Non-coding Sequences Having No Known Regulatory Function Which Are Adaptors Or Linkers For Vector Or Gene Contruction Patents (Class 536/24.2)
  • Patent number: 9446120
    Abstract: The present invention provides a therapeutic or improving agent for a lifestyle-related disease, containing an expression vector encoding a chimeric Hepatitis B virus core antigen polypeptide inserted with an amino acid sequence containing a specific epitope of the lifestyle-related disease-related factor, wherein the amino acid sequence containing the specific epitope is inserted between the amino acid residues 80 and 81 of the hepatitis B virus core antigen polypeptide.
    Type: Grant
    Filed: April 13, 2012
    Date of Patent: September 20, 2016
    Assignees: Osaka University, Anges MG, Inc.
    Inventors: Ryuichi Morishita, Hironori Nakagami, Hiroshi Koriyama, Futoshi Nakagami, Natsuki Yoshida
  • Publication number: 20150133317
    Abstract: Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.
    Type: Application
    Filed: April 27, 2012
    Publication date: May 14, 2015
    Applicants: Department of Veterans Affairs, The Board of Trustees of the Leland Stanford Junior University
    Inventors: William H. Robinson, Yann Chong Tan, Jeremy Sokolove
  • Patent number: 9029526
    Abstract: Polynucleotides and polypeptides which participate in influenza virus infection of cells and nucleic acid molecules, which include a polynucleotide sequence capable of specifically binding the polypeptides of the present invention. Also provided are methods of using such nucleic acid molecules, polynucleotides and antibodies directed thereagainst for diagnosing, treating and preventing influenza virus infection.
    Type: Grant
    Filed: November 19, 2012
    Date of Patent: May 12, 2015
    Assignee: Yeda Research and Development Co. Ltd.
    Inventors: Ruth Arnon, Sung-Ho Jeon, Basak Kayhan, Tamar Ben-Yedidia
  • Patent number: 9018365
    Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.
    Type: Grant
    Filed: March 28, 2013
    Date of Patent: April 28, 2015
    Assignee: Population Genetics Technologies Ltd
    Inventor: Sydney Brenner
  • Patent number: 9000142
    Abstract: There is disclosed a photocleavable sense-antisense nucleobase polymer complex capable of modulating gene expression comprising an unnatural antisense nucleobase polymer that targets an mRNA, and a photocleavable sense nucleobase polymer noncovalently bound to the antisense nucleobase polymer, wherein the photocleavable sense nucleobase polymer comprises a plurality of nucleobase polymers connected by a photocleavable linkage. There is also disclosed a method for controlling the time and spatial position of gene expression comprising selecting a target mRNA, introducing the photocleavable sense-antisense nucleobase polymer complex into a cell, and selectively irradiating the cell with light.
    Type: Grant
    Filed: June 23, 2009
    Date of Patent: April 7, 2015
    Assignee: Syntrix Biosystems, Inc.
    Inventor: John A. Zebala
  • Patent number: 8999673
    Abstract: Provided is a method for selectively obtaining, for a given target gene, a “joined DNA fragment” wherein just a target gene fragment is joined with desired other DNA fragments, regardless of whether a DNA fragment containing a target gene sequence has been purified. In the provided method, a double-stranded joining DNA fragment containing a sequence A and/or a sequence B is selectively joined to the ends of a target gene fragment. A mixture of a double-stranded gene fragment, the 3? end of which is protruding, and the double-stranded joining DNA fragment, which are related in a prescribed manner, undergoes at least two cycles of thermal denaturation, reassociation, and DNA synthesis, resulting in a “joined DNA fragment,” which is a double-stranded DNA fragment including at least one instance of a sequence resulting from joining sequence A, the target gene sequence, and sequence B. A “single-side joined DNA fragment” can also be obtained, by a similar method.
    Type: Grant
    Filed: September 2, 2010
    Date of Patent: April 7, 2015
    Assignee: National University Corporation University of Toyama
    Inventors: Nobuyuki Kurosawa, Masaharu Isobe
  • Patent number: 8993238
    Abstract: Compositions and methods related to transgenic glyphosate tolerant Brassica plants are provided. Specifically, the present invention provides Brassica plants having a DP-073496-4 event which imparts tolerance to glyphosate. The Brassica plant harboring the DP-073496-4 event at the recited chromosomal location comprises genomic/transgene junctions within SEQ ID NO: 2 or with genomic/transgene junctions as set forth in SEQ ID NO: 12 and/or 13. The characterization of the genomic insertion site of the event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the event are provided.
    Type: Grant
    Filed: October 7, 2013
    Date of Patent: March 31, 2015
    Assignees: E I du Pont de Nemours and Company, Pioneer Hi Bred International Inc
    Inventors: David George Charne, Wenpin Chen, Chadwick Bruce Koscielny, Zhongsen Li, Jayantilal Patel, Ferdinand G Thoonen, Lomas Tulsieram, Yongping Zhang
  • Patent number: 8993532
    Abstract: Provided is an improved design of shRNA based on structural mimics of miR-451 precursors. These miR-451 shRNA mimics are channeled through a novel small RNA biogenesis pathway, require AGO2 catalysis and are processed by Drosha but are independent of DICER processing. This miRNA pathway feeds active elements only into Ago2 because of its unique catalytic activity. These data demonstrate that this newly identified small RNA biogenesis pathway can be exploited in vivo to produce active molecules.
    Type: Grant
    Filed: April 22, 2011
    Date of Patent: March 31, 2015
    Assignee: Cold Spring Harbor Laboratory
    Inventors: Gregory J. Hannon, Sihem Cheloufi
  • Patent number: 8951790
    Abstract: The present invention relates to the construction and utilization of a new mammalian expression vector that contains a unique multiple cloning site (MCS), designated pUHAB. The pUHAB vector comprises a high copy replication origin (ColE1), a drug resistance gene (TK-Hygromycin), and a human cytomegalovirus promoter operably associated with a unique intron (hCMV/intron). Further, pUHAB comprises a selectable marker conferring resistance to kanamycin in bacterial cells, and a phage f1(+) region. pUHAB can be used to transiently or stably express cloned genes when transfected into mammalian cells. The invention also encompasses kits and host cells and cell lines comprising pUHAB, and methods of producing a recombinant protein using pUHAB.
    Type: Grant
    Filed: January 6, 2012
    Date of Patent: February 10, 2015
    Assignee: Merck Sharp & Dohme Corp.
    Inventor: Deba P. Saha
  • Patent number: 8927245
    Abstract: Provided herein is a method of preparing an RNA sample comprising: a) obtaining an RNA sample comprising: i. long RNA molecules that may be unfragmented or fragmented to contain 5?-OH group and a 2?-3?-cyclic phosphate group; and ii. short RNA molecules that comprise a 5? phosphate group and a 3? OH group; and b) contacting the RNA sample with an adaptor comprising either a 2?-PO group and 3?-OH group or a 2?,3?-cyclic phosphate group in the presence of a eukaryotic tRNA ligase, thereby producing a ligated RNA sample in which a) the short RNA molecules are selectively ligated to the adaptor or b) the short RNA molecules and long RNA fragments are selectively ligated to the adaptor.
    Type: Grant
    Filed: December 15, 2011
    Date of Patent: January 6, 2015
    Assignee: Agilent Technologies, Inc.
    Inventors: Gusti Zeiner, Robert A. Ach
  • Patent number: 8911945
    Abstract: The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers.
    Type: Grant
    Filed: June 27, 2014
    Date of Patent: December 16, 2014
    Assignee: KeyGene N.V.
    Inventors: Michael Josephus Theresia Van Eijk, Anker Preben Sørensen, Marco Gerardus Maria Van Schriek
  • Patent number: 8900869
    Abstract: Methods and compositions using populations of randomized modified FRT recombination sites to identify, isolate and/or characterize modified FRT recombination sites are provided. The recombinogenic modified FRT recombination sites can be employed in a variety of methods for targeted recombination of polynucleotides of interest, including methods to recombine polynucleotides, assess promoter activity, directly select transformed organisms, minimize or eliminate expression resulting from random integration into the genome of an organism, such as a plant, remove polynucleotides of interest, combine multiple transfer cassettes, invert or excise a polynucleotide, and identify and/or characterize transcriptional regulating regions are also provided.
    Type: Grant
    Filed: October 25, 2012
    Date of Patent: December 2, 2014
    Assignee: Pioneer Hi-Bred International, Inc.
    Inventors: Yumin Tao, Dennis L. Bidney, William J. Gordon-Kamm, Leszek A. Lyznik
  • Patent number: 8877502
    Abstract: The present invention relates to plasmid curing, and particularly to efficient and stress-free methods for displacing resident or endogenous plasmids from a host cell, such as a bacterium. The invention extends to method of displacing a plasmid comprising a post-segregational killing system from a host cell, the method comprising introducing a recombinant nucleic acid molecule into a host cell harboring a plasmid comprising a post-segregational killing (PSK) system, characterized in that the recombinant nucleic acid molecule is adapted to neutralize the toxic effects of the plasmid's post-segregational killing system, and wherein the nucleic acid molecule is also adapted to outcompete or inhibit replication of the plasmid. The invention further extends to recombinant nucleic acid molecules that can be used in this method, as well as further uses of the methods and nucleic acid molecules of the invention.
    Type: Grant
    Filed: May 9, 2007
    Date of Patent: November 4, 2014
    Assignee: The University of Birmingham
    Inventor: Christopher Morton Thomas
  • Patent number: 8859229
    Abstract: A method of mRNA production for use in transfection is provided, that involves in vitro transcription of PCR generated templates. This RNA can efficiently transfect different kinds of cells. This approach results in increased efficiency (fidelity and productivity) of mRNA synthesis and is less time consuming because it does not require cloning, and also consequently eliminates the unwanted errors and effects related to RNA made on DNA templates obtained with cloning techniques. The results of transfection of RNAs demonstrate that RNA transfection can be very effective in cells that are exceedingly difficult to transfect efficiently with DNA constructs. The method can be used to deliver genes into cells not- or only poorly transfectable for DNA, in vitro and in vivo.
    Type: Grant
    Filed: February 4, 2008
    Date of Patent: October 14, 2014
    Assignee: Yale University
    Inventors: Peter M. Rabinovich, Sherman M. Weissman, Marina E. Komarovskaya, Erkut Bahceci
  • Publication number: 20140303004
    Abstract: The present invention provides a method for producing a circular DNA molecule having a specific structure that enables to distinguish circular DNA formed from a single DNA molecule (single-molecule circular DNA), from circular DNA formed from multiple DNA molecules (multiple-molecule circular DNA) and also from single-molecule circular DNA derived from the circular DNA formed from multiple DNA molecules. According to the present invention, only single-molecule circular DNA that is not derived from multiple-molecule circular DNA can be selected in the production of circular DNA.
    Type: Application
    Filed: August 24, 2012
    Publication date: October 9, 2014
    Inventors: Shinichi Mizuno, Hidetoshi Ozawa, Koji Nagafuji, Takashi Okamura
  • Patent number: 8846385
    Abstract: Lentiviral vectors modified at the 5? LTR or both the 5? and 3? LTR's are useful in the production of recombinant lentivirus vectors. Such vectors can be produced in the absence of a functional tat gene. Multiple transformation of the host cell with the vector carrying the transgene enhances virus production.
    Type: Grant
    Filed: July 26, 2006
    Date of Patent: September 30, 2014
    Assignee: GBP IP, LLC
    Inventors: Luigi Naldini, Thomas Dull, Deborah A. Farson, Rochelle Witt
  • Patent number: 8841089
    Abstract: The present invention relates to polynucleotides comprising a first nucleic acid sequence for a chromatin element, which is capable of enhancing expression, and at least one second nucleic acid sequence comprising a curved origin motif. Furthermore, the invention relates to a host cell, a non-human transgenic organism, a vector and a kit comprising the aforementioned polynucleotide. Moreover, the invention relates to methods for expressing a polynucleotide of interest.
    Type: Grant
    Filed: March 28, 2008
    Date of Patent: September 23, 2014
    Assignee: Hochschule Mannheim
    Inventors: Manfred Frey, Heiko Flammann, Mathias Hafner
  • Patent number: 8841431
    Abstract: The present invention is related to a nucleic acid capable of binding to hepcidin.
    Type: Grant
    Filed: April 30, 2010
    Date of Patent: September 23, 2014
    Assignee: NOXXON Pharma AG
    Inventors: Simone Sell, Frank Morich, Christian Maasch, Sven Klussmann, Nicole Dinse, Klaus Buchner, Frank Schwobel
  • Patent number: 8841271
    Abstract: Compositions and methods of treatments of cells are provided for altering the phenotype of a cell by administering an oligonucleotide complex to the cell, the complex having two strands and chemical modifications.
    Type: Grant
    Filed: March 13, 2012
    Date of Patent: September 23, 2014
    Assignee: The General Hospital Corporation
    Inventors: David R. Tabatadze, Paul C. Zamecnik, Malay K. Raychowdhury, Horacio F. Cantiello
  • Publication number: 20140271551
    Abstract: This invention relates to synthetic adeno-associated virus (AAV) inverted terminal repeats (ITRs) that exhibit altered activities compared to a naturally occurring AAV ITR and methods of using the same for delivery of nucleic acids to a cell or a subject. The synthetic ITRs provide a larger packaging capacity and the ability to manipulate activities such as transduction efficiency, cellular response to transduction, and transcription.
    Type: Application
    Filed: March 14, 2014
    Publication date: September 18, 2014
    Applicant: THE UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL
    Inventors: MATTHEW LOUIS HIRSCH, RICHARD JUDE SAMULSKI
  • Patent number: 8835114
    Abstract: 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: Grant
    Filed: September 30, 2013
    Date of Patent: September 16, 2014
    Assignee: Gen-Probe Incorporated
    Inventors: Sylvia A. Norman, Jennifer J. Bungo, William L. Hanna, Neeraj P. Rao
  • Patent number: 8829177
    Abstract: We describe methods and DNA constructs/engineered mammalian promoters to enhance native promoter activity while retaining inherent regulation by inserting multi-copy response elements (REs) into non-adjacent locations. Multiple copies of REs are clustered in a group forming a transcription factor response element segment. The segment is at least duplicated in tandem upstream of the ATG start codon. Spacers of 0.2-0.7 kilo base pairs are introduced between the two segments and smaller spacers of about between 9-15 bp are introduced between the copies of REs within a segment.
    Type: Grant
    Filed: June 5, 2010
    Date of Patent: September 9, 2014
    Assignee: The General Hospital Corporation
    Inventors: David B. Rhoads, Jianmin Huang, Lynne L. Levitsky
  • Patent number: 8828690
    Abstract: Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding multizymes (i.e., single polypeptides having at least two independent and separable enzymatic activities) along with a method of making long-chain polyunsaturated fatty acids (PUFAs) using these multizymes in plants and oleaginous yeast are disclosed.
    Type: Grant
    Filed: April 3, 2008
    Date of Patent: September 9, 2014
    Assignee: E I du Pont de Nemours and Company
    Inventors: Howard G. Damude, Anthony J. Kinney, Kevin G. Ripp, Quinn Qun Zhu
  • Patent number: 8829171
    Abstract: Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids.
    Type: Grant
    Filed: February 10, 2011
    Date of Patent: September 9, 2014
    Assignee: Illumina, Inc.
    Inventors: Frank J. Steemers, Kevin Gunderson, Thomas Royce, Natasha Pignatelli
  • Patent number: 8828660
    Abstract: 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: Grant
    Filed: October 2, 2013
    Date of Patent: September 9, 2014
    Assignee: Gen-Probe Incorporated
    Inventors: Sylvia A. Norman, Jennifer J. Bungo, William L. Hanna, Neeraj P. Rao
  • Patent number: 8815512
    Abstract: The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers.
    Type: Grant
    Filed: November 1, 2012
    Date of Patent: August 26, 2014
    Assignee: KeyGene N.V.
    Inventors: Michael Josephus Theresia Van Eijk, Anker Preben Sørensen, Marco Geradus Maria Van Schriek
  • Publication number: 20140208457
    Abstract: The present invention is concerned with nuclease fusion proteins and various uses thereof. Specifically, it relates to a polynucleotide encoding a polypeptide comprising (i) a first module comprising at least a first DNA binding domain derived from a homing endonuclease, (ii) a linker, and (iii) a second module comprising at least a second DNA binding domain and a cleavage domain derived from a restriction endonuclease, wherein said polypeptide functionally interacts only with DNA comprising a DNA recognition site for the first DNA binding domain and a DNA recognition site for the second DNA binding domain, and wherein said cleavage domain cleaves DNA within a specific DNA cleavage site upon binding of the polypeptide. Further contemplated are a vector and a non-human transgenic organism comprising said polynucleotide as well as a polypeptide encoded by the polynucleotide of the invention.
    Type: Application
    Filed: June 8, 2012
    Publication date: July 24, 2014
    Applicant: BASF PLANT SCIENCE COMPANY GMBH
    Inventors: Ines Fonfara, Wolfgang Wende, Alfred Pingoud
  • Patent number: 8785414
    Abstract: The identification of differentially expressed microRNAs in patients with Sjögren's syndrome is disclosed herein. Provided is a method of diagnosing a subject as having Sjögren's syndrome by measuring the level of at least one differentially expressed miR gene product identified herein. An alteration in the level of the at least one miR gene product in the biological sample of the subject relative to a control indicates the subject has Sjögren's syndrome. Also provided is a method of treating a patient with Sjögren's syndrome by administering to the patient a therapeutically effective amount of an agent that inhibits expression of a miR gene product that is up-regulated in the patient with Sjögren's syndrome relative to a control, or by administering to the patient a therapeutically effective amount of an isolated miR gene product that is down-regulated in the patient with Sjögren's syndrome relative to a control. A method of restoring salivary flow in a patient with Sjögren's syndrome is also provided.
    Type: Grant
    Filed: March 31, 2010
    Date of Patent: July 22, 2014
    Assignee: The United States of America, as represented by the Secretary, Department of Health and Human Services
    Inventors: Ilias Alevizos, Gabor Illei
  • Patent number: 8785125
    Abstract: 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: Grant
    Filed: September 27, 2013
    Date of Patent: July 22, 2014
    Assignee: Gen-Probe Incorporated
    Inventors: Sylvia A. Norman, Jennifer J. Bungo, William L. Hanna, Neeraj P. Rao
  • Patent number: 8765926
    Abstract: The present invention pertains to a supramolecular structure based on i-motif tetramers of Cm—X—Cn oligonucleotides, wherein m and n are integers comprised between 2 and 9, and X is a linker such as A, T, G, a modified deoxynucleotide or a diol spacer. These supramolecular structures can be dissociated, when necessary, by a mere pH change. The present invention also relates to methods for obtaining such a supramolecular structure.
    Type: Grant
    Filed: December 17, 2012
    Date of Patent: July 1, 2014
    Assignee: Centre National de la Recherche Scientifique
    Inventors: Denis Pompon, Jean-Louis Leroy, Aude Laisne
  • Patent number: 8754198
    Abstract: The present invention relates to microorganisms that express, or have attached to their surface, a TNF? binding polypeptide. Peptides expressed or attached on the surface of microorganism are more resistant to chemical and enzymatic degradation in the gastrointestinal tract. Such microorganisms are capable of binding TNF? and therefore reducing the content of free TNF? and alleviating its pro-inflammatory effects in the gut. The invention also relates to the use of such microorganisms as medicament in the treatment of inflammatory bowel disease.
    Type: Grant
    Filed: January 5, 2011
    Date of Patent: June 17, 2014
    Assignees: University of Ljubljana, Institute Jozef Stefan, Labena d.o.o.
    Inventors: Mojca Lunder, Matjaz Ravnikar, Borut Strukelj, Ales Berlec, Boris Ceh
  • Patent number: 8753847
    Abstract: Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.
    Type: Grant
    Filed: August 13, 2013
    Date of Patent: June 17, 2014
    Assignee: New England Biolabs, Inc.
    Inventors: Yu Zheng, Richard J. Roberts
  • Patent number: 8741569
    Abstract: The present teachings are generally directed to methods for normalizing at least one species of small nucleic acid that is present in a population of small nucleic acid species, wherein the relative concentration of at least one small nucleic acid species is substantially greater than the relative concentration of at least one other small nucleic acid species in the population. At least one small nucleic acid species is normalized using a multiplicity of primers comprising degenerate sequences. In some embodiments, a small nucleic acid species is identified by inserting at least part of an extension product from a normalized population into a vector and subsequently sequencing the insert. In some embodiments, a small nucleic acid species is identified by determining the sequence of at least part of an extension product.
    Type: Grant
    Filed: October 23, 2009
    Date of Patent: June 3, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Lao, Neil Straus, John Burns
  • Patent number: 8741565
    Abstract: A method for detecting a target nucleic acid of a pathogen in a test sample, the method comprising preparing a target nucleic acid detecting reagent and contacting the target nucleic acid detecting reagent with an oligonucleotide microarray. A kit for detecting a target nucleic acid of a pathogen in a test sample is also described. The kit comprises at least one primer pair and an oligonucleotide microarray comprising at least one probe.
    Type: Grant
    Filed: December 28, 2006
    Date of Patent: June 3, 2014
    Assignee: Honeywell International Inc.
    Inventors: Yuandong Gu, Leon Xu
  • Patent number: 8715927
    Abstract: Disclosed herein is the identification of human DNA polymerase ? (pol ?) as the polymerase that mediates repair of DNA containing interstrand cros slinks (ICLs). The mechanism of action of a number of chemotherapeutic and antimicrobial agents is the induction of ICLs. Thus, provided herein is a method of enhancing the efficacy of a chemotherapeutic or antimicrobial agent in a subject, including selecting a subject in need of treatment with an ICL -inducing agent and administering to the subject an ICL-inducing agent and a therapeutically effective amount of an inhibitor of pol ?. Also provided is a composition for treating a hyperproliferative disease, an autoimmune disease or an infectious disease, comprising an ICL-inducing agent and an amount of an inhibitor of pol ? sufficient to enhance the efficacy of the ICL-inducing agent. Further provided is a method of identifying a DNA polymerase inhibitor.
    Type: Grant
    Filed: April 22, 2009
    Date of Patent: May 6, 2014
    Assignee: Oregon Health & Science University
    Inventors: R. Stephen Lloyd, Irina G. Minko, Amanda K. McCullough
  • Patent number: 8710208
    Abstract: The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3? end of a target polynucleotide, using a ligase that can ligate the 3? end of RNA to the 5? end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleotides that vary by as little as one nucleotide.
    Type: Grant
    Filed: April 26, 2012
    Date of Patent: April 29, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Ruoying Tan, Caifu Chen, Karl J. Guegler
  • Patent number: 8673570
    Abstract: The invention provides a series of reagent compositions and methods for making and amplifying novel cDNA based probe sets from RNA samples to improve analysis with gene expression arrays. The methods globally produce probe sets with common universal linkers at one or both ends, called WRAP-Probes, wherein the linkers do not bind to the target sequences and they can efficiently bind added reporters to the probes. The universal linkers are also designed as primer binding sites for copying and amplifying the probes, either linearly with one linker, or exponentially with double linkers. The capacity to globally and exponentially amplify the probe set by PCR is a primary advantage. Adding reporters by terminal linkers also improves quantification since each probe gets equivalent signaling. The invention allows expression analysis of small research, clinical and forensic samples to enable improved diagnostics, drug discovery, therapeutic monitoring, and medical, agricultural and general research.
    Type: Grant
    Filed: February 23, 2012
    Date of Patent: March 18, 2014
    Assignee: Genetag Technology, Inc.
    Inventor: David A. Shafer
  • Patent number: 8669418
    Abstract: The present invention belongs to the field of functional proteomics and more particularly to the field of protein aggregation. The invention discloses a method for interfering with the function of a target protein and uses a non-naturally, user-designed molecule, designated as interferor, that has a specificity for a target protein and which induces aggregation upon contact with said target protein. The present invention also discloses such interferor molecules and their use in agrobiotech applications.
    Type: Grant
    Filed: May 6, 2011
    Date of Patent: March 11, 2014
    Assignees: VIB VZW, Vrije Universiteit Brussel
    Inventors: Joost Schymkowitz, Frederic Rousseau
  • Patent number: 8669072
    Abstract: The present invention relates to non-steroidal ligands for use in nuclear receptor-based inducible gene expression system, and a method to modulate exogenous gene expression in which an ecdysone receptor complex comprising: a DNA binding domain; a ligand binding domain; a transactivation domain; and a ligand is contacted with a DNA construct comprising: the exogenous gene and a response element; wherein the exogenous gene is under the control of the response element and binding of the DNA binding domain to the response element in the presence of the ligand results in activation or suppression of the gene.
    Type: Grant
    Filed: August 13, 2007
    Date of Patent: March 11, 2014
    Assignee: Intrexon Corporation
    Inventors: Robert Eugene Hormann, Orestes Chortyk, Dat Phat Le
  • Patent number: 8664164
    Abstract: The present invention provides a method for detecting or enriching for a target deoxyribonucleic acid (DNA) present in a nucleic acid sample, said method comprising: (a) fragmenting a nucleic acid sample to generate nucleic acid fragments including a target fragment containing said target DNA and non-specifically ligating an adaptor sequence to an end of said fragments; (b) rendering said fragments at least partially single-stranded; (c) contacting the at least partially single-stranded fragments of step (b) with oligonucleotides A and B of a single target-specific nucleic acid probe; (d) ligating oligonucleotide B of said probe to the part of the single-stranded portion of said target fragment which is hybridised to oligonucleotide A of said probe to produce a probe-target fragment hybrid; and (e) detecting or enriching for said probe-target fragment hybrid.
    Type: Grant
    Filed: July 23, 2010
    Date of Patent: March 4, 2014
    Assignee: Agilent Technologies, Inc.
    Inventors: Olof Ericsson, Magnus Isaksson, Henrik Johansson, Ulf Landegren
  • Patent number: 8624014
    Abstract: A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 1168 24mers is described.
    Type: Grant
    Filed: December 21, 2009
    Date of Patent: January 7, 2014
    Assignee: Luminex Molecular Diagnostics, Inc.
    Inventors: Daniel Kobler, Daniel Fieldhouse
  • Patent number: 8617880
    Abstract: This invention provides monoclonal antibodies that recognize the Toll-like Receptor 4/MD-2 receptor complex, and monoclonal antibodies that recognize the TLR4/MD2 complex as well as TLR4 when not complexed with MD-2. The invention further provides methods of using the monoclonal antibodies as therapeutics. This invention also provides soluble chimeric proteins, methods of expressing and purifying soluble chimeric proteins, and methods of using soluble chimeric proteins as therapeutics, in screening assays and in the production of antibodies.
    Type: Grant
    Filed: January 31, 2012
    Date of Patent: December 31, 2013
    Assignee: Novimmune S.A.
    Inventor: Greg Elson
  • Patent number: 8609341
    Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.
    Type: Grant
    Filed: May 16, 2012
    Date of Patent: December 17, 2013
    Assignee: Illumina, Inc.
    Inventors: Frank Steemers, Jonathan Mark Boutell
  • Patent number: 8609383
    Abstract: Provided are methods of making carrier polypeptide that include incorporating a first unnatural amino acid into a carrier polypeptide variant, incorporating a second unnatural amino acid into a target polypeptide variant, and reacting the first and second unnatural amino acids to produce the conjugate. Conjugates produced using the provided methods are also provided. In addition, orthogonal translation systems in methylotrophic yeast and methods of using these systems to produce carrier and target polypeptide variants comprising unnatural amino acids are provided.
    Type: Grant
    Filed: December 9, 2009
    Date of Patent: December 17, 2013
    Assignee: The Scripps Research Institute
    Inventors: Travis Young, Peter G. Schultz
  • Patent number: 8598335
    Abstract: The present disclosure relates to RNAi agents useful in methods of treating Beta-ENaC-related diseases such as cystic fibrosis, pseudohypoaldosteronism type 1 (PHA1), Liddle's syndrome, hypertension, alkalosis, hypokalemia, and obesity-associated hypertension, using a therapeutically effective amount of a RNAi agent to Beta-ENaC.
    Type: Grant
    Filed: September 13, 2012
    Date of Patent: December 3, 2013
    Assignee: Novartis AG
    Inventors: Antonin De Fougerolles, John Diener, Emma Hickman, Gregory Hinkle, Stuart Milstein, Anne-Marie Pulichino, Andrew Griffin Sprague
  • Patent number: 8586361
    Abstract: Methods and compositions using populations of randomized modified FRT recombination sites to identify, isolate and/or characterize modified FRT recombination sites are provided. The recombinogenic modified FRT recombination sites can be employed in a variety of methods for targeted recombination of polynucleotides of interest, including methods to recombine polynucleotides, assess promoter activity, directly select transformed organisms, minimize or eliminate expression resulting from random integration into the genome of an organism, such as a plant, remove polynucleotides of interest, combine multiple transfer cassettes, invert or excise a polynucleotide, and identify and/or characterize transcriptional regulating regions are also provided.
    Type: Grant
    Filed: September 29, 2010
    Date of Patent: November 19, 2013
    Assignee: Pioneer Hi-Bred International, Inc.
    Inventors: Yumin Tao, Dennis L. Bidney, William J. Gordon-Kamm, Leszek A. Lyznik
  • Patent number: 8569258
    Abstract: The invention provides interfering RNA molecule-ligand conjugates useful as a delivery system for delivering interfering RNA molecules to a cell in vitro or in vivo. The conjugates comprise a ligand that can bind to a low density lipoprotein receptor (LDLR) or LDLR family member. Therapeutic uses for the conjugates are also provided.
    Type: Grant
    Filed: August 13, 2012
    Date of Patent: October 29, 2013
    Assignee: Alcon Research, Ltd.
    Inventor: Jon E. Chatterton
  • Patent number: 8551702
    Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.
    Type: Grant
    Filed: December 15, 2008
    Date of Patent: October 8, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Publication number: 20130196331
    Abstract: A method for analyzing biomolecular interactions, which method can be carried out without performing affinity selection using an immobilized bait, is provided. mRNA portions of assignment molecules that interacted with each other are linked together by annealing via a DNA linker for linking mRNA portions of assignment molecules together, the DNA linker comprising, at the 5?-end, an mRNA-complementary region complementary to a sequence at the 5?-end of each mRNA portion, and, at the 3?-end, a self-complementary region complementary between molecules of the DNA linker, the DNA linker being phosphorylated at the 5?-end.
    Type: Application
    Filed: March 31, 2011
    Publication date: August 1, 2013
    Inventors: Etsuko Miyamoto, Toru Tsuji, Shigeo Fujimori, Masamichi Ishizaka
  • Patent number: RE45196
    Abstract: The present invention provides compositions comprising conjugate molecules that are structurally stable at a temperature of between about 2 degrees C. and 8 degrees C. In some examples, a conjugate molecule comprises an antigen, such as an allergen. In some examples, a conjugate molecule comprises the Ragweed antigen Amb a 1. The present invention provides methods for making and using such compositions. Provided herein are methods for modulating an immune response in an individual comprising administration of a composition comprising a structurally stable conjugate molecule as described herein.
    Type: Grant
    Filed: May 18, 2012
    Date of Patent: October 14, 2014
    Assignee: Dynavax Technologies Corporation
    Inventors: Stephen F. Tuck, Roberto Rodriguez