Probes For Detection Of Specific Nucleotide Sequences Or Primers For The Synthesis Of Dna Or Rna Patents (Class 536/24.3)
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Patent number: 8796441Abstract: Identified herein are different forms of sweet and umami receptor encoding sequences that occur in different human populations. In particular, there are provided several single nucleotide polymorphisms (SNPs) that occur within the exons/coding sequence (and are therefore coding SNPs, cSNPs) of one of the three T1R genes. Some SNPs cause amino acid substitutions, while others introduce a chain termination codon, rendering a truncated product. Differences in these genes are believed to affect the sense of taste of individuals, such that individuals with different SNPs (or different haplotypes) are believed to perceive the taste of sweet or umami (e.g., glutamate) substances differently than the rest of the population. The ability to assay this allelic information is useful in the development of flavorings and flavor enhancers, as it can be used to define groups and populations who perceive tastes differently. This in turn allows the taste preferences of these groups to be addressed at the molecular level.Type: GrantFiled: April 13, 2006Date of Patent: August 5, 2014Assignee: The United States of America as represented by the Secretary of the Department of Health and Human ServicesInventors: Dennis T. Drayna, Un-Kyung Kim
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Patent number: 8795966Abstract: In a multiplexed assay method carried out in solution, wherein the solution contains nucleic acid targets and, wherein several different types of oligonucleotide probes, each type having a different sequence in a region designated as a target binding domain, are used to detect the nucleic acid targets, said assay method including a method for increasing the effective concentration of the nucleic acid targets at the surface of a bead to which the oligonucleotide probes are bound, by one or more of the following steps: adjusting assay conditions so as to increase the effective concentration of the targets available for binding to the probes, by one or more of the following: (i) selecting a particular probe density on the surface of the bead; (ii) selecting a solution having an ionic strength greater than a threshold; (ii) selecting a target domain of a size less than a threshold; or (iii) selecting target domains within a specified proximity to a terminal end of the targets.Type: GrantFiled: February 18, 2010Date of Patent: August 5, 2014Assignee: BioArray Solutions, Ltd.Inventors: Michael Seul, Yi Zhang, Sukanta Banerjee, Jiacheng Yang, Chiu Chau
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Patent number: 8796432Abstract: This invention provides a nucleotide analogue comprising (i) a base selected from the group consisting of adenine, guanine, cytosine, thymine and uracil, (ii) a deoxyribose, (iii) an allyl moiety bound to the 3?-oxygen of the deoxyribose and (iv) a fluorophore bound to the base via an allyl linker, and methods of nucleic acid sequencing employing the nucleotide analogue.Type: GrantFiled: October 31, 2006Date of Patent: August 5, 2014Assignee: The Trustees of Columbia University in the City of New YorkInventors: Jingyue Ju, Lanrong Bi, Dae H. Kim, Qinglin Meng
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Patent number: 8795972Abstract: Provided herein are methods, kits and compositions to classify fungi. Methods are provided for classification of fungi according to established phenotypes, for example, antimicrobial susceptibility profiles. More specifically, the invention provides methods for the use of PNA probes in diagnostic applications, which will aid in the direction of appropriate therapy against fungi.Type: GrantFiled: October 15, 2008Date of Patent: August 5, 2014Assignee: AdvanDx, Inc.Inventors: Mark Fiandaca, Henrik Stender
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Patent number: 8790919Abstract: The present invention provides compositions and methods for the optimization of cleavage of RNA species by RNase H. In some embodiments, the invention provides oligonucleotides that possess two or more regions of differing conformation, and at least one transitional nucleobase positioned between the regions that is capable of modulating transfer of the helical conformation characteristic of the region bound to the 3?hydroxy thereof, to the region bound to the 5? hydroxyl thereof.Type: GrantFiled: March 15, 2005Date of Patent: July 29, 2014Assignee: Isis Pharmaceuticals, Inc.Inventors: Michael T. Migawa, Walter F. Lima, Eric E. Swayze, Joshua Nichols, Hongjiang Wu, Thazha P. Prakash, Tadeusz Krzysztof Wyrzykiewicz, Balkrishen Bhat, Stanley T. Crooke
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Publication number: 20140208449Abstract: This invention relates to the genetics of gender discrimination in the dioecious date palm. Methods of the present invention involve analyzing DNA or RNA from a date palm plant, tissue, germplasm, or seed for the presence of (i) a nucleic acid sequence or genotype that identifies the sex of the plant, tissue, germplasm, or seed or (ii) a molecular marker in linkage disequilibrium with the nucleic acid sequence or genotype. Also disclosed are kits for selecting male and female date palm plants prior to flowering, methods of breeding a date palm plant, and a method of planting a date palm seed of a known sex.Type: ApplicationFiled: March 29, 2012Publication date: July 24, 2014Applicant: CORNELL UNIVERSITYInventor: Joel A. Malek
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Patent number: 8785615Abstract: The various embodiments of the present disclosure relate generally to single molecule sensitive probes for detecting RNA, and more particularly to multivalent fluorescent probes for detecting a single molecule of RNA in a cell. The present invention includes a RNA imaging probe comprising: a multivalent core comprising a plurality of attachment sites; a plurality of RNA/DNA chimeric oligonucleotides having a specificity for a target RNA, wherein a RNA/DNA chimeric oligonucleotide is bound to an attachment site of the multivalent core; and a plurality of fluorophores, wherein a fluorophore is bound to the RNA/DNA chimeric oligonucleotide.Type: GrantFiled: March 25, 2010Date of Patent: July 22, 2014Assignee: Georgia Tech Research CorporationInventor: Philip J. Santangelo
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Patent number: 8785125Abstract: Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.Type: GrantFiled: September 27, 2013Date of Patent: July 22, 2014Assignee: Gen-Probe IncorporatedInventors: Sylvia A. Norman, Jennifer J. Bungo, William L. Hanna, Neeraj P. Rao
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Patent number: 8785133Abstract: A process of detection of pandemic swine flu virus H1N1 type in a sample is provided herein. Also provided are highly specific oligonucleotides useful for rapid detection of swine flu virus in a sample, as well as swine flu virus specific isothermal gene amplification assay for early clinical diagnosis of H1N1 human patients.Type: GrantFiled: November 11, 2010Date of Patent: July 22, 2014Assignee: Defence Research & Development OrganisationInventors: Manmohan Parida, Jyoti Shukla, Santhosh Sannarangiah, Sashi Sharma, Venkata Lakshmana Putcha Rao, Rajagopalan Vijayaraghavan
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Patent number: 8785728Abstract: This invention relates to soybean event pDAB4472-1606 (Event 1606). This invention includes a novel aad-12 transformation event in soybean plants comprising a polynucleotide sequence, as described herein, inserted into a specific site within the genome of a soybean cell. This invention also relates in part to plant breeding and herbicide tolerant plants. In some embodiments, said event/polynucleotide sequence can be “stacked” with other traits, including, for example, other herbicide tolerance gene(s) and/or insect-inhibitory proteins.Type: GrantFiled: September 7, 2011Date of Patent: July 22, 2014Assignee: Dow AgroSciences, LLC.Inventors: Yunxing C. Cui, Thomas Hoffman, Ning Zhou, Gregory J. Gilles, Terry R. Wright, Dawn M. Parkhurst, Julissa Colon, Yonghe Bai
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Patent number: 8785122Abstract: Methods of identifying polymorphisms associated with ataxia-ocular apraxia 2 (AOA2), are described. The polymorphisms associated with AOA2 include specific mutations in the senataxin (SETX) gene. Also described are methods of diagnosis of AOA2, as well as methods of assessing an individual for carrier status for AOA2.Type: GrantFiled: June 4, 2012Date of Patent: July 22, 2014Assignee: Athena Diagnostics, Inc.Inventors: Corey D. Braastad, Narasimhan Nagan, Jeffrey G. Jones, William K. Seltzer, Susan Allen, Sat Dev Batish, Hui Zhu
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Patent number: 8785614Abstract: The present invention provides a method for detecting pancreatic carcinoma in a subject. The method includes contacting a nucleic acid-containing specimen from the subject with an agent that provides a determination of the methylation state of at least one gene or associated regulatory region of the gene and identifying aberrant methylation of regions of the gene or regulatory region, wherein aberrant methylation is identified as being different when compared to the same regions of the gene or associated regulatory region in a subject not having the pancreatic carcinoma, thereby detecting pancreatic carcinoma in the subject.Type: GrantFiled: January 9, 2009Date of Patent: July 22, 2014Assignee: The Johns Hopkins UniversityInventors: Michael G. Goggins, Norihiro Sato
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Patent number: 8785126Abstract: The invention provides a method for reducing stutter in the amplification of a microsatellite comprising the steps of providing a sample comprising a microsatellite having a G+C content of 50% or less; contacting the sample with at least one enzyme having nucleic acid polymerase activity; and incubating the sample with the enzyme for a sufficient amount of time and under conditions sufficient to amplify the microsatellite; wherein the incubation is performed in the presence of an amount of betaine, sorbitol or mixtures thereof, effective to reduce stutter relative to the amount of stutter observed in the absence of betaine and/or sorbitol. The invention also provides compositions containing betaine and/or sorbitol, kits for amplifying microsatellites having a G+C content of 50% or less, and methods of using all of the foregoing.Type: GrantFiled: September 12, 2012Date of Patent: July 22, 2014Assignee: Applied Biosystems, LLCInventors: Sulekha Rao Coticone, William Bloch
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Patent number: 8778676Abstract: MicroRNA genes are highly associated with chromosomal features involved in the etiology of different cancers. The perturbations in the genomic structure or chromosomal architecture of a cell caused by these cancer-associated chromosomal features can affect the expression of the miR gene(s) located in close proximity to that chromosomal feature. Evaluation of miR gene expression can therefore be used to indicate the presence of a cancer-causing chromosomal lesion in a subject. As the change in miR gene expression level caused by a cancer-associated chromosomal feature may also contribute to cancerigenesis, a given cancer can be treated by restoring the level of miR gene expression to normal. microRNA expression profiling can be used to diagnose cancer and predict whether a particular cancer is associated with an adverse prognosis. The identification of specific mutations associated with genomic regions that harbor miR genes in CLL patients provides a means for diagnosing CLL and possibly other cancers.Type: GrantFiled: August 21, 2013Date of Patent: July 15, 2014Assignee: Thomas Jefferson UniversityInventors: Carlo M. Croce, Chang-Gong Liu, George A. Calin, Cinzia Sevignani
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Patent number: 8778664Abstract: A probe, a set of probes, and a probe carrier on which the probe or the set of probes is immobilized, are provided for classification of fungus species. The probe or the set of probes is capable of collectively detecting fungus of the same species and distinguishingly detecting those fungus from fungus of other species. The probe is an oligonucleotide probe for detecting a pathogenic fungus DNA and includes at least one of base sequences of SEQ ID NOS. 1 to 4 and mutated sequences thereof.Type: GrantFiled: June 19, 2012Date of Patent: July 15, 2014Assignee: Canon Kabushiki KaishaInventors: Nobuhiro Tomatsu, Toshifumi Fukui, Nobuyoshi Shimizu, Atsushi Takayanagi
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Publication number: 20140194611Abstract: The present invention provides a new class of solids supports for synthesis of modified oligomers of nucleic acids, and nucleic acid probes that have a format expediently synthesized on the new supports. Exemplary solid supports include at least one quencher bound through a linker to the solid support. Various exemplary embodiments include a moiety that stabilizes a duplex, triplex or higher order aggregation (e.g., hybridization) of nucleic acids of which the oligomer of the invention is a component. Other components of the solid support include moieties that stabilize aggregations of nucleic acids, e.g., intercalators, minor groove binding moieties, bases modified with a stabilizing moiety (e.g., alkynyl moieties, and fluoroalkyl moieties), and conformational stabilizing moieties, such as those described in commonly owned U.S. Patent Application Publication No. 2007/0059752.Type: ApplicationFiled: March 17, 2014Publication date: July 10, 2014Applicant: Biosearch Technologies, Inc.Inventors: Ronald M. Cook, Matt Lyttle
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Publication number: 20140196160Abstract: Methods and means are provided for monitoring and modulating reduction of gene expression in eukaryotic organisms, using double stranded RNA comprising, in addition to the dsRNA region comprising nucleotide sequences homologous to the target gene, additional dsRNA regions designed to down regulate a second gene or which are unrelated to the target gene.Type: ApplicationFiled: December 9, 2013Publication date: July 10, 2014Applicant: Commonwealth Scientific & Industrial Research OrganisationInventors: Peter Waterhouse, Susan Wesley, Chris Helliwell
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Patent number: 8771940Abstract: The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.Type: GrantFiled: May 28, 2009Date of Patent: July 8, 2014Assignee: The Regents of the University of CaliforniaInventors: Gary L. Andersen, Todd D. DeSantis
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Patent number: 8772467Abstract: An assay system and methods are described where patient samples containing genomic DNA are analyzed for the presence of known genetic polymorphisms using a universal reporter strategy. In a preferred embodiment, the amplified DNA is localized at test sites in an array of sites on a microchip followed by a series of hybridization reactions that screen for the presence of a single mutation from among a number of mutations, and allow the identification of specific mutations. In addition to universal reporters, the assay may use blockers and discriminators for screening and identification of known polymorphisms.Type: GrantFiled: October 7, 2009Date of Patent: July 8, 2014Assignee: Gamida for Life B.V.Inventors: Ray R. Radtkey, Lance C. Held, Robert B. Wallace, Karen Menge, David Canter
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Patent number: 8771939Abstract: The present invention relates to a method for methylation analysis. It comprises the providing of a double stranded nucleic acid; its conversion, whereby unmethylated bases become distinguishable in their base-pairing behavior from methylated bases, and the analysis of both of the converted nucleic acid strands.Type: GrantFiled: August 1, 2007Date of Patent: July 8, 2014Assignee: Epigenomics AGInventors: Reimo Tetzner, Joern Lewin
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Patent number: 8771938Abstract: Disclosed are example methods and devices for detecting one or more targets. An example method includes placing a sample including a first target with in a microfluidic device and hybridizing a plurality of copies of the first target with a plurality of nanostructures. The example method includes applying an electric current to the plurality of nanostructures and using an electric field created by the electric current to move the plurality of nanostructures. In addition, the plurality of nanostructures are sorted and evaluated to determine at least one of a presence, an absence, or a quantity of the first target.Type: GrantFiled: October 7, 2008Date of Patent: July 8, 2014Assignee: University of Notre Dame du LacInventors: Hsueh-Chia Chang, Jason Gordon, Satyajyoti Senpati, Zachary Gagnon, Sagnik Basuray
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Patent number: 8771943Abstract: A method and assay for predicting athletic performance potential of a subject, such as a thoroughbred race horse, comprising the steps of assaying a biological sample from a subject for the presence of a single nucleotide polymorphism in one or more genes associated with athletic performance. The athletic performance genes may be selected from one or more of MSTN, COX4I2, PDK4, CKM and COX4I1.Type: GrantFiled: September 11, 2009Date of Patent: July 8, 2014Assignee: University College Dublin—National University of Ireland, DublinInventors: Emmeline Hill, David MacHugh, Nick Orr, JingJing Gu, Lisa Katz
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Publication number: 20140187434Abstract: Nucleic acid labeling compounds are disclosed. The compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.Type: ApplicationFiled: June 27, 2013Publication date: July 3, 2014Applicant: Affymetrix, Inc.Inventors: Glenn Hugh McGall, Anthony Dale Barone
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Publication number: 20140187724Abstract: Provided are a solid-phase carrier for solid-phase synthesis of nucleic acid having improved amino group reactivity, and an aminated oligonucleotide to which an amino group has been attached. The present invention relates to an aminated oligonucleotide represented by formula (I).Type: ApplicationFiled: July 31, 2012Publication date: July 3, 2014Applicant: National Institute of Advanced Industrial Science and TechnologyInventors: Yasuo Komatsu, Naoshi Kojima
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Publication number: 20140187763Abstract: The present invention provides a family of dark quenchers, termed Black Hole Quenchers (“BHQs”), that are efficient quenchers of excited state energy but which are themselves substantially non-fluorescent. Also provided are methods of using the BHQs, probes incorporating the BHQs and methods of using the probes.Type: ApplicationFiled: October 29, 2013Publication date: July 3, 2014Inventors: Ronald M. COOK, Matt LYTTLE, Daren DICK
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Publication number: 20140189902Abstract: Molecular markers useful for identifying, selecting, and/or providing soybean plants displaying tolerance, improved tolerance, or susceptibility to iron deficiency, methods of their use, and compositions having one or more marker loci are provided. Methods comprise detecting at least one marker locus, detecting a haplotype, and/or detecting a marker profile. Methods may further comprise crossing a selected soybean plant with a second soybean plant. Isolated polynucleotides, primers, probes, kits, systems, as well as soybean plants, seeds, and parts thereof are also provided.Type: ApplicationFiled: March 13, 2013Publication date: July 3, 2014Applicant: PIONEER HI BRED INTERNATIONAL INC.Inventors: Julian M. Chaky, Martin A. Fabrizius, David L. Hyten, JR., Nadejda N. Krasheninnik, Jordan Spear, John B. Woodward, Yanwen Xiong
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Publication number: 20140189905Abstract: The present invention relates to a method for determining the genotype of a Cruciferous vegetable plant for a plant with an increased glucosinolate level, comprising obtaining a sample of nucleic acids from said plant or a portion thereof and detecting in said nucleic acids a polymorphism at the Myb28 locus that is genetically linked to an increased glucosinolate level.Type: ApplicationFiled: September 12, 2013Publication date: July 3, 2014Applicants: PLANT BIOSCIENCE LIMITED, SEMINIS VEGETABLE SEEDS, INC.Inventors: RICHARD F. MITHEN, Maria Traka, Bart W. Brugmans
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Patent number: 8765928Abstract: Provided herein are isolated genomic polynucleotide fragments from the from the p15 region of chromosome 11 encoding human and tumor suppressing subtransferable candidate 4 (TSSC4) and methods of use.Type: GrantFiled: March 18, 2013Date of Patent: July 1, 2014Assignee: Ryogen LLCInventor: James Ryan
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Patent number: 8765927Abstract: Provided herein are isolated genomic polynucleotide fragments from the p15 arm of chromosome 11 and methods of use.Type: GrantFiled: March 18, 2013Date of Patent: July 1, 2014Inventor: James Ryan
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Patent number: 8765369Abstract: The invention relates to methods and reagents for detecting minute amounts of targets having affinity for nucleic acid. The present invention more particularly relates to target detection using aggregates of cationic polymer chains and nucleic acid capture probes linked to particles, such as controllable mobility particles.Type: GrantFiled: July 11, 2008Date of Patent: July 1, 2014Assignee: National Research Council of CanadaInventors: Sebastien Dubus, Hoang-Anh Ho, Mario Leclerc, Denis Boudreau
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Patent number: 8765372Abstract: The invention relates to diagnostic methods to predict whether a subject is predisposed for acquiring a disease or to predict the therapy responsiveness of an individual patient. Provided is a method for determining whether a subject is predisposed for developing an autoimmune disease, comprising determining in a sample isolated from said subject the amount of intact genes, or gene products thereof, of the Fc?RII/Fc?RIII gene cluster, said gene cluster comprising the FCGR2C, FCGR3A, FCGR2A and FCGR3B genes encoding an activating Fc?R, and FCGR2B encoding an inhibitory Fc?R; and correlating said amount to the amount observed in a healthy population. Also provided is a method to predict the responsiveness of a subject to therapy with intravenous immunoglobulin (IVIg) therapy or a monospecific biological, such as a humanized or human monoclonal antibody or a chimeric molecule, comprising the C-terminal Fc-tail of IgG.Type: GrantFiled: February 2, 2011Date of Patent: July 1, 2014Assignee: Stichting Sanquin BloedvoorzieningInventors: Dirk Roos, Taco Willem Kuijpers
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Patent number: 8765374Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.Type: GrantFiled: December 20, 2012Date of Patent: July 1, 2014Assignee: The Penn State Research FoundationInventors: Stephen J Benkovic, Frank Salinas
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Patent number: 8765417Abstract: Primers for DNA elongation are immobilized onto a substrate having on the surface thereof a polymer substance which contains a first unit having a group derived from a phosphoester composing the hydrophilic section of a phospholipid, and a second unit having an activated ester group, and DNA elongation reaction is allowed to proceed in a reaction system having introduced therein a sample which contains DNA fragments having desired sequences and nucleotide monomers, by heating the reaction system up to a temperature causing thermal unfolding of the DNA chains, and then by cooling the reaction system down to a temperature for annealing.Type: GrantFiled: November 29, 2005Date of Patent: July 1, 2014Assignees: Sumitomo Bakelite Co., Ltd., DNA Chip Research Inc.Inventor: Kenji Kinoshita
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Publication number: 20140178866Abstract: Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode.Type: ApplicationFiled: March 1, 2013Publication date: June 26, 2014Applicant: PIONEER HI-BRED INTERNATIONAL, INC.Inventors: JOSHUA M. SHENDELMAN, JOHN B. WOODWARD, MEIZHU YANG
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Publication number: 20140178878Abstract: The present application discloses a labeled nucleotide comprising a label attached via a linker, wherein said labeled nucleotide has the formula wherein R1 is a residue with a negative net charge, preferably selected from the group consisting of a phosphate group, and a sulphate group; wherein R2, R3 and R4 are independently selected from the group consisting of H2, OH2, and O; wherein “n” is an integer between 0 and 16; wherein “a” is an integer between 1 and 10; wherein SP is absent or a spacer; wherein X is said label; and wherein Y is a nucleotide or nucleoside. Furthermore, oligonucleotides comprising a labeled nucleotide according to the present invention and the use as a primer in amplification based methods is disclosed herein.Type: ApplicationFiled: May 4, 2012Publication date: June 26, 2014Inventors: Daniel Müller, Francesca Di Pasquale
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Publication number: 20140182009Abstract: Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.Type: ApplicationFiled: March 6, 2013Publication date: June 26, 2014Applicant: PIONEER HI-BRED INTERNATIONAL, INC.Inventors: Jonathan B. Allen, Bryce Daines, David Hyten, Jr., Donald Kyle, Clinton W. Mapel, Joshua M. Shendelman, Jeffrey A. Thompson, John B. Woodward, Yanwen Xiong, Meizhu Yang
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Publication number: 20140178867Abstract: Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with tolerance or improved tolerance to Phytophthora infection. In certain embodiments, the method comprises detecting at least one marker locus that is associated with tolerance to Phytophthora infection. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with tolerance to Phytophthora infection. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with tolerance or improved tolerance to Phytophthora infection.Type: ApplicationFiled: March 1, 2013Publication date: June 26, 2014Applicant: Pioneer Hi-Bred International, Inc.Inventors: Julian M. Chaky, Holly J. Jessen, Joshua M. Shendelman, Paul A. Stephens, David M. Webb, John B. Woodward, Meizhu Yang
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Patent number: 8759000Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.Type: GrantFiled: December 20, 2012Date of Patent: June 24, 2014Assignee: The Penn State Research FoundationInventors: Stephen J Benkovic, Frank Salinas
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Patent number: 8758995Abstract: This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.Type: GrantFiled: August 6, 2010Date of Patent: June 24, 2014Assignee: Sequenom, Inc.Inventors: Charles R. Cantor, Hubert Koster
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Patent number: 8758999Abstract: The present invention relates to primers for the universal amplification and detection of Archaea, which primers are designed based on a multiple sequence alignment of Archaea Type II chaperonin (thermo-some) genes. For detection of Archaea having templates with a GC content of below 60%, primers are designed so that inosine residues are found at degenerate positions. For amplification of higher GC content templates, degenerate positions are replaced with specific nucleotide bases found in the high GC organism. The primers are useful for detecting, identifying and quantifying Archaea in a sample and for determining a phylogenetic relationship of a test Archaea organism.Type: GrantFiled: March 8, 2011Date of Patent: June 24, 2014Assignee: University of SaskatchewanInventors: Janet Elizabeth Hill, Bonnie Laura Chaban
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Patent number: 8758997Abstract: A probe for detecting a polymorphism at position ?1639 of the VKORC1 gene, the probe comprising an oligonucleotide having a nucleotide sequence having a length of 10 to 50 nucleotides, which nucleotide sequence comprises the nucleotides 80 to 89 of SEQ ID NO:1 or 2 and has a homology to SEQ ID NO:1 or 2 except that the nucleotide corresponding to the nucleotide at position 80 in SEQ ID NO:1 or 2 is cytosine, which nucleotide corresponding to the nucleotide at position 80 is labeled with a fluorescent dye.Type: GrantFiled: June 1, 2011Date of Patent: June 24, 2014Assignee: Arkray, Inc.Inventor: Mariko Komori
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Publication number: 20140170654Abstract: The present invention relates to a proximity-probe based detection assay for detecting an analyte in a sample and in particular to a method that comprises the use of at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte directly or indirectly, wherein the nucleic acid domain of at least one of said proximity probes comprises a hairpin structure that can be unfolded by cleavage of the nucleic acid domain to generate at least one ligatable free end or region of complementarity to another nucleic acid molecule in said sample, wherein when the probes bind to said analyte unfolding said hairpin structure allows the nucleic acid domains of said at least first and second proximity probes to interact directly or indirectly.Type: ApplicationFiled: May 11, 2012Publication date: June 19, 2014Applicant: Olink ABInventors: Ulf Landegren, Rachel Yuan Nong, Ola Söderberg, Irene Weibrecht
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Patent number: 8753811Abstract: The present invention provides methods of making a population of nucleic acid molecules, wherein each nucleic acid molecule comprises a predetermined nucleic acid sequence, each of said methods comprising the steps of: (a) synthesizing, on a substrate, a population of nucleic acid molecules wherein: i) each synthesized nucleic acid molecule comprises a predetermined nucleic acid sequence; and ii) each synthesized nucleic acid molecule is localized to a defined area of said substrate; (b) harvesting said population of synthesized nucleic acid molecules from said substrate to yield harvested nucleic acid molecules; and (c) introducing said harvested nucleic acid molecules into vector molecules.Type: GrantFiled: February 16, 2012Date of Patent: June 17, 2014Assignee: Cold Spring Harbor LaboratoryInventors: Stephen H. Friend, Michele A. Cleary, Ernest M. Coffey, Kristopher A. Killian, Gregory J. Hannon, Patrick Paddison
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Patent number: 8754055Abstract: Methods, pharmaceutical compositions, and kits are provided which includes accurately sampling a RNA from a tissue of an animal and analyzing RNA in the tissue of the animal as an indicator of physiological state, infectious disease, neoplastic disease, autoimmune disease, inflammatory disease, cardiovascular disease, atherosclerotic disease, or neurological disease in the animal. A method is provided which includes administering at least one compound to an animal wherein the at least one compound is configured to prevent the cleavage of at least one tissue RNA by a ribonuclease. The method further includes collecting a sample of at least a portion of tissue from the animal.Type: GrantFiled: September 5, 2008Date of Patent: June 17, 2014Assignee: The Invention Science Fund I, LLCInventors: Paul G. Allen, Edward S. Boyden, Roderick A. Hyde, Muriel Y. Ishikawa, Stephen L. Malaska, Dennis J. Rivet, Leif T. Stordal, Lowell L. Wood, Jr.
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Transferases and Oxidoreductases, Nucleic Acids Encoding Them and Methods for Making and Using Them.
Publication number: 20140165221Abstract: This invention relates generally to enzymes, polynucleotides encoding the enzymes, the use of such polynucleotides and polypeptides and more specifically to enzymes having transferase activity, e.g., transaminase activity, e.g., d-amino-acid transferase activity, and/or oxidoreductase activity, e.g., dehydrogenase activity, e.g., d-amino-acid dehydrogenase activity, and/or catalyze the transfer of a chemical group, catalyze transamination, catalyze the reaction: D-alanine+2-oxoglutarate<=>pyruvate+D-glutamate, and/or catalyze an oxidation-reduction reaction, catalyze the removal of hydrogen atoms, and/or catalyze the reaction: D-amino acid+H2O+acceptor<=>a 2-oxo acid+NH3+reduced acceptor.Type: ApplicationFiled: February 18, 2014Publication date: June 12, 2014Applicant: VERENIUM CORPORATIONInventors: DAVID P. WEINER, PETER LUGINBUHL, ANALIA BUENO, JOSLIN M. CUENCA, ERIN MARASCO -
Publication number: 20140162250Abstract: Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with tolerance to chloride salt stress. In certain embodiments, the method comprises detecting at least one marker locus that is associated with tolerance to chloride salt stress. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with chloride salt stress tolerance. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with tolerance to chloride salt stress.Type: ApplicationFiled: March 1, 2013Publication date: June 12, 2014Applicant: Pioneer Hi-Bred International, Inc.Inventors: Mark J. Hood, David L. Hyten, Andrea B. Kalvig, Jason C. Raines, Joshua M. Shendelman, John B. Woodward, Yanwen Xiong
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Patent number: 8748096Abstract: The present invention provides an isolated nucleic acid molecule containing a repeat region of an isolated spinocerebellar ataxia type 8 (SCA8) coding sequence, the coding sequence located within the long arm of chromosome 13, and the complement of the nucleic acid molecule. Diagnostic methods based on identification of this repeat region are also provided.Type: GrantFiled: August 20, 2012Date of Patent: June 10, 2014Assignee: Regents of the University of MinnesotaInventors: Laura P. W. Ranum, Michael D. Koob, Kellie A. Benzow, Melinda L. Moseley-Alldredge
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Patent number: 8748100Abstract: Disclosed herein are methods and kits for selectively amplifying, detecting or quantifying a DNA fragment with a specific end sequence, especially generated following restriction enzyme digestion. This method can be used, for example, to detect a hypomethylated DNA fragment. This methods and kits are especially useful in detecting or quantifying a hypomethylated fetal DNA fragment in a maternal plasma sample containing a corresponding hypermethylated maternal DNA fragment.Type: GrantFiled: August 30, 2007Date of Patent: June 10, 2014Assignee: The Chinese University of Hong KongInventors: Yuk Ming Dennis Lo, Yu Kwan Tong, Wai Kwun Rossa Chiu, Chunming Ding
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Patent number: 8748090Abstract: The present invention relates to methods for screening for binding interactions using multiple sets of microparticles, wherein said set has the same identifiable characteristic and wherein one of more sets comprise subsets of microparticles and said subset presents at least one unique probe that acts as a binding partner for a target molecule in a biological sample. In particular, the invention provides for methods of detecting tissue-typing antigens in donor tissue or recipient tissue using these multiple sets of microparticles.Type: GrantFiled: May 2, 2008Date of Patent: June 10, 2014Assignee: One Lambda, Inc.Inventors: Jar-How Lee, Terrence Chen, Thoa Nong
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Patent number: 8748093Abstract: A method of detecting a fungus belonging to genus Geosmithia, including identifying a fungus belonging to genus Geosmithia using a nucleic acid represented by the nucleotide sequence defined in the following (a) or (b): (a) a partial nucleotide sequence of ?-tubulin gene shown in any one of SEQ ID NOS: 1 to 3, or a complementary sequence thereof; (b) a nucleotide sequence including deletion, substitution, insertion or addition of one or several nucleotide(s) in the nucleotide sequence shown in any one of SEQ ID NOS: 1 to 3, or a complementary sequence thereof.Type: GrantFiled: November 11, 2009Date of Patent: June 10, 2014Assignee: Kao CorporationInventors: Kouichi Hosoya, Motokazu Nakayama, Hajime Tokuda, Takashi Yaguchi, Yusuke Hiro