Rhodococcus spp., Pseudomonas spp., Bacillus spp., or Xanthobacter spp., or a mixture thereof. A closed apparatus, FIG. 1A, containing a tri-phasic system is used to expose the bacteria to hydrocarbons, iron, cyanide, and/or ammonium compounds; the method induces the biocatalyst to biosynthesize volatile compound(s) that plant hormone production to enhance or accelerate plant development.Type: ApplicationFiled: September 11, 2016Publication date: December 29, 2016Inventor: Guenevere Diane Perry
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Publication number: 20160376620Abstract: The present invention relates to compositions comprising: a polypeptide having cellulolytic enhancing activity and a heterocyclic compound. The present invention also relates to methods of using the compositions.Type: ApplicationFiled: June 27, 2016Publication date: December 29, 2016Inventors: Jason Quinlan, Feng Xu, Matthew Sweeney
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Publication number: 20160376621Abstract: A method for optimization of a fed batch hydrolysis process wherein the hydrolysis time is minimized by controlling the feed addition volume and/or batch addition frequency of the prehydrolysate and optionally also the enzyme feed. The increase over time in hydrolysate consistency and volume and/or concentration of sugars released in the reactor, so that the enzymatic hydrolysis is controlled, significantly reduces the impact of cellulase feedback inhibition, especially for enzyme contents lower than 1%. The overall time to reach conversion of the total prehydrolysate feed is reduced significantly where the batch addition frequency is equal to one batch each time 70% to 90%, preferably 80%, conversion of the previous batch is reached in the reaction mixture. At an enzyme load of 0.3% in the reaction mixture, the optimum frequency each time 80% conversion was reached was found to be one batch every 80 to 105 minutes.Type: ApplicationFiled: September 8, 2016Publication date: December 29, 2016Inventors: Robert Ashley Cooper BENSON, Regis-Olivier BENECH
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Publication number: 20160376622Abstract: The present invention relates to recombinant filamentous fungal host cells producing cellulolytic enzyme compositions and methods of producing and using the compositions.Type: ApplicationFiled: September 14, 2016Publication date: December 29, 2016Inventors: Jeffrey Shasky, Suchindra Maiyuran, Amanda Fischer
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Publication number: 20160376623Abstract: The present invention relates to an isolated DNA molecule encoding a fagopyritol synthase. A method for producing a fagopyritol, an insulin mediator, an insulin mediator analogue, an insulin mediator homologue, or an insulin mediator inhibitor is also described. The method includes providing a fagopyritol synthase, providing a substrate comprising a galactosyl donor and a galactosyl acceptor, and combining the fagopyritol synthase with the substrate under conditions effective produce a fagopyritol, an insulin mediator, an insulin mediator analogue, an insulin mediator homologue, or an insulin mediator inhibitor.Type: ApplicationFiled: June 27, 2016Publication date: December 29, 2016Inventors: Ralph L. OBENDORF, Takashi UEDA
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Publication number: 20160376624Abstract: Polypeptides having target levels of C-terminal variants are described.Type: ApplicationFiled: September 9, 2016Publication date: December 29, 2016Applicant: Momenta Pharmaceuticals, Inc.Inventor: Holly Prentice
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Publication number: 20160376625Abstract: The subject of the present invention is a whole-cell catalysis process for converting substrates of cytochrome P450 monooxygenases of eukaryotic origin into valuable biotechnological products. The subject of the present invention is also microorganisms genetically engineered to achieve those biotransformations with high rates and processes to prepare these microorganism strains.Type: ApplicationFiled: June 17, 2014Publication date: December 29, 2016Inventors: Adrian Gerber, Frank Hannemann, Sabrina Bleif, Michael Kleser, Rita Bernhardt
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Publication number: 20160376626Abstract: The present invention provides: a reagent composition having higher storage stability; a sensor involving the reagent composition; and others. According to the present invention, a specific heterocyclic compound is added to a reagent composition to improve the storage stability of the reagent composition and reduce the degree of fluctuation in current values in a sensor that utilizes reagent composition.Type: ApplicationFiled: August 30, 2016Publication date: December 29, 2016Inventors: Motonori UCHIYAMA, Takuo KOUNO
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Publication number: 20160376627Abstract: Methods, apparatuses, and systems for screening, analyzing and selecting microorganisms from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and synthesizing microbial ensembles based thereon are disclosed. Methods for identifying and determining the absolute cell count of microorganism types and strains, along with identifying the network relationships between active microorganisms and environmental parameters, are also disclosed.Type: ApplicationFiled: July 22, 2016Publication date: December 29, 2016Inventors: Karsten ZENGLER, Mallory EMBREE
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Publication number: 20160376628Abstract: A method for screening an antimicrobial agent which is capable of controlling microorganisms causing offensive odor in an air-conditioning system and a method for removing offensive odor in an air-conditioning system are provided. The method for screening an antimicrobial agent and the method for removing offensive odor in an air-conditioning system may be used for various purposes of industrial application. For example, they may be used to develop a novel antimicrobial agent capable of inhibiting the growth of the microorganisms or to develop an air freshener for removing offensive odor by elucidating the chemical properties of the metabolites of the microorganisms. In addition, they may be used to fundamentally remove the cause of offensive odor by providing an air-conditioning system with an environment where the microorganisms may not live.Type: ApplicationFiled: December 10, 2014Publication date: December 29, 2016Inventors: Tae Hee Lee, Ji Wan Kim, So Yoon Park
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Publication number: 20160376629Abstract: Provided herein provided is an assay system for monitoring drug susceptibility of a pathogenic bacteria comprising color-producing substrates for a beta-lactamase of the pathogenic bacteria, an assay device for visibly detecting a product of the beta-lactamase on the substrate thereof and a reader configured to quantify the visibly detected product. Also provided is an in vitro method to determine susceptibility to a drug effective against a pathogenic bacteria, for example, a pathogenic Mycobacteria, that has a beta-lactamase activity. An excitation wavelength is delivered to a biological sample obtained from a subject having an infection from the pathogenic bacteria in the presence of a beta-lactamase substrate. The intensity of a signal, such as a fluorescent, luminescent or colorimetric signal, at an emission wavelength of a product of the beta-lactamase on the subject is correlated to drug susceptibility.Type: ApplicationFiled: September 12, 2016Publication date: December 29, 2016Applicants: The Texas A&M University System, The Board of Trustees of the Leland Stanford Junior UniversityInventors: Jeffrey D. Cirillo, Jianghong Rao
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Publication number: 20160376630Abstract: The present invention relates to a method for determining an amount of a peroxide in a sample, wherein the method comprises the steps of: —providing a sample, —contacting the sample with a terbium(III) benzene dicarboxylic acid complex, and —determining the luminescence of the terbium(III) benzene dicarboxylic acid complex.Type: ApplicationFiled: July 1, 2014Publication date: December 29, 2016Applicant: UNIVERSITAT LEIPZIGInventors: Thomas KREISING, Agneta PRASSE, Kristin ZCHARNACK, Thole ZUCHNER
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Publication number: 20160376631Abstract: The subject invention provides materials and methods for detecting the presence of an electron donor. In a specific embodiment, the device detects the presence of dihydronicotinamide adenine dinucleotide (NADH) via a colorimetric change output by the sensing device. In another specific embodiment, the presence of an enzyme capable of catalyzing, or an agent capable of inhibiting, the production of NADH can also be detected by a colorimetric readout using the same device. In some embodiments, dihydronicotinamide adenine dinucleotide phosphate (NADPH) can also be detected using the device provided herein. Advantageously, preferred embodiments of the subject invention provide a low-cost, sensitive device for monitoring the presence of critical biological analytes in a variety of applications.Type: ApplicationFiled: June 28, 2015Publication date: December 29, 2016Applicant: The Florida International University Board of TrusteesInventors: Pingping LIANG, Haixiang YU, Yi XIAO
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Publication number: 20160376632Abstract: The invention provides a method for detecting the activities of two or more kinases. The method enables multiplexed detection with high signal to noise in a high-throughput-compatible format and a platform that could be applied to other lanthanide metal and fluorophore combinations to achieve even greater multiplexing without the need for phosphospecific antibodies.Type: ApplicationFiled: June 28, 2016Publication date: December 29, 2016Inventors: Laurie L. Parker, Andrew M. Lipchik
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Publication number: 20160376633Abstract: A composition, method and kit for performing a two-reagent enzymatic homocysteine assay, wherein a single homocysteinase enzyme and a Schiff-based conjugate of N,N-dibutyl-p-phenyldiamine (DBPDA) with pyridoxal 5?-phosphate (PLP) are used to measure total homocysteine in plasma or serum. The assay measures a chromophore reaction product of H2S and the DBPDA released from the Schiff-base conjugate in the presence of a Fe+3 containing compound. The resulting chromophore may be measured absorbance or fluorescence spectrophotometry.Type: ApplicationFiled: September 9, 2016Publication date: December 29, 2016Inventors: Yuying Tan, Shukuan Li
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Publication number: 20160376634Abstract: The present invention relates to medicine, and specifically to hematology, and can be used in particular for diagnostic and research purposes when determining coagulation characteristics of blood and its components, and also in biotechnology and fundamental biological research. One of the aspects of the present invention is a polypeptide for inhibition of contact activation in a sample of blood or its product to be tested, which comprises the sequence of an infestin-4 mutant MutB (SEQ ID NO: 1) and which substantially corresponds thereto, where said sequence can have modifications outside the area of the inhibitory loop which significantly maintain the activity of the said polypeptide, which acts as a high-selectivity fXIIa inhibitor, the selectivity of which is higher than that of native infestin-4 and Mut15, or the activity of which is higher than that of native infestin-4 and Mut15.Type: ApplicationFiled: November 25, 2014Publication date: December 29, 2016Applicant: OBSCHESTVO S OGRANICHENNOY OTVETSTVENNOSTYU <<GEMATOLOGICHESKAYA KORPORATSIYAInventors: Vladimir Nikolaevich KOLYADKO, Fazoil Inoyatovich ATAULLAKHANOV, Mikhail Aleksandrovich PANTELEEV, Tatyana Alekseevna VUYMO, Ruzanna Armenovna OVSEPYAN, Stepan Sergeevich SUROV, Vera Anatoljevna KORNEEVA
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Publication number: 20160376635Abstract: The present invention relates to a PCR kit for improving detection of particular nucleic acid motifs and for increasing the reliability of the results obtained. More precisely, the invention proposes to use modified primers having particular characteristics making it possible, during electrophoresis treatment, to detect, on samples containing nucleic acids, the equivalent of a characteristic encoding of particular nucleic acid motifs, this encoding being such that it makes it possible to better detect the presence of these motifs. The invention also proposes a method for detecting nucleic acid motifs of interest (for example STRs, mini-STRs or VNTRs) using such primers. It advantageously finds—but is not limited to—application in the field of capillary electrophoresis.Type: ApplicationFiled: June 22, 2016Publication date: December 29, 2016Applicants: Safran Identity & Security, Safran Identity & SecurityInventors: Marcelin RAGOT, Benoit TONSON, Marina POUET, Rafael ALOS
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Publication number: 20160376636Abstract: The invention relates generally to compositions and methods for disrupting cells (e.g., disrupting cellular and nuclear membranes). In particular, the invention provides modified solid surfaces (e.g., bead surfaces) and their use in disruption of cellular membranes (e.g., during cellular lysis procedures (e.g., for recovery of nucleic acid (e.g., DNA or RNA) from mechanical cell lysis)). Compositions and methods of the invention find use in a wide range of applications including molecular biology and medical science.Type: ApplicationFiled: September 12, 2016Publication date: December 29, 2016Inventor: Thomas N. Chiesl
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Publication number: 20160376637Abstract: Methods, materials, and kits for distinguishing a population of cells or organisms truly present in a clinical specimen from contaminating cells or organisms is disclosed. The methods and kits use a suppressor to avoid false positive detection of contaminants in nucleic acid amplification reactions.Type: ApplicationFiled: June 26, 2015Publication date: December 29, 2016Inventors: Wanyuan AO, Robert D. JENISON, Jamie PURCELL
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QUANTITATIVE ANALYSIS METHOD USING MICROORGANISM 16S RDNA GENE HAVING SINGLE NUCLEOTIDE POLYMORPHISM
Publication number: 20160376638Abstract: The present invention relates to utilization of an artificially synthesized nucleic acid, and more particularly, to a quantitative analysis method capable of quantitatively adjusting gene-based microbial community analysis results by preparing a microorganism 16S rDNA gene, which has a single nucleotide polymorphism (SNP) at a particular location so as to be differentiated from a gene of a target microorganism on the nucleotide sequence, and then using the microorganism 16S rDNA gene as an internal standard material which is quantifiable through nucleotide sequencing.Type: ApplicationFiled: November 18, 2014Publication date: December 29, 2016Applicant: KOREA RESEARCH INSTITUTE OF STANDARDS AND SCIENCEInventors: Inchul Yang, Hannah Yu, Hyo-jin Yang, Sook-Kyung Kim, Sang-Ryoul Park -
Publication number: 20160376639Abstract: The present invention comprises methods and systems to profile individual chromosomes using target-specific DNA probes in biological samples. The invention relates to generation of chromosome profiles either singly or in combination (multiplex). The invention can refer to the generation of chromosome profiles using target-specific DNA probes for various biological samples such as cell free DNA from the peripheral blood of a pregnant woman or from a cancer patient. The invention further involving generation of chromosome profiles using target-specific DNA probes for individual intact cells from the peripheral blood of a pregnant woman, from a cancer patient or from an embryo created using artificial reproductive technologies. The invention further involving detection of target-specific DNA hybridizations through direct fluorescence by special spectral filters or fluorescence intensity by fluorimeters.Type: ApplicationFiled: June 22, 2016Publication date: December 29, 2016Inventor: Ramesh Vallabhaneni
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Publication number: 20160376640Abstract: Methods and apparatuses for determining exosome purity are disclosed. In an example embodiment, a laboratory instrument apparatus includes an analytical centrifuge configured to rotate a solution causing a plurality of particles to separate. The analytical centrifuge is also configured to perform an interference measurement on the solution and/or three absorbance measurements on the solution. A computer processor communicatively coupled to the analytical centrifuge is configured to determine an exosome purity of the solution based on the three absorbance measurements and/or the interference measurement.Type: ApplicationFiled: June 23, 2016Publication date: December 29, 2016Inventors: Carley Denise Ross, Thomas Hans Ramin
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Publication number: 20160376641Abstract: Disclosed herein are methods and compositions for detecting differential expression of certain miRNAs in cancer cells or their surrounding normal tissues in the tumor microenvironment. The disclosure describes an automated, highly sensitive and specific method for detection of any cellular RNA molecule, including microRNA, messenger RNA and non-coding RNA. The technology includes probe design as well as probe use in an automated fashion for detection of RNA molecules in formalin-fixed paraffin-embedded tissue (FFPET) samples.Type: ApplicationFiled: August 23, 2016Publication date: December 29, 2016Inventors: Michael Farrell, William Day, Zeyu Jiang, Anne Pedata
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Publication number: 20160376642Abstract: The present invention provides a method for performing a localised RCA reaction comprising at least two rounds of RCA, wherein the product of a second RCA reaction is attached, and hence localised, to a product of a first RCA reaction, said method comprising: (a) providing a first RCA product; (b) directly or indirectly hybridising to said first RCA product a probe which comprises or provides a primer for a second RCA reaction; and (c) performing a second RCA reaction using said RCA primer of (b) to form a second RCA product, wherein in said reaction: (i) said probe and said primer are not able to prime extension using said first RCA product as template or any such extension is limited to avoid displacement of any probe hybridised to the first RCA product; (ii) the direct or indirect hybridisation of the RCA primer of (b) to the first RCA product is maintained and, by virtue of said hybridisation, the second RCA product is attached to the first RCA product; (iii) a RCA template for said second RCA reaction isType: ApplicationFiled: November 14, 2013Publication date: December 29, 2016Applicant: OLINK ABInventors: Ulf LANDEGREN, Lei CHEN, Di WU, Yuan NONG, Caroline GALLANT
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Publication number: 20160376643Abstract: The present invention relates to a method for quantifying a target nucleic acid sequence by use of a common internal control. The present invention allows to determine an absolute initial amount of a target nucleic acid sequence with no use of a standard curve. The present invention amplifies not only a control reaction mixture comprising a known-amount standard and an internal control but also a sample reaction mixture comprising an internal control identical to the internal control in the control reaction mixture and the target nucleic acid sequence to be quantified. In the present invention, a relative ratio of the amount of the standard and the amount of the target nucleic acid sequence is calculated by using the internal control and then an initial amount of the target nucleic acid sequence is determined by using a known amount of the standard.Type: ApplicationFiled: May 2, 2014Publication date: December 29, 2016Inventors: Jong Yoon CHUN, Young Jo LEE
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Publication number: 20160376644Abstract: This invention is directed to a guide positioning sequencing technology of whole-genome DNA methylation. The invention provides a new detection method of nucleic acid methylation. In particular, a concept of “positioning” in the detection of nucleic acid methylation is provided. Specifically, a portion of a sequence is used for genome wide positioning and the other portion of the sequence is used for methylation detection in sequencing, thereby solving/defeating previously existing challenges in methylation detection and bioinformatics analysis of a genome.Type: ApplicationFiled: November 13, 2014Publication date: December 29, 2016Applicant: FUDAN UNIVERSITYInventors: Wenqiang YU, Yan LI, Feizhen WU
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Publication number: 20160376645Abstract: Improvements on the basic method used for BEAMing increase sensitivity and increase the signal-to-noise ratio. The improvements have permitted the determination of intrinsic error rates of various DNA polymerases and have permitted the detection of rare and subtle mutations in DNA isolated from plasma of cancer patients.Type: ApplicationFiled: June 6, 2016Publication date: December 29, 2016Applicant: The Johns Hopkins UniversityInventors: Bert Vogelstein, Frank Diehl, Kenneth W. Kinzler, Meng Li
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Publication number: 20160376646Abstract: The present invention relates to systems, compositions, and methods for nucleic acid sequencing and analysis in free-solution using protein polymer drag-tags. As such, the present invention provides protein-based molecular compositions that find use as drag-tags for use in sequencing and nucleic acid analysis methods and provides systems and methods for automated sequencing and analysis of nucleic acids in free solution.Type: ApplicationFiled: April 1, 2016Publication date: December 29, 2016Inventors: Robert J. Meagher, Jong-In Won, Annelise E. Barron
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Publication number: 20160376647Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.Type: ApplicationFiled: August 19, 2016Publication date: December 29, 2016Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
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Publication number: 20160376648Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.Type: ApplicationFiled: July 22, 2016Publication date: December 29, 2016Inventors: Stephen P.A. Fodor, Glenn K. Fu
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Publication number: 20160376649Abstract: Disclosed herein are compositions and methods for sequencing nucleic acids.Type: ApplicationFiled: September 12, 2016Publication date: December 29, 2016Applicant: Illumina Cambridge LimitedInventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Betley, Niall Anthony Gormley
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Publication number: 20160376650Abstract: The present invention relates to methods of treating and diagnosing oxidative damage in a subject comprising administering an agent that binds oxidized extracellular nucleic acid, and methods of treating diseases and conditions in a subject comprising administering an adjuvant therapy comprising an agent that binds oxidized extracellular nucleic acid. The oxidized fraction of extracellular DNA can also be detected through electrochemical methods or by mass-spectrometry.Type: ApplicationFiled: November 6, 2014Publication date: December 29, 2016Inventors: Anna BARANOVA, Svetlana KOSTYUK, Natalya VEIKO
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Publication number: 20160376651Abstract: The present invention provides a method for determining increased risk of premature birth in a pregnant woman by detecting altered expression level of one or more marker genes in the woman's blood. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for preventing or reducing the likelihood of premature birth.Type: ApplicationFiled: June 20, 2014Publication date: December 29, 2016Inventors: Siu-Chung Stephen CHIM, Chee Yin CHEUNG, Wan Chee CHEUNG, Tak Yeung EUNG, Wing Shan LEE
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Publication number: 20160376652Abstract: Provided herein are methods, compositions, systems, and kits for diagnosing acute rejection of solid organ transplants using at least 5 genes selected from a 10-gene panel.Type: ApplicationFiled: September 5, 2014Publication date: December 29, 2016Inventor: Minnie M. Sarwal
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Publication number: 20160376653Abstract: Methods are provided for determining whether a subject has a graft tolerant phenotype. In practicing the subject methods, the expression level of one or more gene in a sample from the subject, e.g., a blood sample, is assayed to obtain a gene expression result, where the gene expression result includes a result for a biomarker of graft tolerance. The obtained gene expression result is then employed to determine whether the subject has a graft tolerant phenotype. Also provided are compositions, systems and kits that find use in practicing the subject methods. The methods and compositions find use in a variety of applications, including the determination of an immunosuppressive therapy regimen.Type: ApplicationFiled: February 9, 2016Publication date: December 29, 2016Inventors: MINNIE M. SARWAL, LI LI, Samuel STROBER
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Publication number: 20160376654Abstract: Methods and compositions disclosed herein generally relate to methods of identifying, validating, and measuring clinically relevant, quantifiable biomarkers of diagnostic and therapeutic responses for blood, vascular, cardiac, and respiratory tract dysfunction, particularly as those responses relate to septic shock in pediatric patients. In particular, the invention relates to identifying one or more biomarkers associated with septic shock in pediatric patients, obtaining a sample from a pediatric patient having at least one indication of septic shock, then quantifying from the sample an amount of one or more of said biomarkers, wherein the level of said biomarker correlates with a predicted outcome.Type: ApplicationFiled: November 25, 2014Publication date: December 29, 2016Applicant: CHILDREN'S HOSPITAL MEDICAL CENTERInventors: Christopher John Lindsell, Hector R. Wong
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Publication number: 20160376655Abstract: Focal and segmental glomerulosclerosis (FSGS) is a kidney disorder of unknown etiology and up to 20% of patients on dialysis have this diagnosis. A large family with hereditary FSGS carries a missense mutation in the TRPC6 gene on chromosome 11q, encoding the ion channel protein Transient Receptor Potential Cation Channel 6. The missense mutation is a P112Q substitution, which occurs in a highly conserved region of the protein, enhances TRPC6-mediated calcium signals in response to agonists such as angiotensin II, and alters the intracellular distribution of TRPC6 protein. Previous work has emphasized the importance of cytoskeletal and structural proteins in proteinuric kidney diseases. Our findings suggest a novel mechanism for glomerular disease pathogenesis.Type: ApplicationFiled: June 1, 2016Publication date: December 29, 2016Applicant: Duke UniversityInventors: Michelle WINN, Margaret A. Pericak-Vance, Jeffery M. Vance