Transferring Phosphorus Containing Group (e.g., Kineases, Etc.(2.7)) Patents (Class 435/194)
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Publication number: 20130202536Abstract: The invention relates to novel luminescent compositions of matter containing a fluorophore, synthetic methods for making the compositions, macromolecular conjugates of the compositions, and the use of the compositions in various methods of detection. The invention also provides kits containing the compositions and their conjugates for use in the methods of detection.Type: ApplicationFiled: January 13, 2011Publication date: August 8, 2013Applicants: NEW JERSEY INSTITUTE OF TECHNOLOGY, UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEYInventors: Arkady Mustaev, Maxim Kozlov, Salvatore Marras, Lev Krasnoperov, Laura Wirpsza, Shyamala Pillai
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Publication number: 20130203088Abstract: The present invention relates generally to methods for diagnosing the presence or the risk of development or the therapy control of spondyloarthritis (Spa), in particular, of ankylosing spondylitis (AS) and undifferentiated spondyloarthritis in a subject, in particular in mammals. In addition, the present invention relates to test kits for use in the diagnosis of the presence or the risk of development, or for the therapy control of Spa, like AS and undifferentiated spondyloarthritis, in a subject. In particular, the present invention relates to a method for diagnosing the presence or the risk of development, or for the therapy control of Spa, like AS and undifferentiated spondyloarthritis, in a subject analysing for the presence of autoantibodies against CD74 and/or IKBKB in a subject. The presence of autoantibodies against CD74 and/or IKBKB is indicative for the presence or the risk of development, or for the therapy control of Spa, like AS and undifferentiated spondyloarthritis.Type: ApplicationFiled: August 16, 2011Publication date: August 8, 2013Inventors: Niklas Thomas Baerlecken, Torsten Witte
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Publication number: 20130203115Abstract: The present disclosure provides modified nucleosides, nucleotides, and nucleic acids, and methods of using thereof.Type: ApplicationFiled: January 11, 2013Publication date: August 8, 2013Applicant: MODERNA THERAPEUTICS, INC.Inventor: MODERNA THERAPEUTICS, INC.
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Publication number: 20130196327Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.Type: ApplicationFiled: May 10, 2012Publication date: August 1, 2013Applicant: NEW ENGLAND BIOLABS, INC.Inventor: Andrew Gardner
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Publication number: 20130196409Abstract: Processes and C/D box small nucleolar RNAs (snoRNAs) for altering telomerase activity and altering telomerase length are described. The processes of the invention involve the use of C/D box snoRNAs for targeted 2?-O-methylation modification of nucleotides in a pseudoknot region of the telomerase RNA. Depending on their position, the 2?-O-methylation modifications can cause an increase in telomerase activity and subsequent telomere lengthening or a decrease in telomerase activity and subsequent telomere shortening.Type: ApplicationFiled: July 15, 2011Publication date: August 1, 2013Applicant: UNIVERSITY OF ROCHESTERInventors: Yi-Tao Yu, Chao Huang
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Publication number: 20130195843Abstract: The disclosure provides a method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) such as testing a sample from a subject for a mutation in one or more biomarkers. Also described are methods for classifying or monitoring a subject having, or suspected of having, B-cell non-Hodgkin lymphoma comprising testing the sample for a mutation in one or more biomarkers.Type: ApplicationFiled: March 15, 2013Publication date: August 1, 2013Applicant: British Columbia Cancer Agency BranchInventor: British Columbia Cancer Agency Branch
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Publication number: 20130195835Abstract: Described herein are methods and genetically engineered cells useful for producing an altered N-glycosylation form of a target molecule. Also described are methods and molecules with altered N-glycosylation useful for treating a variety of disorders such as metabolic disorders.Type: ApplicationFiled: September 14, 2012Publication date: August 1, 2013Applicants: OXYRANE UK LIMITED, UNIVERSITEIT GENT, VIB VZWInventors: Nico Luc Marc Callewaert, Wouter Vervecken, Karen Jacqueline Marcel De Pourcq, Steven Christian Jozef Geysens, Mouna Guerfal
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Publication number: 20130196382Abstract: Disclosed are DNA polymerases having increased reverse transcriptase efficiency relative to a corresponding, unmodified polymerase. The polymerases are useful in a variety of disclosed primer extension methods. Also disclosed are related compositions, including recombinant nucleic acids, vectors, and host cells, which are useful, e.g., for production of the DNA polymerases.Type: ApplicationFiled: July 26, 2012Publication date: August 1, 2013Applicant: Roche Molecular Systems, Inc.Inventors: Keith Bauer, Thomas W. Myers, Fred Reichert, Shawn Suko
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Publication number: 20130189758Abstract: The present invention relates to a gene that encodes a hyperactive reverse transcriptase having DNA polymerase activity and substantially reduced RNase H activity, vectors containing the gene and host cells transformed with the invention. The present invention also includes a method of producing the hyperactive reverse transcriptase, producing cDNA from mRNA using the reverse transcriptase of the invention, kits and assay templates made using the hyperactive reverse transcriptase.Type: ApplicationFiled: December 28, 2012Publication date: July 25, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventor: Life Technologies Corporation
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Publication number: 20130189733Abstract: The present invention relates to a method to improve the secretion of a protein of interest by a filamentous fungal cell comprising inducing a phenotype in the cell selected from the group consisting of a lowered ERAD, an elevated UPR that does not induce an elevated ERAD, wherein ERAD preferably is lowered. The invention further relates to the filamentous fungal cell comprising the phenotype described above. The invention also relates to polynucleotides and polypeptides whose expression can be modulated in the filamentous fungal cell to obtain the above-described phenotype.Type: ApplicationFiled: January 25, 2013Publication date: July 25, 2013Applicant: DSM IP ASSETS B.V.Inventors: CORNELIS MARIA JACOBUS SAGT, CORNELIS THEODORUS VERRIPS, WALRAVEN HENRY MULLER, NOEL NICOLAAS MARIA ELISABETH VAN PEIJ
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Publication number: 20130183718Abstract: The present invention relates to a method of RNA synthesis by RNA-dependent RNA polymerases (RdRp) displaying an RNA polymerase activity on single-stranded DNA templates and to a kit for carrying out the method. The RdRp showing DNA-dependent RNA polymerase activity has a “right hand conformation” and the amino acid sequence of said RdRp comprises a conserved arrangement of the following sequence motifs: a. XXDYS, b. GXPSG, c. YGDD, d. XXYGL, e. XXXXFLXRXX (with the following meanings: D: aspartate, Y: tyrosine, S: serine, G: glycine, P: proline, L: leucine, F: phenylalanine, R: arginine, X: any amino acid). This class of RdRp is exemplified by the RdRp enzymes of viruses of the Caliciviridae family. The present invention also relates to a method for transferring at least one ribonucleotide (rC, rA, rU or rG) to the 3?-end of a single-stranded DNA by using the RdRp of the invention.Type: ApplicationFiled: September 20, 2011Publication date: July 18, 2013Applicant: RibpxX GmbHInventor: Jacques Rohayem
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Publication number: 20130183677Abstract: A method for predicting differentiation-inducing properties of naive T-cells to regulatory T-cells comprising: measuring an amount of ZAK in naive T-cells contained in the body fluid collected from the living body; and predicting differentiation-inducing properties of the naive T-cells to regulatory T-cells based on the measurement results is disclosed. A method for determining the risk of development of Graft versus Host Disease and a biomarker for predicting differentiation-inducing properties of naive T-cells to regulatory T-cells are also disclosed.Type: ApplicationFiled: January 16, 2013Publication date: July 18, 2013Applicant: SYSMEX CORPORATIONInventor: SYSMEX CORPORATION
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Patent number: 8486645Abstract: Novel gene deletions and translocations involving chromosome 2 resulting in fusion proteins combining part of Anaplastic Lymphoma Kinase (ALK) kinase with part of a secondary protein have now been identified in human solid tumors, e.g. non-small cell lung carcinoma (NSCLC). Secondary proteins include Echinoderm Microtubule-Associated Protein-Like 4 (EML-4) and TRK-Fusion Gene (TFG). The EML4-ALK fusion protein, which retains ALK tyrosine kinase activity, was confirmed to drive the proliferation and survival of NSCLC characterized by this mutation. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant polypeptides, probes for detecting it, isolated mutant polypeptides, and reagents for detecting the fusion and truncated polypeptides.Type: GrantFiled: April 3, 2012Date of Patent: July 16, 2013Assignee: Cell Signaling Technology, Inc.Inventors: Klarisa Rikova, Herbert Haack, Laura Sullivan, Ailan Guo, Anthony Possemato, Joan MacNeill, Ting-Lei Gu, Jian Yu
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Patent number: 8487078Abstract: Compositions, methods, and kits for detecting and monitoring kinase, phosphatase and protein post-translational modification activity are described. The compositions typically include a peptide, a detectable moiety, and a protease cleavage site. Modification of a peptide by a kinase, phosphatase or other protein post-translational modification alters the proteolytic sensitivity of the peptide, resulting in a change of a detectable property of the composition. Panel assays for determining substrates or modulators of kinase, phosphatase or other protein post-translational modification activity are also described.Type: GrantFiled: October 4, 2011Date of Patent: July 16, 2013Assignee: Life Technologies CorporationInventors: Tony Klink, Jane Beebe, David Lasky, Karen Kleman-Leyer, Richard Somberg
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Patent number: 8486671Abstract: The present invention relates to a process for producing polyunsaturated fatty acids in an organism by introducing nucleic acids into the organism which code for polypeptides having acyl-CoA:lysophospholipid a cyltransferase activity. Advantageously, these nucleic acid sequences may, if appropriate together with further nucleic acid sequences coding for biosynthesis polypeptides of the fatty acid or lipid metabolism, be expressed in the transgenic organism. The invention furthermore relates to the nucleic acid sequences, to nucleic acid constructs comprising the nucleic acid sequences of the invention, to vectors comprising the nucleic acid sequences and/or the nucleic acid constructs and to transgenic organisms comprising the abovementioned nucleic acid sequences, nucleic acid constructs and/or vectors. A further part of the invention relates to oils, lipids and/or fatty acids produced by the process of the invention and to their use.Type: GrantFiled: April 2, 2009Date of Patent: July 16, 2013Assignee: BASF Plant Science GmbHInventors: Andreas Renz, Ernst Heinz, Amine Abbadi, Frederic Domergue, Thorsten Zank
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Publication number: 20130177919Abstract: The invention concerns the field of protein production and cell culture technology. CERT is identified as a novel in vivo PKD substrate. Phosphorylation on serine 132 by PKD decreases the affinity of CERT towards its lipid target phosphatidylinositol 4-phosphate at Golgi membranes and reduces ceramide transfer activity, identifying PKD as a regulator of lipid homeostasis. The present invention shows that CERT in turn is critical for PKD activation and PKD dependent protein cargo transport to the plasma membrane. The interdependence of PKD and CERT is thus a key to the maintenance of Golgi membrane integrity and secretory transport.Type: ApplicationFiled: February 29, 2008Publication date: July 11, 2013Applicant: BOEHRINGER INGELHEIM PHARMA GMBH & CO. KGInventors: Hitto Kaufmann, Lore Florin, Eric Becker, Monilola Olayioye, Angelika Hausser, Tim Fugmann
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Patent number: 8481279Abstract: In accordance with the invention, novel gene deletions and translocations involving chromosome 2 resulting in fusion proteins combining part of Anaplastic Lymphoma Kinase (ALK) kinase with part of a secondary protein have now been identified in human solid tumors, e.g. non-small cell lung carcinoma (NSCLC). Secondary proteins include Echinoderm Microtubule-Associated Protein-Like 4 (EML-4) and TRK-Fusion Gene (TFG). The EML4-ALK fusion protein, which retains ALK tyrosine kinase activity, was confirmed to drive the proliferation and survival of NSCLC characterized by this mutation. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ALK kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides.Type: GrantFiled: February 6, 2012Date of Patent: July 9, 2013Assignee: Cell Signaling Technology, Inc.Inventors: Klarisa Rikova, Herbert Haack, Laura Sullivan, Ailan Guo, Anthony Possemato, Joan MacNeill, Ting-Lei Gu, Jian Yu
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Patent number: 8481685Abstract: The present invention provides, among other things, modified DNA polymerases containing amino acid alterations based on mutations identified in directed evolution experiments designed to select enzymes that are better suited for applications in recombinant DNA technologies.Type: GrantFiled: November 3, 2009Date of Patent: July 9, 2013Assignee: Kapa BiosystemsInventors: William Bourn, Bjarne Faurholm, John Foskett
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Publication number: 20130171328Abstract: Recombinant microorganisms, plants, and plant cells are disclosed that have been engineered to express novel recombinant genes encoding steviol biosynthetic enzymes and UDP-glycosyltransferases (UGTs). Such microorganisms, plants, or plant cells can produce steviol or steviol glycosides, e.g., rubusoside or Rebaudioside A, which can be used as natural sweeteners in food products and dietary supplements.Type: ApplicationFiled: June 2, 2011Publication date: July 4, 2013Inventors: Ganesh M. Kishore, Michael Motion, Paula M. Hicks, Jorgen Hansen, Jens Houghton-Larsen, Esben Halkjær Hansen, Michael Dalgaard Mikkelsen, Sabina Tavares, Charlotte Blom
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Publication number: 20130171140Abstract: The present disclosure relates to recombinant fusion proteins, such as human antibody-based molecules called Vaccibodies, which are able to trigger both a T cell- and B cell immune response. The present disclosure also relates to a method of treating a cancer or an infectious disease by means of these specific fusion proteins.Type: ApplicationFiled: June 24, 2011Publication date: July 4, 2013Applicant: VACCIBODY ASInventors: Pier Adelchi Ruffini, Bjarne Bogen, Agnete Brunsvik Fredriksen
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Publication number: 20130172204Abstract: The invention concerns a first diagnostic method for glaucoma based on an analysis of autoimmune reactivity in body fluids against at least one sample of at least partially purified ocular antigens, wherein the autoimmune reactivity against individual antigens is measured and transformed into a glaucoma score to determine the diagnostic result. Further aspects of the invention include antigen carrying elements carrying at least one sample of the at least partially purified ocular antigens and kits for diagnosis of glaucoma. Further aspects include methods of collecting a body fluid such as tears for the use in the diagnostic method for glaucoma. Yet further aspects include ocular antigens serving as diagnostic markers and/or for preparing pharmaceutical compositions for treatment of glaucoma.Type: ApplicationFiled: April 13, 2011Publication date: July 4, 2013Applicant: M-LAB AGInventors: Franz Grus, Nils Boehm, Norbert Pfeiffer, Katharina Bell
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Patent number: 8476045Abstract: This invention provides for methods of sequencing and performing polymerase reactions using an improved generation of nucleic acid polymerases. The improvement is the fusion of a sequence-non-specific nucleic-acid-binding domain to the enzyme in a manner that enhances the processivity of the polymerase.Type: GrantFiled: July 27, 2012Date of Patent: July 2, 2013Assignee: Bio-Rad Laboratories, Inc.Inventors: Yan Wang, Peter Vander Horn, Lei Xi
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Publication number: 20130164271Abstract: The present invention relates to a method for preparing an expression vector encoding a tailored recombinase, which tailored recombinase is capable of recombining asymmetric target sequences within the long terminal repeat (LTR) of proviral DNA of a plurality of retrovirus strains inserted into the genome of a host cell, as well as to the obtained expression vector, cells transfected with this, expressed recombinase and pharmaceutical compositions comprising the expression vector, cells and/or recombinase. Pharmaceutical compositions are useful, e.g., in treatment and/or prevention of retrovirus infection. In particular, asymmetric target sequences present in a plurality of HIV strains are disclosed, as well as tailored recombinases capable of combining these sequences (Tre 3.0 and 4.0) and expression vectors encoding them.Type: ApplicationFiled: May 27, 2011Publication date: June 27, 2013Applicants: MAX-PLANCK-GESELLSCHAFT ZUR FOEDERUG DER WISSENSCH E.V., HENRICH-PETTE-INSTITUT LEIBNZ-INSTITUT FOR EXPERIM VIROLOGIE-STIFTUNG BInventors: Joachim Hauber, Jan Chemnitz, Frank Buchholz, Janet Chusainow
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Publication number: 20130164782Abstract: A method for the secretory production of a glycoprotein having a human-type sugar chain, comprising a step of introducing a gene of an enzyme capable of performing a transfer reaction of a galactose residue to a non-reducing terminal acetylglucosamine residue, and a gene of heterologous glycoprotein, to obtain a transformed plant cell, a step of culturing the plant cell, and a step of recovering the culture medium of the plant cell.Type: ApplicationFiled: September 14, 2012Publication date: June 27, 2013Applicant: Phyton Holdings, LLCInventors: Kazuhito FUJIYAMA, Tatsuji Seki
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Publication number: 20130164788Abstract: The present invention is directed to compositions and methods useful for the amplification of nucleic acid molecules by reverse transcriptase-polymerase chain reaction (RT-PCR). Specifically, the invention provides compositions and methods for the amplification of nucleic acid molecules in a simplified one- or two-step RT-PCR procedure using combinations of reverse transcriptase and thermostable DNA polymerase enzymes in conjunction with sulfur-containing molecules or acetate-containing molecules (or combinations of such sulfur-containing molecules and acetate-containing molecules), and optionally bovine serum albumin. The invention thus facilitates the rapid and efficient amplification of nucleic acid molecules and the detection and quantitation of RNA molecules. The invention also is useful in the rapid production and amplification of cDNAs which may be used for a variety of industrial, medical and forensic purposes.Type: ApplicationFiled: February 11, 2013Publication date: June 27, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventor: LIFE TECHNOLOGIES CORPORATION
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Patent number: 8470563Abstract: A method of obtaining DNA amplification of a nucleic acid target from a volume of whole blood comprising performing DNA amplification in a PCR assay mixture with a blood-resistant polymerase.Type: GrantFiled: December 8, 2008Date of Patent: June 25, 2013Assignee: DNA Polymerase Technology Inc.Inventors: Milko B. Kermekchiev, Wayne Morris Barnes
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Patent number: 8470573Abstract: The present invention provides DNA polymerases having increased efficiency of amplification of long amplicons. The present invention also provides for methods of amplifying target nucleic acid molecules with the DNA polymerases for increasing the efficiency of amplification of long amplicons.Type: GrantFiled: June 21, 2011Date of Patent: June 25, 2013Assignee: Bio-Rad Laboratories, Inc.Inventors: Yan Wang, John Sullivan
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Patent number: 8470566Abstract: A non-naturally occurring microbial organism having an isopropanol, 4-hydroxybutryate, or 1,4-butanediol pathway includes at least one exogenous nucleic acid encoding an isopropanol, 4-hydroxybutryate, or 1,4-butanediol pathway enzyme expressed in a sufficient amount to produce isopropanol, 4-hydroxybutryate, or 1,4-butanediol. The aforementioned organisms are cultured to produce isopropanol, 4-hydroxybutryate, or 1,4-butanediol.Type: GrantFiled: February 10, 2012Date of Patent: June 25, 2013Assignee: Genomatica, Inc.Inventors: John D. Trawick, Mark J. Burk, Anthony P. Burgard
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Publication number: 20130157258Abstract: The invention provides polypeptides comprising an amino acid sequence comprising at least one variation from wild-type HCV NS5B polymerase, the at least one variation selected from the group consisting of cysteine, isoleucine, valine, or proline at amino acid position 419; alanine, valine, or asparagine at amino acid position 482; valine, isoleucine, threonine, or serine at amino acid position 486; and isoleucine at amino acid position 494, as the amino acid positions are defined in SEQ ID NO: 1, and having Hepatitis C Virus (HCV) NS5B polymerase activity. Polynucleotides encoding the polypeptide, antibodies, host cells, compositions, and methods for detecting an HCV NS5B polymerase having resistance to a polymerase inhibitor also are provided.Type: ApplicationFiled: June 15, 2011Publication date: June 20, 2013Applicant: VERTEX PHARMACEUTICALS INCORPORATEDInventors: Douglas J. Bartels, Min Jiang, Tara Lynn Kieffer, Olivier Nicolas
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Publication number: 20130157259Abstract: Provided are methods of efficiently amplifying DNA from RNA in sample, methods of efficiently estimating an amount of RNA in a sample, and compositions for efficiently amplifying DNA from RNA in a sample.Type: ApplicationFiled: December 14, 2012Publication date: June 20, 2013Applicant: SAMSUNG ELECTRONICS CO., LTD.Inventor: SAMSUNG ELECTRONICS CO., LTD.
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Publication number: 20130158095Abstract: The present inventors found that a fusion gene present in some cancer patients is an oncogene. The present invention relates to a polypeptide as a novel fusion protein, a polynucleotide encoding the polypeptide, a vector comprising the polynucleotide, a transformed cell comprising the vector, a method for detecting the fusion protein or polynucleotide, a method for screening a therapeutic agent for cancer, and a method for treating cancer that is shown to be positive for the fusion gene. Further, the present invention relates kit, primer set, and probe useful in the detection of cancer that is shown to be positive for the fusion gene.Type: ApplicationFiled: May 10, 2012Publication date: June 20, 2013Applicants: CureGene K.K., Astellas Pharma Inc.Inventors: Hiroyuki Mano, Sadao Kuromitsu, Nobuaki Shindo, Takatoshi Soga, Takashi Furutani
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Publication number: 20130157268Abstract: The present invention relates generally to the field of phosphatidylinositol based signaling pathways, and more specifically to the use of novel members of these pathways for disease prognosis and treatment. In some aspects, the present invention relates to the use of novel splice variants of type I phosphatidylinositol phosphate kinase ?, named PIPKI? 700 and PIPKI? 707, to determine breast cancer and breast cancer prognosis.Type: ApplicationFiled: November 30, 2012Publication date: June 20, 2013Applicant: Wisconsin Alumni Research FoundationInventor: Wisconsin Alumni Research Foundation
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Publication number: 20130149749Abstract: An engineered DNA polymerase characterised in that the polymerase exhibits an enhanced ability to process nucleic acid in the presence of environmental and biological inhibitors compared to wild type DNA polymerase.Type: ApplicationFiled: February 18, 2013Publication date: June 13, 2013Applicant: Medical Research CouncilInventor: Medical Research Council
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Publication number: 20130150294Abstract: A method for regulating Src and its downstream signaling pathway which includes binding between Src and Na+/K+-ATPase is disclosed. The Na+/K+-ATPase/Src complex is a functional receptor for cardiotonic steroids such as ouabain. Also disclosed are Src inhibitors or activators which include either Na+/K+-ATPase or Src that interfere with the interaction between the Na/K-ATPase and Src, act via a different mechanism from ATP analogues, and is pathway (Na+/K+-ATPase) specific.Type: ApplicationFiled: September 24, 2012Publication date: June 13, 2013Applicant: THE UNIVERSITY OF TOLEDOInventor: The University of Toledo
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Publication number: 20130149748Abstract: Disclosed are DNA polymerases having increased reverse transcriptase efficiency relative to a corresponding, unmodified polymerase. The polymerases are useful in a variety of disclosed primer extension methods. Also disclosed are related compositions, including recombinant nucleic acids, vectors, and host cells, which are useful, e.g., for production of the DNA polymerases.Type: ApplicationFiled: December 5, 2012Publication date: June 13, 2013Applicant: Roche Molecular Systems, Inc.Inventor: Roche Molecular Systems, Inc.
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Publication number: 20130149747Abstract: Disclosed are DNA polymerases having increased reverse transcriptase efficiency relative to a corresponding, unmodified polymerase. The polymerases are useful in a variety of disclosed primer extension methods. Also disclosed are related compositions, including recombinant nucleic acids, vectors, and host cells, which are useful, e.g., for production of the DNA polymerases.Type: ApplicationFiled: December 5, 2012Publication date: June 13, 2013Applicant: Roche Molecular Systems, Inc.Inventor: Roche Molecular Systems, Inc.
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Patent number: 8460910Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.Type: GrantFiled: September 10, 2004Date of Patent: June 11, 2013Assignee: Illumina Cambridge LimitedInventors: Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches, Harold Swerdlow, David James Earnshaw
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Patent number: 8460870Abstract: A method of altering the conformation of a polypeptide having a known three-dimensional structure is described. The method comprises attaching a first end of a polymer to a first portion of the polypeptide, attaching a second end of the polymer to a second portion of the polypeptide, and altering the mechanical tension of the polymer, thereby altering the conformation of the polypeptide. The alteration of the conformation of the polypeptide may increase or decrease the binding affinity of the polypeptide for a substrate bound by the polypeptide, or alter the catalytic rate of an enzyme. Typically, the polymer is a polynucleotide or polypeptide.Type: GrantFiled: July 20, 2011Date of Patent: June 11, 2013Assignee: The Regents of the University of CaliforniaInventors: Giovanni Zocchi, Brian Choi
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Publication number: 20130143300Abstract: The invention provides novel compositions with polymerase activity and methods of using the compositions.Type: ApplicationFiled: January 29, 2013Publication date: June 6, 2013Applicant: Bio-Rad Laboratories, Inc.Inventor: Bio-Rad Laboratories, Inc.
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Publication number: 20130143911Abstract: Nucleic acids and proteins having a mutant MEK sequence, and methods concerning identification of patients having resistance to treatment with anti-cancer agents, specifically inhibitors of RAF or MEK are provided. Methods of treatment and for optimizing treatment for patients having a mutation in a MEK1 sequence are also provided.Type: ApplicationFiled: June 9, 2011Publication date: June 6, 2013Applicant: Dana-Farber Cancer Institute, Inc.Inventors: Levi A. Garraway, Caroline Emery, Nikhil Wagle
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Publication number: 20130143225Abstract: The present invention provides a versatile mutant reverse transcriptase with high thermal stability, a nucleic acid thereof and a method for producing a mutant reverse transcriptase, a versatile kits for reverse transcription and detection, a method for improving thermal stability of a nucleic acid-related enzyme, which significantly improves thermal stability of a nucleic acid-related enzyme, and a reverse transcription method, which efficiently performs a reverse transcription. An amino acid residue in a nucleic acid interaction region of a wild-type enzyme is substituted with a positively-charged amino acid residue or a nonpolar amino acid residue, to form a nucleic acid interaction region having a positive effective charge larger than the nucleic acid interaction region of a wild-type enzyme.Type: ApplicationFiled: August 9, 2011Publication date: June 6, 2013Applicant: Kyoto UniversityInventors: Kiyoshi Yasukawa, Kuniyo Inouye
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Patent number: 8455214Abstract: The present invention provides methods for determining a putative antibacterial, the methods comprising determining whether the putative antibacterial inhibits GlgE or Rv3032. The present invention also provides the antibacterial, the pharmaceutical composition and the method of making the antibacterial as well as a method of treating a subject infected with a bacterial comprising administration of the antibacterial.Type: GrantFiled: October 26, 2010Date of Patent: June 4, 2013Assignees: Albert Einstein College of Medicine of Yeshiva University, Plant Bioscience LimitedInventors: William R. Jacobs, Jr., Rainer Kalscheuer, Stephen Bornemann, Karl Syson
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Publication number: 20130137125Abstract: The present invention relates to human Janus Kinase 3 (JAK3) and JAK3-like binding pockets. The present invention provides a computer comprising a data storage medium encoded with the structure coordinates of such binding pockets. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen for and design compounds, including inhibitory compounds, that bind to JAK3 protein or JAK3 protein homologues, or complexes thereof. The invention also relates to crystallizable compositions and crystals comprising JAK3 kinase domain and JAK3 kinase domain complexes with AMP-PNP.Type: ApplicationFiled: May 24, 2012Publication date: May 30, 2013Applicant: VERTEX PHARMACEUTICALS INCORPORATEDInventors: Harmon Zuccola, Marc Jacobs, Lovorka Swenson, Kumkum Saxena
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Publication number: 20130137145Abstract: 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: ApplicationFiled: December 20, 2012Publication date: May 30, 2013Inventors: Stephen J Benkovic, Frank Salinas
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Publication number: 20130137708Abstract: The present invention sets forth a new chemical genetic approach for engineering kinase enzymes with a cysteine gatekeeper residue as well as for developing electrophilic inhibitors thereto. The present invention also provides a Src proto-oncogenic tyrosine kinase with a cysteine gatekeeper that recapitulates wild type activity and can be irreversibly inhibited both in vitro and in cells. The present invention also provides methods and compositions for modulating kinases and for treating kinase-associated diseases.Type: ApplicationFiled: November 30, 2012Publication date: May 30, 2013Applicant: The Regents of The University of CaliforniaInventor: The Regents of The University of California
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Publication number: 20130137160Abstract: The invention relates to methods of altering expression of a genomic locus of interest or specifically targeting a genomic locus of interest in an animal cell, which may involve contacting the genomic locus with a non-naturally occurring or engineered composition that includes a deoxyribonucleic acid (DNA) binding polypeptide having a N-terminal capping region, a DNA binding domain comprising at least five or more Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and a C-terminal capping region, wherein the polypeptide includes at least one or more effector domains, and wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to the DNA of the genomic locus.Type: ApplicationFiled: December 31, 2012Publication date: May 30, 2013Applicants: MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE BROAD INSTITUTE INC.Inventors: The Broad Institute Inc., Massachusetts Institute of Technology
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Publication number: 20130137161Abstract: The invention relates to methods of altering expression of a genomic locus of interest or specifically targeting a genomic locus of interest in an animal cell, which may involve contacting the genomic locus with a non-naturally occurring or engineered composition that includes a deoxyribonucleic acid (DNA) binding polypeptide having a N-terminal capping region, a DNA binding domain comprising at least five or more Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and a C-terminal capping region, wherein the polypeptide includes at least one or more effector domains, and wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to the DNA of the genomic locus.Type: ApplicationFiled: December 31, 2012Publication date: May 30, 2013Applicants: MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE BROAD INSTITUTE INC.Inventors: The Broad Institute Inc., Massachusetts Institute Of Technology
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Publication number: 20130130352Abstract: Methods and kits for generating contamination-free reagents and reagent solutions for use in nucleic acid amplification are provided. Methods include processing of polymerase solutions, nucleotide solutions and primer solutions to render contaminating nucleic acid inert. The methods employ the proofreading activity of the polymerase and/or exonucleases to de-contaminate the reagents and reagent solutions. Methods and kits for contamination-free nucleic acid amplification are provided.Type: ApplicationFiled: December 28, 2012Publication date: May 23, 2013Applicant: GENERAL ELECTRIC COMPANYInventor: GENERAL ELECTRIC COMPANY
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Publication number: 20130130249Abstract: A method for producing a nucleic acid molecule from a template nucleic acid sequence and a linking unit attached to a primer, which method comprises a step of contacting the template nucleic acid sequence with a nucleic acid polymerase under conditions which allow the nucleic acid polymerase to produce the nucleic acid molecule from the primer based on the template nucleic acid sequence, wherein the linking unit is attached to a target site in the template nucleic acid sequence with a covalent linkage.Type: ApplicationFiled: November 16, 2012Publication date: May 23, 2013Applicant: Vilnius UniversityInventor: Vilnius University
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Publication number: 20130130320Abstract: The invention relates to a nucleic acid polymerase capable of producing a non-DNA nucleotide polymer from a DNA nucleotide polymer template, said polymerase comprising amino acid sequence having at least 36% identity to the amino acid sequence of SEQ ID NO:1, wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at one or more residues of the thumb region, said residues selected from: amino acids 651 to 679 (patch 10A); wherein said amino acid sequence is mutated relative to the amino acid sequence of SEQ ID NO:1 at residue E664. In one embodiment said polymerase comprises the mutations Y409G and E664K. In one embodiment said polymerase comprises amino acid sequence corresponding to SEQ ID NO:12.Type: ApplicationFiled: April 14, 2011Publication date: May 23, 2013Inventors: Philipp Holliger, Christopher Cozens, Vitor B. Pinheiro