Patents Examined by Ardin Marschel
  • Patent number: 9404147
    Abstract: The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.
    Type: Grant
    Filed: December 19, 2012
    Date of Patent: August 2, 2016
    Assignee: GEN-PROBE INCORPORATED
    Inventors: Norman C. Nelson, Jijumon Chelliserry
  • Patent number: 9309561
    Abstract: Extended rhodamine compounds exhibiting favorable fluorescence characteristics having the structure are disclosed. In addition, novel intermediates for synthesis of these dyes are disclosed, such intermediates having the structure In addition, methods of making and using the dyes as fluorescent labels are disclosed.
    Type: Grant
    Filed: December 5, 2013
    Date of Patent: April 12, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Joe Y. L. Lam, Scott C. Benson, Steven M. Menchen
  • Patent number: 9284602
    Abstract: Provided herein are primers and primer systems having improved specificity and kinetics over existing primers, and methods of use thereof.
    Type: Grant
    Filed: October 27, 2011
    Date of Patent: March 15, 2016
    Assignee: President and Fellows of Harvard College
    Inventors: David Yu Zhang, Peng Yin
  • Patent number: 9267111
    Abstract: Described herein are methods of treating a female subject in need of in vitro fertilization to become pregnant by detecting a loss of non-atretic follicles in the female subject and providing in vitro fertilization to the female subject.
    Type: Grant
    Filed: January 14, 2011
    Date of Patent: February 23, 2016
    Assignee: The General Hospital Corporation
    Inventors: Jonathan L. Tilly, Joshua Johnson
  • Patent number: 9261518
    Abstract: The application relates to a method for producing a medical bioprosthesis that can be transplanted in a patient and comprises substances from animal tissue, said method comprising a step during which a bioprosthesis is positively selected for implantation in the body of said patient when (i) the phenotype in the ABO/ABH system of said bioprosthesis is compatible with (ii) the phenotype in the ABO/ABH system of said patient.
    Type: Grant
    Filed: October 13, 2010
    Date of Patent: February 16, 2016
    Inventor: Olivier Schussler
  • Patent number: 9255293
    Abstract: The invention provides efficient methods of preparing a target nucleic acid in a form suitable for sequencing. The methods are particularly amenable for preparing high quality nucleic acids for massively parallel sequencing. The methods involve capturing a target nucleic acid from a sample and PCR amplification of the target nucleic acid. The target nucleic acid is captured by binding to a capture probe, which in turn binds to an immobilized probe. The immobilized probe is typically immobilized via a magnetic bead. The captured target nucleic acid is PCR amplified by thermocycling without prior dissociation of the target nucleic acid from the beads. The efficiency of the method lies in part in that both the capture and amplification steps are performed in a single vessel. The amplified nucleic acid can then be sequenced.
    Type: Grant
    Filed: November 1, 2011
    Date of Patent: February 9, 2016
    Assignee: GEN-PROBE INCORPORATED
    Inventors: Reinhold Pollner, Shyun-Shyun Lee
  • Patent number: 9249457
    Abstract: The purpose of the subject invention is to provide a method of manufacturing a mixture of amplified double-stranded nucleic acids comprising unknown sequence including the complete 5? end sequence. A method of manufacturing a mixture of amplified double-stranded nucleic acids comprising: (a) preparing a single-stranded nucleic acid comprising a single-stranded adapter 1, a single-stranded nucleic acid fragment and a single-stranded adapter 2, and (b) conducting PCR with said single-stranded nucleic acid prepared in step (a), a primer 1, and a primer 2 to amplify double-stranded nucleic acids.
    Type: Grant
    Filed: June 18, 2009
    Date of Patent: February 2, 2016
    Assignee: Riken
    Inventors: Piero Carninci, Charles Plessy, Roberto Simone
  • Patent number: 9243272
    Abstract: Disclosed is a thermostable DNA polymerase preparation which can illimitably reduce the risk of false positivity in the detection of a subject microorganism utilizing a gene amplification reaction and therefore enables the selective amplification of DNA for detecting the subject microorganism even when the amount of the subject microorganism is small and therefore the amount of DNA collected therefrom is extremely small, and can be produced at a reduced cost. Also disclosed is a method for quantifying or quantifying/identifying a subject organism to be detected rapidly, conveniently and with high sensitivity using the preparation of the present invention.
    Type: Grant
    Filed: January 15, 2010
    Date of Patent: January 26, 2016
    Assignees: HOKKAIDO MITSUI CHEMICALS INC., NATIONAL UNIVERSITY CORPORATION UNIVERSITY OF TOYAMA
    Inventors: Homare Tabata, Hiroshi Minami, Hideki Niimi, Isao Kitajima, Tomohiro Ueno, Shiroh Hayashi, Masashi Mori
  • Patent number: 9217177
    Abstract: The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages.
    Type: Grant
    Filed: January 9, 2013
    Date of Patent: December 22, 2015
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Patent number: 9212387
    Abstract: Provided is a detection kit for detecting target genes of miRNA. Also provided is a method of detecting target genes of miRNA in a simple manner without the need for performing a transfection operation of a gene into cells via a vector. The detection kit is a detection kit for target genes of microRNA, including a cell extraction reagent, and a labeling reagent for microRNA or labeled microRNA, and further including a reaction reagent for the labeling substance for microRNA. mRNA corresponding to target genes of miRNA can be easily pulled down by producing a cell extract under mild conditions, adding labeled miRNA to the cell extract, and recovering the labeling substance. cDNA is produced from the pulled down mRNA to detect target genes of miRNA.
    Type: Grant
    Filed: June 15, 2011
    Date of Patent: December 15, 2015
    Assignee: National University Corporation Okayama University
    Inventors: Mamoru Ouchida, Sachio Ito
  • Patent number: 9207690
    Abstract: A processing apparatus includes a carrier receiving region configured to receive a sample carrier with at least one channel that carries at least one sample. The apparatus further includes a thermal control device configured to thermal cycle the sample carrier when the sample carrier is installed in the carrier receiving region, thereby thermal cycling the sample carried therein. The apparatus further includes a thermal control system configured to control the temperature control device based on a predetermined set of target sample temperatures and a temperature map, which maps the predetermined set of target sample temperatures to a set of temperatures of the temperature control device. The set of temperatures of the temperature control device is different from the predetermined set of target sample temperatures, and the set of temperatures of the temperature control device thermal cycle the sample carrier with the temperatures of the predetermined set of target sample temperatures.
    Type: Grant
    Filed: September 23, 2011
    Date of Patent: December 8, 2015
    Assignee: Analogic Corporation
    Inventor: Mark Tverskoy
  • Patent number: 9200291
    Abstract: The present invention provides compositions comprising randomized in-frame fusion polynucleotides and methods for introducing them into a host organism to identify desirable phenotypic changes that disrupt or alter existing genetic or biochemical mechanisms or pathways, thus creating novel characteristics of the transformed organism. Methods for using the compositions for increasing diversity within populations of organisms are also presented.
    Type: Grant
    Filed: December 19, 2013
    Date of Patent: December 1, 2015
    Inventor: Helge Zieler
  • Patent number: 9193993
    Abstract: The invention is directed to a method for isothermally amplifying a DNA sequence involving hybridizing a destabilizing DNA template to complementary nucleotide fragments to form a first nicked duplex; ligating the first nicked duplex to form a product duplex comprising the DNA sequence and the template, wherein the product duplex is capable of dissociating to release the DNA sequence and the template; and repeating these steps to generate multiple copies of the template and the DNA sequence. Further, the method may also involve hybridizing the DNA sequence to complementary destabilizing fragments or probes to form a second nicked duplex; ligating the second nicked duplex to form the product duplex comprising the DNA sequence and the template, wherein the product duplex dissociates to release the DNA sequence and the template; and repeating these steps to generate multiple copies of the template and the DNA sequence.
    Type: Grant
    Filed: March 7, 2013
    Date of Patent: November 24, 2015
    Inventors: Julianne M Gibbs-Davis, Rosalie Dawn McKay, Yimeng Li, Jade Lam, Abu Kausar, Catherine Jennifer Mitran
  • Patent number: 9193997
    Abstract: Methods are provided for the detection and analysis of clonality in a cell population, where parallel sequencing is applied to a nucleic acid sample obtained from the cell population, optionally a population of lymphocytes. Replicate samples are amplified, and sequenced, where identification of coincident sequences in two or more replicates is indicative of clonal expansion.
    Type: Grant
    Filed: December 15, 2011
    Date of Patent: November 24, 2015
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Andrew Fire, Scott D. Boyd, Jason Merker, Kyunga Seo, Eleanor L. Marshall
  • Patent number: 9194861
    Abstract: System, including methods, apparatus, compositions, and kits, for the mixing of small volumes of fluid by coalescence of multiple emulsions.
    Type: Grant
    Filed: August 24, 2010
    Date of Patent: November 24, 2015
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Benjamin J. Hindson, Billy W. Colston, Jr., Kevin D. Ness, Donald A. Masquelier
  • Patent number: 9194006
    Abstract: Provided herein are methods for identifying the presence or absence of a target nucleic acid from a microorganism using direct amplification without a step of extraction of the nucleic acids, but retaining substantially the same specificity and sensitivity of methods assaying extracted nucleic acids.
    Type: Grant
    Filed: July 6, 2012
    Date of Patent: November 24, 2015
    Assignee: QUEST DIAGNOSTICS INVESTMENTS INCORPORATED
    Inventors: Maurice Exner, Luca Jacky, Yin-Peng Chen, Huong Mai, Jules Chen, Michelle M. Tabb, Michael Aye, Emberlee Eleazar
  • Patent number: 9187781
    Abstract: The present invention is to provide a method for identifying a polymorphism. The method includes performing a nucleic acid chain extension reaction and identifying the polymorphism of the nucleic acid contained in the test nucleic acid sample. The extension reaction is conducted with use of a nucleic acid in a test nucleic acid sample as a template, a type I detection primer which hybridizes with a region including the polymorphic site of a nucleic acid whose polymorphic site nucleotide sequence consisting of a first nucleotide sequence, and a polymerase. The reaction is conducted with the presence of an inhibitory oligonucleotide, which hybridizes with the type I detection primer. The region of the type I detection primer to hybridize with the inhibitory oligonucleotide is located on the 5? side of the polymorphism detection site of the type I detection primer to hybridize with the polymorphic site.
    Type: Grant
    Filed: April 13, 2010
    Date of Patent: November 17, 2015
    Assignee: OLYMPUS CORPORATION
    Inventor: Tetsuya Tanabe
  • Patent number: 9175349
    Abstract: The present invention provides biomarkers for the diagnosis and prognosis of endometriosis. Generally, the methods of this invention find use in diagnosing or for providing a prognosis for endometriosis by detecting the expression levels of biomarkers, which are differentially expressed (up- or down-regulated) in endometrial cells from a patient with endometriosis. Similarly, these markers can be used to diagnose reduced fertility in a patient with endometriosis or to provide a prognosis for a fertility trial in a patient suffering from endometriosis. The present invention also provides methods of identifying a compound for treating or preventing endometriosis. Finally, the present invention provides kits for the diagnosis or prognosis of endometriosis.
    Type: Grant
    Filed: October 1, 2013
    Date of Patent: November 3, 2015
    Assignee: The Regents of the University of California
    Inventor: Linda C. Giudice
  • Patent number: 9168531
    Abstract: A thermal cycler for a microfluidic device includes a controller operable to provide a series of electrical signals, a heat sink, and a heating element in thermal communication with the heat sink and operable to receive the series of electrical signals from the controller. The thermal cycler also includes a thermal chuck in thermal communication with the heating element. The thermal chuck comprises a heating surface operable to make thermal contact with the microfluidic device. The heating surface is characterized by a temperature ramp rate between 2.5 degrees Celsius per second and 5.5 degrees Celsius per second and a temperature difference between a first portion of the heating surface supporting a first portion of the microfluidic device and a second portion of the heating surface supporting a second portion of the microfluidic device is less than 0.25° C.
    Type: Grant
    Filed: March 26, 2012
    Date of Patent: October 27, 2015
    Assignee: FLUIDIGM CORPORATION
    Inventors: Jake Kimball, Brandon Ripley, Gang Sun, Dominique Toppani, Myo Thu Maung
  • Patent number: 9163277
    Abstract: Microfluidic devices of the present disclosure relate to quick and inexpensive microfluidic manipulation/handling. A number of channels may be provided for supply of fluid ingredients to a number of cavities. A separating material may provide fluid separation between a number of cavities, such as corresponding cavities of a reaction chamber. Once the cavities are supplied with fluid ingredient, channels connecting the cavities may be sealed off; that is, the cavities may be subject to fluid isolation. In some embodiments, a sealing material may be compressed so as to deform into the channels obstructing fluid flow. The separating material may be manipulated so that the initial fluid separation between cavities is removed. Removal of this fluid separation subsequently permits mixing of fluid ingredient(s) contained within previously separated cavities. In some embodiments, the fluid separation may be removed by heating or dissolving portions of the separating material.
    Type: Grant
    Filed: March 14, 2013
    Date of Patent: October 20, 2015
    Assignee: Formulatrix, Inc.
    Inventors: Kabir James Yamana, Sean Yamana-Hayes