Patents Examined by Jeffrey Fredman
  • Direct, externally imposed control of polypeptides
    Patent number: 6953656
    Abstract: Methods and compositions for rendering proteins directly responsive to an external signal utilizing modulators that themselves respond to the external signal and are associated with the proteins. In response to the external signal, the modulator alters physical properties of the specific protein molecule(s) with which it is associated, thereby altering the structural and functional properties thereof. The modulator may, for example, transfer applied energy to a protein, or to a portion of the protein, thereby changing the protein structure and function.
    Type: Grant
    Filed: July 13, 2001
    Date of Patent: October 11, 2005
    Assignee: Massachusetts Institute of Technology
    Inventors: Joseph M. Jacobson, John J. Schwartz, Kimberly Hamad, Shuguang Zhang
  • High-throughput microbial culturing
    Patent number: 6951714
    Abstract: Methods for isolating microbial species, particularly previously uncultured species, from non-laboratory source environments (such as soil, freshwater, seawater, etc.) are disclosed. These methods can include the use of cultures in arrays, and cells deposited on solid surfaces in arrays for detection, and flow cytometry and/or cell sorting and/or dilution cultures.
    Type: Grant
    Filed: January 16, 2002
    Date of Patent: October 4, 2005
    Assignee: State of Oregon acting by and through the State Board of Higher Education on behalf of Oregon State University
    Inventors: Stephen Giovannoni, Stephanie Connon
  • Process for obtaining recombined nucleotide sequences in vitro, libraries of sequences and sequences thus obtained
    Patent number: 6951719
    Abstract: Ligation-mediated method of recombining polynucleotides in vitro. Polynucleotides from a library are fragmented and the fragments are hybridized to an assembly template. The hybridized fragments are iteratively re-hybridized and ligated until the ends of the hybridized fragments are adjacent to the ends of other hybridized fragments on the assembly template. A final ligation produces recombined polynucleotides.
    Type: Grant
    Filed: November 28, 2000
    Date of Patent: October 4, 2005
    Assignee: Proteus S.A.
    Inventors: Daniel Dupret, Jean-Michel Masson, Fabrice Lefevre
  • Real-time PCR assay of the bacterium Edwardsiella ictaluri in channel catfish
    Patent number: 6951726
    Abstract: A rapid and sensitive PCR-based assay is provided to facilitate early detection of Edwardsiella ictaluri in channel catfish. This bacteria is the causative agent in the disease, Enteric septicemia of catfish (ESC). Also provided is a method of selecting breeding stock for use in selective breeding programs to improve disease resistance in channel catfish. Also provided is a method of determining the efficacy of vaccines produced against ESC.
    Type: Grant
    Filed: September 24, 2002
    Date of Patent: October 4, 2005
    Assignees: Mississippi State University, The United States of America as represented by the Department of Agriculture
    Inventors: Anita L. Bilodeau, William R. Wolters, Geoffrey C. Waldbieser, David J. Wise
  • Rhodococcus cloning and expression vectors
    Patent number: 6949362
    Abstract: A plasmid has been isolated from Rhodococcus erythropolis strain AN12 comprising a unique replication protein. The replication protein may be used in a variety of cloning and expression vectors and particularly in shuttle vectors for the expression of heterologous genes in Rhodococcus sp.
    Type: Grant
    Filed: December 5, 2001
    Date of Patent: September 27, 2005
    Assignee: E. I. du Pont de Nemours and Company
    Inventors: Michael G. Bramucci, Qiong Cheng, Kristy N. Kostichka, Jean-Francois Tomb
  • Dideoxy dye terminators
    Patent number: 6949635
    Abstract: A kit for DNA sequencing comprising a first, second, third and fourth dye terminator molecules, each of the dye terminator molecules comprising a dye molecule, a linker of at least 10 atoms in length and either ddATP, ddCTP, ddGTP or ddTTP as a mono or tri-phosphate and a thermostable DNA polymerase.
    Type: Grant
    Filed: October 26, 2000
    Date of Patent: September 27, 2005
    Assignee: Amersham Biosciences Corp
    Inventors: Shiy Kumar, Satyam Nampalli, Bernard F. McArdle, Carl W. Fuller
  • Design of artificial genes for use as controls in gene expression analysis systems
    Patent number: 6943242
    Abstract: Method of producing controls for use in gene expression analysis systems such as macroarrays, real-time PCR, northern blots, SAGE and microarrays. The controls are generated either from near-random sequence of DNA, or from inter- or intragenic regions of a genome. Ten specific control sequences are also disclosed. Also presented are methods of using these controls, including as negative controls, positive controls, and as calibrators of a gene expression analysis system.
    Type: Grant
    Filed: May 7, 2002
    Date of Patent: September 13, 2005
    Assignee: Amersham Biosciences Corp.
    Inventors: Hrissi Samartzidou, Leah Turner, Steven Daniel, Thomas Houts
  • Methods and compositions for effecting homologous recombination
    Patent number: 6936418
    Abstract: This invention concerns a method for effecting directed mutagenesis based on a guided homologous recombination system that comprises (i) a triple helix forming oligonucleotide, (ii) a donor nucleic acid segment, and (iii) an adapter segment comprising an oligonucleotide sequence able to bind at least a portion of said donor nucleic acid through Watson-Crick base pairing.
    Type: Grant
    Filed: January 18, 2002
    Date of Patent: August 30, 2005
    Assignees: Institut Curie, Centre National de la Recherche Scientifique, Museum National D'Histoire Naturelle, Institut National de la Sante et de la Recherche Medicale
    Inventors: Marie Dutreix, Jian-Sheng Sun, Elodie Biet, Rosalie Maurisse, Jean-Paul Feugeas
  • Diagnostic compositions, elements, methods and test kits for amplification and detection of two or more DNA's using primers having matched melting temperatures
    Patent number: 6936415
    Abstract: An aqueous composition containing primers for opposing strands of two or more target nucleic acids can be used in polymerase chain reaction to provide simultaneously rapid and efficient amplification and detection of those nucleic acids. The primers for each target DNA differ in length by no more than 5 nucleotides and have a Tm within the range of from about 65 to about 74° C., while the Tm's are within about 5° C. of each other. Such compositions are useful in diagnostic test kits and methods for amplification and detection of multiple nucleic acids, or in “multiplexing”, using multiple capture probes. All of the capture probes have Tm's which are greater than 50° C. and are within 15° C. of each other.
    Type: Grant
    Filed: September 29, 2000
    Date of Patent: August 30, 2005
    Inventors: Thomas J. Cummins, Susan Melissa Atwood, Lynn Bergmeyer, John Bruce Findlay, John W. H. Sutherland, JoAnne H. Kerschner
  • Gene expression in bladder tumors
    Patent number: 6936417
    Abstract: Methods for analyzing tumor cells, particularly bladder tumor cells employ gene expression analysis of samples. Gene expression patterns are formed and compared to reference patterns. Alternatively gene expression patterns are manipulated to exclude genes which are expressed in contaminating cell populations. Another alternative employs subtraction of the expression of genes which are expressed in contaminating cell types. These methods provide improved accuracy as well as alternative basis for analysis from diagnostic and prognostic tools currently available.
    Type: Grant
    Filed: September 14, 2001
    Date of Patent: August 30, 2005
    Assignee: AROS Applied Biotechnology ApS
    Inventor: Torben F. Orntoft
  • Detection and typing of human papillomavirus using PNA probes
    Patent number: 6936443
    Abstract: The invention provides materials and methods for detection and typing of HPV infection using PNA probes. More specifically, methods are provided for detecting high-risk types of HPV infection with minimal numbers of PNA probes or using PNA probes to selectively amplify only high-risk types of HPV. Novel primer sequences are also provided.
    Type: Grant
    Filed: November 1, 2002
    Date of Patent: August 30, 2005
    Assignee: Cytyc Corporation
    Inventors: Menashi A. Cohenford, Brian Lentrichia
  • Reagents and methods for automated hybridization
    Patent number: 6933117
    Abstract: The invention provides novel reagents, reagent kits, and methods for automated hybridization. More particularly, the invention provides reagents, reagent kits, and methods for automated in situ hybridization and automated hybridization on a microarray. The use of automated instruments for in situ hybridization and microarray hybridization dramatically reduces the amount of labor and time involved and also facilitates standardization of protocols and consistency between results.
    Type: Grant
    Filed: April 30, 2002
    Date of Patent: August 23, 2005
    Assignee: Ventana Medical Systems, Inc.
    Inventors: Catherine Wolf, Hiroaki Nitta, Thomas Grogan, Jacques Cavadenti, Lidija Pestic-Dragovich, Anthony Hartman, Angela Sattler, Jennifer Wong
  • Method of determining biological/molecular age
    Patent number: 6933120
    Abstract: Methods of obtaining a measurement indicative of oxidative stress and the molecular age of an individual include the step of detecting a mitochondrial DNA deletion and correlating the quantity of the deletion with a measurement of a parameter related to oxygen metabolism.
    Type: Grant
    Filed: October 15, 2002
    Date of Patent: August 23, 2005
    Inventor: Michael D. Seidman
  • Glufosinate tolerant rice
    Patent number: 6933111
    Abstract: This invention pertains to plants, plant material and seeds characterized by harboring a specific transformation event particularly by the presence of the bar gene under control of a CaMV 35S promoter, at a specific location in the rice genome. The rice plants of the invention combine glufosinate tolerance with optimal overall agronomic performance, genetic stability and adaptability to different genetic backgrounds.
    Type: Grant
    Filed: April 28, 2000
    Date of Patent: August 23, 2005
    Assignee: Bayer BioScience N.V.
    Inventors: Marc De Beuckeleer, Frank Michiels, Kirk Johnson
  • Secreted and transmembrane polypeptides and nucleic acids encoding the same
    Patent number: 6930172
    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 27, 2001
    Date of Patent: August 16, 2005
    Assignee: Genentech, Inc.
    Inventors: Napoleone Ferrara, Wei-Qiang Gao, Audrey Goddard, Austin L. Gurney, Colin K. Watanabe, William I. Wood
  • Method for determining genetic affiliation, substructure and gene flow within human populations
    Patent number: 6929911
    Abstract: The present invention provides novel polymorphisms on the Y chromosome and methods of using these polymorphisms as well as known polymorphisms on the Y chromosome as indicators of evolutionary heritage. The polymorphisms of the present invention clustered to specific regions of the Y chromosome, and polymorphisms of particular use to the present methods are found in the non-recombining region of the human Y chromosome (NRY). These polymorphisms, including SNPs, insertions, and deletions, may be useful for numerous applications, including forensics, paternity testing, diagnosis and the like.
    Type: Grant
    Filed: November 1, 2001
    Date of Patent: August 16, 2005
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Peter J. Oefner, Peter A. Underhill
  • Methods for nucleic acid manipulation
    Patent number: 6929915
    Abstract: 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: Grant
    Filed: April 19, 2002
    Date of Patent: August 16, 2005
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Nucleic acid multiplex formation
    Patent number: 6927027
    Abstract: Heteropolymeric triplexes and quadruplexes and methods for making them; the use of accelerator agents such as cations to create them; the use of fluorescent intercalators and fluorescent probe-bound non-intercalators to detect them.
    Type: Grant
    Filed: June 20, 2001
    Date of Patent: August 9, 2005
    Assignee: Ingeneus Corporation
    Inventors: Glen H. Erikson, Jasmine I. Daksis, Ivana Kandic, Pierre Picard
  • Methods for identifying anti-microbial agents
    Patent number: 6924101
    Abstract: A method for identifying endogenous microbial proliferation genes for growth and viability is disclosed herein. The method involves exogenous nucleic acids that are used to conditionally produce antisense inhibitors of endogenous complementary mRNAs in a microorganism. Antisense fragments that result in lethality when expressed indicate that the endogenous gene is a proliferation gene. The method can also be used with sequences in sense orientation. The strategy can be used to identify new gene targets for novel antibiotics.
    Type: Grant
    Filed: March 13, 2001
    Date of Patent: August 2, 2005
    Assignee: San Diego State University Foundation
    Inventors: Judith W. Zyskind, R. Allyn Forsyth
  • High-throughput transcriptome and functional validation analysis
    Patent number: 6924109
    Abstract: Methods for correlating genes and gene function are provided. Such methods generally involve selecting a candidate gene that appears to be correlated with a particular cellular state or activity and then validating the role of the candidate gene in establishment of such a cellular state or activity. Certain methods utilize RNA interference techniques in the validation process.
    Type: Grant
    Filed: April 3, 2002
    Date of Patent: August 2, 2005
    Assignee: AGY Therapeutics, Inc.
    Inventors: Thorsten Melcher, Keith Charles McFarland, Li Gan, Shiming Ye, Mirella Gonzalez-Zulueta