Patents Examined by Jeffrey Fredman
  • Patent number: 7629120
    Abstract: A process for assembling a series of DNA fragments generated by PCR into an ordered circular arrangement for replication and genetic work in cells. The PCR fragments are made with a modified nucleotide in the primers that can be removed with a DNA excision repair enzyme to generate a 3? overhang. The 3? overhangs are designed to allow directional annealing and thus sequential PCR fragments can be assembled by annealing the overhangs and subsequent ligation. Sequential addition of PCR fragments is facilitated by growing the chain on a solid support, and the assembled chain can be removed with a site specific recombinase if the first and last primers contain the recombinase site. The circularized assembled fragment can be directly used for cell transformation if the appropriate sequences are included, such as an origin of replication and a selectable marker.
    Type: Grant
    Filed: October 31, 2003
    Date of Patent: December 8, 2009
    Assignee: Rice University
    Inventors: George Nelson Bennett, Mary Lou Harrison
  • Patent number: 7375184
    Abstract: The present invention is directed to novel polypeptides and to nucleic acid molecules encoding those polypeptides. Also provided herein are vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides of the present invention and to methods for producing the polypeptides of the present invention.
    Type: Grant
    Filed: December 7, 2001
    Date of Patent: May 20, 2008
    Assignee: Genentech, Inc.
    Inventors: Audrey Goddard, Paul J. Godowski, Austin L. Gurney, Timothy A. Stewart, William I. Wood
  • Patent number: 7371529
    Abstract: The invention provides novel methods and compositions for modulating gluconeogenesis through modulation of PGC-1 activity or expression. Also provided are methods for identifying compounds that modulate gluconeogenesis through modulation of PGC-1 activity or expression, as well as methods for identifying compounds that modulate the interaction of PGC-1 with PGC-1 target molecules. Further provided are methods for treating disorders characterized by aberrant gluconeogenesis.
    Type: Grant
    Filed: January 6, 2005
    Date of Patent: May 13, 2008
    Assignee: Dana-Farber Cancer Institute, Inc.
    Inventors: Bruce M. Spiegelman, Clifford Hyunsuk Yoon
  • Patent number: 7329489
    Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.
    Type: Grant
    Filed: October 27, 2003
    Date of Patent: February 12, 2008
    Assignees: Matabolon, Inc., Cornell Research Foundation, Inc.
    Inventors: Rima Kaddurah-Daouk, Bruce Kristal
  • Patent number: 7320860
    Abstract: A nucleic acid amplification method, and probes for use within the method are described.
    Type: Grant
    Filed: July 12, 2002
    Date of Patent: January 22, 2008
    Assignee: Olink A.B.
    Inventors: Ulf Landegren, Mats Gullberg, Mats Nilsson
  • Patent number: 7316901
    Abstract: This invention relates to a method for efficiently detecting double-stranded nucleic acids. More particularly, this invention relates to a method for reducing signals derived from an intercalator bound to a single-stranded nucleic acid, wherein a compound that reacts more preferentially with an intercalator bound to a single-stranded nucleic acid than with an intercalator bound to a double-stranded nucleic acid or a compound that is bound to a single-stranded nucleic acid more strongly than an intercalator and is bound to a double-stranded nucleic acid more weakly than an intercalator is added to a mixture comprising double-stranded and single-stranded nucleic acids both having intercalators bound thereto, thereby reducing signals derived from an intercalator bound to a single-stranded nucleic acid.
    Type: Grant
    Filed: June 10, 2002
    Date of Patent: January 8, 2008
    Assignee: Eiken Kagaku Kabushiki Kaisha
    Inventors: Norihiro Tomita, Yasuyoshi Mori
  • Patent number: 7314711
    Abstract: This invention pertains to the general field of chemical and biological assays which employ electrochemiluminscence (ECL), also referred to as electrogenerated chemiluminescence. More particularly, the present invention pertains to certain classes of chemical moieties which strongly quench ECL, and the use of these ECL quenchers in combination with ECL labels, for example, in ECL assay methods which employ an ECL quencher and an ECL label. One class of such quenching moieties are those which comprise at least one benzene moiety. Sub-classes of such quenching moieties are those which comprise at least one phenol moiety, quinone moiety, benzene carboxylic acid, and/or benzene carboxylate moiety.
    Type: Grant
    Filed: May 7, 1998
    Date of Patent: January 1, 2008
    Assignee: BioVeris Corporation
    Inventors: Mark M. Richter, Michael J. Powell, Christopher M. Belisle
  • Patent number: 7312059
    Abstract: The present invention provides a method for identifying a thermostable polymerase having altered fidelity. The method consists of generating a random population of polymerase mutants by mutating at least one amino acid residue of a thermostable polymerase and screening the population for one or more active polymerase mutants by genetic selection. For example, the invention provides a method for identifying a thermostable polymerase having altered fidelity by mutating at least one amino acid residue in an active site O-helix of a thermostable polymerase. The invention also provides thermostable polymerases and nucleic acids encoding thermostable polymerases having altered fidelity, for example, high fidelity polymerases and low fidelity polymerases. The invention additionally provides a method for identifying one or more mutations in a gene by amplifying the gene with a high fidelity polymerase.
    Type: Grant
    Filed: March 31, 2005
    Date of Patent: December 25, 2007
    Assignee: University of Washington
    Inventors: Lawrence A. Loeb, Leroy Hood, Motoshi Suzuki
  • Patent number: 7312052
    Abstract: The subject invention provides novel compositions containing a mixture of (a) an enzyme that possesses substantial 3?–5? exonuclease activity (b) a DNA polymerase with less 3?–5? exonuclease activity than the enzyme with substantial 3?–5? exonuclease activity. Preferably, the DNA polymerase for inclusion in the compositions are DNA polymerases that substantially lack 3?–5? exonuclease activity. A preferred embodiment of the invention is a composition comprising the Taq DNA polymerase (isolated from Thermus aquaticus) and the Pfu DNA polymerase (isolated from Pyrococcus furiosus). Another aspect of the invention is to provide methods for synthesizing polynucleotides, typically DNA, using compositions comprising an enzyme that possesses substantial 3?–5? exonuclease activity and a DNA polymerase with less 3?–5? exonuclease activity than the enzymes possessing substantial 3?–5? exonuclease activity, preferably a DNA polymerase that substantially lacks 3?–5? exonuclease activity.
    Type: Grant
    Filed: September 18, 1995
    Date of Patent: December 25, 2007
    Assignee: Stratagene California
    Inventors: Joseph A. Sorge, Rebecca Lynn Mullinax
  • Patent number: 7309589
    Abstract: A method for identifying an RNA form of a bacteria, comprising reverse transcribing RNA material; conducting PCR using primers for a first highly conserved genetic sequence generic of the bacteria; conducting nested PCR using primers for a second highly conserved genetic sequence within the first genetic sequence of the bacteria; and identifying the bacteria based on unconserved amplified sequences linked to the conserved sequences.
    Type: Grant
    Filed: August 16, 2005
    Date of Patent: December 18, 2007
    Assignee: Vironix LLC
    Inventors: Luc Montagnier, Claude Lavallee
  • Patent number: 7306903
    Abstract: Disclosed herein are methods and compositions for identifying morphogen analogs. The preferred methods and compositions relate to the discovery that morphogen upregulation of the mouse type X collagen promoter activity is mediated by a MEF-2 like sequence and requires an adjacent AP-1 sequence. Certain methods rest on the use of test cells comprising DNA defining a morphogen-responsive transcription activating element operatively associated with a reporter gene. Other methods rest on the use of DNAs for measuring morphogen-inducible DNA-binding. In certain preferred embodiments, the methods and DNAs involve an osteogenic protein 1 (OP-1) responsive transcription activating element. Substances that mediate interaction with and/or activate the OP-1 responsive transcription activating element are considered herein likely to be useful for reproducing in vivo effects of morphogens such as OP-1.
    Type: Grant
    Filed: July 10, 2000
    Date of Patent: December 11, 2007
    Assignee: Curis, Inc.
    Inventors: Kuber T. Sampath, Shun-ichi Harada, Gideon A. Rodan
  • Patent number: 7303874
    Abstract: The present invention relates to methods and compositions for using nucleotide sequence variations of 16S and 23S rRNA within the B. cereus group to discriminate a highly infectious bacterium B. anthracis from closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations and discriminate B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed samples, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.
    Type: Grant
    Filed: August 25, 2003
    Date of Patent: December 4, 2007
    Assignee: The University of Chicago
    Inventors: Sergei G. Bavykin, Natalia V. Mirzabekova, legal representative, Andrei D. Mirzabekov, deceased
  • Patent number: 7297519
    Abstract: The invention provides compositions containing a mixture of (a) an enzyme that possesses substantial 3?-5? exonuclease activity (b) a DNA polymerase with less 3?-5? exonuclease activity than the enzyme with substantial 3?-5? exonuclease activity. Preferably, the DNA polymerase for inclusion in the compositions are DNA polymerases that substantially lack 3?-5? exonuclease activity. A preferred embodiment of the invention is a composition comprising Taq DNA polymerase (isolated from Thermus aquaticus) and Pfu DNA polymerase (isolated from Pvrococcus furiosus). Another aspect of the invention is to provide methods for synthesizing polynucleotides using compositions comprising an enzyme that possesses substantial 3?-5? exonuclease activity and a DNA polymerase with less 3?-5? exonuclease activity than the enzymes possessing substantial 3?-5? exonuclease activity, preferably a DNA polymerase that substantially lacks 3?-5? exonuclease activity.
    Type: Grant
    Filed: December 13, 2002
    Date of Patent: November 20, 2007
    Assignee: Stratagene California
    Inventors: Joseph A. Sorge, Rebecca Lynn Mullinax
  • Patent number: 7294488
    Abstract: The present invention provides amplification and hybridisation method for detecting and typing human papillomavirus (HPV), and the primers and hybridisation probes used in the method. The invention relates to a concrete part of the HPV genome, which is suitable for designing HPV genus-specific and HPV genotype-specific hybridisation oligonucleotide probes.
    Type: Grant
    Filed: March 10, 2003
    Date of Patent: November 13, 2007
    Assignee: Genoid KFT
    Inventors: Csaba Jeney, Tibor Takács
  • Patent number: 7291470
    Abstract: The invention provides a new primer composition for detecting the presence of Shigella sonnei and a method of using the same. The primer composition and method have high specificity and sensitivity on the detection of Shigella sonnei. The invention also provides a method for extracting the nucleic acids of microorganisms in a solution sample.
    Type: Grant
    Filed: August 26, 2005
    Date of Patent: November 6, 2007
    Assignee: National Chung-Hsing University
    Inventors: Jiann-Hwa Chen, Wen-Bin Hsu, Pei-Chum Chen
  • Patent number: 7291460
    Abstract: Methods for the sequencing of polynucleotides are provided. Also provided are multiplex systems for sequencing polynucleotides using the disclosed methods, kits for use with the disclosed methods and methods for diagnosing diseases and adverse drug reactions using the disclosed methods.
    Type: Grant
    Filed: May 30, 2003
    Date of Patent: November 6, 2007
    Assignee: Verenium Corporation
    Inventors: Mike Lafferty, Charles Tweedy, James Butler
  • Patent number: 7288377
    Abstract: The present invention relates to a method for identifying individuals with Parkinson's disease and/or individuals at risk for developing Parkinson's disease, comprising screening nucleic acids from the individual for a mutation in the ADH1C gene, as well as different uses thereof.
    Type: Grant
    Filed: February 12, 2004
    Date of Patent: October 30, 2007
    Assignee: AstraZeneca AB
    Inventors: Silvia Burvenich, Andrea Carmine, Dagmar Galter, Lars Olson, Olof Sydow
  • Patent number: 7288373
    Abstract: The invention provides methods for treating methylated nucleic acids. In one embodiment, the method can include the steps of (a) providing an alkali environment to a nucleic acid sample; (b) reacting the nucleic acid sample with a bisulphite reagent and incubating the reaction so as to form a treated nucleic acid sample where methylated nucleotides in the nucleic acid sample remain unchanged while unmethylated nucleotides are converted to another form; (c) diluting the treated nucleic acid sample so as to reduce salt concentration to a level which will not substantially interfere with a nucleic acid precipitating step; (d) precipitating the diluted treated nucleic acid to substantially remove any unwanted reagents or diluents from treated nucleic acid; and (e) carrying out de-sulphonation of the precipitated treated nucleic acid so as to remove sulphonate groups present on the treated nucleic acid so as to obtain a nucleic acid sample substantially free of sulphonate groups.
    Type: Grant
    Filed: May 2, 2003
    Date of Patent: October 30, 2007
    Assignee: Human Genetic Signatures Pty Ltd.
    Inventors: Douglas Spencer Millar, Cassandra Jean Vockler, Neralie Ann Coulston
  • Patent number: 7288376
    Abstract: Allele specific primers and probes suitable for detecting allelic variants of human SP-A2 gene for applications such as molecular diagnosis, prediction of an individual's susceptibility, and/or the genetic analysis of SP-A2 gene in a population.
    Type: Grant
    Filed: October 17, 2003
    Date of Patent: October 30, 2007
    Assignee: Council of Scientific and Industrial Research
    Inventors: Puranam Usha Sarma, Taruna Madan, Shweta Saxena
  • Patent number: 7288371
    Abstract: The present invention is directed to a novel method of discriminating a highly infectious bacterium Bacillus anthracis from a group of closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations. The identification and analysis of these sequence variations enables positive discrimination of isolates of the B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed probes, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.
    Type: Grant
    Filed: November 4, 2002
    Date of Patent: October 30, 2007
    Assignee: The University of Chicago
    Inventors: Sergei G. Bavykin, Andrei D. Mirzabekov