Patents Examined by Heather G. Calamita
  • Patent number: 7838235
    Abstract: Provided herein are methods for assaying a biological sample for microorganisms having drug resistant and/or drug sensitive phenotypes, wherein the methods are capable of detecting resistant and sensitive phenotypes associated with known and/or unknown mutations. In some aspects, methods are provided for detecting drug resistant Myobacterium tuberculosis (MTb), including multi-drug resistant MTb, wherein drug resistance is associated with one or more novel mutations. Also provided are systems, kits, and compositions related to such methods.
    Type: Grant
    Filed: March 28, 2008
    Date of Patent: November 23, 2010
    Assignee: Signal Diagnostics
    Inventor: Brian Erich Caplin
  • Patent number: 7811753
    Abstract: The present invention provides methods and kits for repair of degraded DNA which may then be used as a template for efficient amplification by a number of different amplification reactions. The method relies upon a series of enzymatic activities provided by DNA repair enzymes.
    Type: Grant
    Filed: July 14, 2004
    Date of Patent: October 12, 2010
    Assignee: Ibis Biosciences, Inc.
    Inventor: Mark W. Eshoo
  • Patent number: 7803549
    Abstract: The present invention provides methods and compositions for confirming the integrity of primers and other components of amplification reactions, including multiplex amplification reactions.
    Type: Grant
    Filed: July 8, 2008
    Date of Patent: September 28, 2010
    Assignee: Cepheid
    Inventor: David Swenson
  • Patent number: 7803529
    Abstract: This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples.
    Type: Grant
    Filed: September 14, 1999
    Date of Patent: September 28, 2010
    Assignee: Sequenom, Inc.
    Inventors: Charles Cantor, Hubert Köster
  • Patent number: 7759062
    Abstract: The present invention relates to systems, methods and kits for low-level detection of nucleic acids, detecting at least two different viral sequences in a single reaction vessel, and increasing the dynamic range of detection of a viral target nucleic acid in a sample. The present invention also relates to T-structure invasive cleavage assays, as well as T-structure related target dependent non-target amplification methods and compositions. The present invention further relates to methods, compositions, devices and systems for consistent nucleic acid dispensing onto surfaces.
    Type: Grant
    Filed: June 11, 2007
    Date of Patent: July 20, 2010
    Assignee: Third Wave Technologies, Inc.
    Inventors: Hatim Taysir Allawi, Vecheslav A. Elagin, Victor A. Lyamichev, Kwok Wu, Walter Iszczyszyn, Chris Fleming, LuAnne Chehak, Scott M. Law
  • Patent number: 7745119
    Abstract: The present invention relates to methods for detecting the presence or amount of a target polynucleotide. A polynucleotide, target nucleic acid analog, and dye are combined to form a mixture. The optical property of the dye is observed after the mixture is exposed to a stimulating means. Optionally, after the stimulating means is employed, the mixture is compared to a reference value characteristic of the rate of change in the optical property of the dye in a similar mixture containing a known amount of a target polynucleotide/nucleic acid analog hybrid to determine a relative rate of change in the optical property. The change in a property of the mixture after exposure thereof to a stimulating means or the relative rate of change in the optical property of dye in the mixture is correlated with the presence or amount of the specified target polynucleotide in the sample.
    Type: Grant
    Filed: November 21, 2005
    Date of Patent: June 29, 2010
    Assignee: Investigen, Inc.
    Inventors: Heather Koshinsky, Michael S. Zwick, K. Yeon Choi
  • Patent number: 7745136
    Abstract: A method for detecting ribosome inactivating protein (RIP) activity in a sample is provided that involves contacting a sample that contains an RIP with an inventive substrate that is depurinated to form product. The product is hybridized to a template and cleaved by an apurinic/apyrimidinic endonuclease such that releasing the blocked 3? end only in a sample that contains RIP activity. The 5? end of the product serves as a primer for extension by a polymerase reaction. The newly synthesized strand complementary to the template is detected by RT-PCR processes. A kit is provided suitable for field or laboratory use.
    Type: Grant
    Filed: January 30, 2009
    Date of Patent: June 29, 2010
    Assignee: The United States of America as represented by the Secretary of the Army
    Inventor: Russell M. Dorsey
  • Patent number: 7745138
    Abstract: The invention provides a diagnostics assay for measuring the responsiveness to a drug by comparing the mRNA levels of a gene that responds to the drug, such as a steroid, to the mRNA levels of a gene that does not respond to the drug. Methods according to the invention are useful for predicting the ability of a patient (or a tissue, body fluid or cell sample in vitro) to respond to a drug or steroid at any stage of their treatment (i.e., before, during or after), and to monitor the patient (or a tissue, body fluid or cell) over time to assess continued responsiveness to the drug or steroid.
    Type: Grant
    Filed: May 11, 2009
    Date of Patent: June 29, 2010
    Assignee: The Trustees of the University of Pennsylvania
    Inventor: Alexander Steven Whitehead
  • Patent number: 7745135
    Abstract: A method for detecting the occurrence of nucleic acid syntheses using an enzyme through the use of a generated insoluble substance as an indicator.
    Type: Grant
    Filed: April 21, 2008
    Date of Patent: June 29, 2010
    Assignee: Eiken Kagaku Kabushiki Kaisya
    Inventors: Yasuyoshi Mori, Kentaro Nagamine
  • Patent number: 7741031
    Abstract: A coding scheme for microcarriers suitable for use in distributed arrays includes labeling the carriers with quenched signaling hairpin molecules with any one of three to eight distinguishable fluorophores wherein the hairpins are of at least two types, most preferably three types, that open and fluoresce differentially as a chemical or physical condition, for example temperature, is changed. Mixtures of microcarriers having immobilized capture probes can be decoded by measuring fluorescence from said fluorophores under conditions under which only one type of hairpin is open, under which two types of hairpin are open, and so on. Mixtures of coded microcarriers with capture probes are used in assays for nucleic acids utilizing microarray methods.
    Type: Grant
    Filed: March 2, 2004
    Date of Patent: June 22, 2010
    Assignee: The Public Health Research Institute of the City of New York
    Inventors: Fred R. Kramer, Sanjay Tyagi, Salvatore A. E. Marras, Hiyam Elhajj Trunfio
  • Patent number: 7741043
    Abstract: Methods of identifying therapeutic agents that inhibit, potentiate or mimic the ability of a km23 polypeptide mutant form, or a nucleic acid encoding the mutant form to modulate the signal transduction activity of a growth factor or cytokine are provided. The methods involve treating a cell with a candidate compound so as to alter at least one cell process associated with the TGF? signaling pathway, and measuring the effect of the candidate on the cell. Further provided are cell and non-cell based methods of screening for a therapeutic agent that inhibits or stimulates the interaction of an altered form of wild-type km23 with a specific binding protein, such as the dynein intermediate chain (DIC), Smad2 or RI and RII TGF? receptors. These methods involve determining the inhibition or stimulation of a therapeutic candidate on the interaction of the specific binding protein with the km23 altered form.
    Type: Grant
    Filed: January 3, 2007
    Date of Patent: June 22, 2010
    Inventor: Kathleen M. Mulder
  • Patent number: 7736850
    Abstract: The invention relates to a novel strain of severe acute respiratory syndrome (SARS)-associated coronavirus, resulting from a sample collected in Hanoi (Vietnam), reference number 031589, nucleic acid molecules originating from the genome of same, proteins and peptides coded by said nucleic acid molecules and, more specifically, protein N and the applications thereof, for example, as diagnostic reagents and/or as a vaccine.
    Type: Grant
    Filed: December 2, 2004
    Date of Patent: June 15, 2010
    Assignees: Institute Pasteur, Centre National de la Recherche Scientifique, Universite Paris 7
    Inventors: Sylvie Van Der Werf, Nicolas Escriou, Bernadette Crescenzo-Chaigne, Jean-Claude Manuguerra, Frederick Kunst, Benoît Callendret, Jean-Michel Betton, Valérie Lorin, Sylvie Gerbaud, Ana Maria Burguiere, Saliha Azebi, Pierre Charneau, Frédéric Tangy, Chantal Combredet, Jean-François Delagneau, Monique Martin
  • Patent number: 7727722
    Abstract: Provided herein are methods and agents for ligation-based exponential ribonucleic acid amplification followed by detection using a nucleic acid polymerization reaction employing terminal-phosphate-labeled nucleotides including three or more phosphates as substrates for nucleic acid polymerase.
    Type: Grant
    Filed: January 8, 2007
    Date of Patent: June 1, 2010
    Assignee: General Electric Company
    Inventors: John Richard Nelson, Robert Scott Duthie
  • Patent number: 7723041
    Abstract: Primers and probes derived from SARS-CoV nucleic acid that facilitate detection and/or quantification of the replicase gene are disclosed. The disclosed sequences may be used in a variety of amplification and non-amplification formats for detection of SARS-CoV infection.
    Type: Grant
    Filed: February 3, 2009
    Date of Patent: May 25, 2010
    Assignee: Becton, Dickinson and Company
    Inventors: Jianrong Lou, James A. Price, Jr., Daretta A. Yursis, David M. Wolfe, Lisa M. Keller, Tobin Hellyer
  • Patent number: 7713700
    Abstract: An object of the present invention is to provide a nucleic acid amplification method for amplifying a desired nucleic acid while suppressing amplification of byproducts in a PCR reaction, a reagent kit used for nucleic acid amplification, a method of detecting single nucleotide polymorphism to detect single nucleotide polymorphism by utilizing that amplification of byproducts is suppressed in a PCR reaction, and a reagent kit used for detecting single nucleotide polymorphism. The method of amplifying nucleic acids by PCR is characterized by admixing in a reaction solution, a homologous recombinant protein which contains at least one of a RecA protein derived from Thermus thermophilus, and a modified RecA protein obtained by modification of the RecA protein and having a function similar to that of the RecA protein, and carrying out PCR.
    Type: Grant
    Filed: April 3, 2008
    Date of Patent: May 11, 2010
    Assignees: Aisin Cosmos R&D Co., Ltd., Riken, Kazusa DNA Research Institute
    Inventors: Yasushi Shigemori, Takehiko Shibata, Tsutomu Mikawa, Michio Oishi, Osamu Ohara
  • Patent number: 7704693
    Abstract: Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays, systems, methods and kits for the age determination of an individual from bloodstains or samples of unknown origin. The methodology is based on gene expression profiling analysis in which novel human newborn fetal specific genes are identified by detecting the presence of appropriate messenger RNA species.
    Type: Grant
    Filed: May 25, 2007
    Date of Patent: April 27, 2010
    Assignee: University of Central Florida Research Foundation, Inc.
    Inventors: John Ballantyne, Michelle Alvarez
  • Patent number: 7700275
    Abstract: A method for detecting the presence of a target nucleic acid sequence in a sample, said method comprising: performing nucleic acid amplification on the sample in the presence of (a) a DNA duplex binding agent, (b) a nucleic acid polymerase and (c) a reagent comprising an amplification primer which can hybridize to said target sequence when in single stranded form and which is connected at its 5? end to a probe which carries a label by way of a chemical linking group, said labeled probe being of a sequence which is similar to that of the said target nucleic acid sequence, such that it can hybridize to a complementary region in an amplification product, and wherein the label is able to absorb fluorescence from or donate fluorescent energy to the DNA duplex binding agent; and monitoring fluorescence of said sample.
    Type: Grant
    Filed: May 24, 2002
    Date of Patent: April 20, 2010
    Assignee: The Secretary of State of Defense
    Inventor: Martin Alan Lee
  • Patent number: 7700283
    Abstract: Methods and compositions are provided for repairing a polynucleotide so that it can be synthesized efficiently with improved fidelity and yield in, for example, an amplification reaction. This involves the use of a reaction mixture that includes a ligase and a cofactor selected from NAD+ or ATP and incubating the polynucleotide with the reaction mixture in the absence of Endonuclease VI. The reaction mixture may further contain an AP endonuclease and a polymerase. These enzymes are optionally selected according to their ability to withstand high temperatures so they can be included in an amplification mixture. The reaction mixture may be used prior to a polynucleotide synthesis reaction in which case enzymes that are not thermophilic may be used. The repair reaction is not time sensitive with respect to seconds, minutes or hours of incubation in the enzyme mixture.
    Type: Grant
    Filed: October 20, 2005
    Date of Patent: April 20, 2010
    Assignee: New England Biolabs, Inc.
    Inventors: Thomas C. Evans, Barton Slatko, Lixin Chen, Romaldas Vaisvila, Chudi Guan
  • Patent number: 7695904
    Abstract: The present invention provides for compositions and methods for amplifying target nucleic acids using nucleic acid primers designed to limit non-target nucleic acid dependent priming events. The present invention permits amplifying and quantitating the number of repetitive units in a repetitive region, such as the number of telomere repetitive units.
    Type: Grant
    Filed: January 31, 2003
    Date of Patent: April 13, 2010
    Assignee: University of Utah Research Foundation
    Inventor: Richard M Cawthon
  • Patent number: 7695905
    Abstract: The present invention relates to magnetic fine particles having a lower critical solution temperature to which at least one substance selected from biotin and avidin is immobilized, and a method of converting a substance, a method of separating or concentrating a microorganism, a method of modifying a denatured protein, a method of detecting a nucleic acid, a separating agent, and a method of separating a biological substance using the same.
    Type: Grant
    Filed: August 20, 2001
    Date of Patent: April 13, 2010
    Assignees: National Institute of Advanced Industrial Science and Technology, Chisso Corporation
    Inventors: Hirotaka Furukawa, Noriyuki Ohnishi, Kazunori Kataoka, Katsuhiko Ueno