Patents Assigned to Applied Biosystems, LLC.
  • Fluid processing device including size-changing barrier
    Patent number: 8383062
    Abstract: A diagnostic device is provided that includes a plurality of retainment regions interconnected through at least one fluid processing passageway or separated by at least one barrier. A fluid flow modulator can be provided in the fluid processing passageway if a fluid processing passageway is provided. The barrier and/or fluid flow modulator can comprise a polysaccharide, a derivative of a polysaccharide, or a combination thereof. For example, the barrier can comprise a chitosan material.
    Type: Grant
    Filed: November 12, 2010
    Date of Patent: February 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Umberto Ulmanella, Debjyoti Banerjee, Konrad Faulstich, Aldrich Lau, Jun Xie
  • Luminescence reference standards
    Patent number: 8373854
    Abstract: The present teachings provide for systems, and components thereof, for detecting and/or analyzing light. These systems can include, among others, optical reference standards utilizing luminophores, such as nanocrystals, for calibrating, validating, and/or monitoring light-detection systems, before, during, and/or after sample analysis.
    Type: Grant
    Filed: June 10, 2010
    Date of Patent: February 12, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: J. Michael Phillips, Kevin S. Bodner, Aldrich N. K. Lau, Steven J. Boege, Mark F. Oldham, Donald R. Sandell, David H. Tracy
  • High speed, high resolution compositions, methods and kits for capillary electrophoresis
    Patent number: 8366900
    Abstract: The invention provides compositions, methods and kits for high speed, high resolution of analytes by capillary electrophoresis starting with uncoated capillaries. The compositions comprise a sieving component, comprising a non-crosslinked acrylamide polymer, and a surface interaction component, comprising at least one uncharged and non-crosslinked water-soluble silica-adsorbing polymer. Methods for employing the novel compositions in capillary electrophoresis are provided. Kits comprising the novel compositions for use in the novel methods are also provided.
    Type: Grant
    Filed: March 16, 2010
    Date of Patent: February 5, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Karl O. Voss, Aldrich N. K. Lau
  • Recombinant reverse transcriptases
    Patent number: 8361754
    Abstract: The present invention relates to a gene that encodes a hyperactive reverse transcriptase having DNA polymerase activity and substantially reduced RNase H activity, vectors containing the gene and host cells transformed with the invention. The present invention also includes a method of producing the hyperactive reverse transcriptase, producing cDNA from mRNA using the reverse transcriptase of the invention, kits and assay templates made using the hyperactive reverse transcriptase.
    Type: Grant
    Filed: September 28, 2009
    Date of Patent: January 29, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Liangjing Chen, Robert A. Setterquist, Gary Latham
  • Device and method for making discrete volumes of a first fluid in contact with a second fluid, which are immiscible with each other
    Patent number: 8361807
    Abstract: Various embodiments described in the application relate to an apparatus, system, and method for generating, within a conduit, discrete volumes of one or more fluids that are immiscible with a second fluid. The discrete volumes can be used for biochemical or molecular biology procedures involving small volumes, for example, microliter-sized volumes, nanoliter-sized volumes, or smaller. The system can comprise an apparatus comprising at least one conduit operatively connected to one or more pumps for providing discrete volumes separated from one another by a fluid that is immiscible with the fluid(s) of the discrete volumes, for example, aqueous immiscible-fluid-discrete volumes separated by an oil.
    Type: Grant
    Filed: March 22, 2011
    Date of Patent: January 29, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Willy Wiyatno, Linda Lee, David Cox, Richard Reel, Mark Oldham, Jim Nurse, Douglas Greiner, Dennis Lehto, Janusz Wojtowicz, Sam Woo
  • Optical instrument comprising multi-notch beam splitter
    Patent number: 8361785
    Abstract: An instrument is provided that can monitor nucleic acid sequence amplification reactions, for example, PCR amplification of DNA and DNA fragments. The instrument includes a multi-notch filter disposed along one or both of an excitation beam path and an emission beam path. Methods are also provided for monitoring nucleic acid sequence amplifications using an instrument that includes a multi-notch filter disposed along a beam path.
    Type: Grant
    Filed: January 26, 2009
    Date of Patent: January 29, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Mark F. Oldham, Eugene F. Young
  • Optoelectronic separation of biomolecules
    Patent number: 8357282
    Abstract: The present teachings relate to systems and methods for separation of substances such as cells, nucleic acids, and carbon nanotubes. The substances are combined with a separation medium in a liquid sample cavity, for example a microchannel, and transit through the separation by optically activated dielectrophoretic forces. The substances are advantageously labeled and visualized using a microscope and camera.
    Type: Grant
    Filed: November 20, 2009
    Date of Patent: January 22, 2013
    Assignee: Applied Biosystems, LLC
    Inventor: Aldrich N. K. Lau
  • Method and system for genotyping samples in a normalized allelic space
    Patent number: 8359166
    Abstract: Aspects of the present invention describe an apparatus and method for generating genotype calls for a sample. The genotyping initially models allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation. The model and parameters are then used to transform the allelic signals to a normalized normalized allelic space that serves to compensate for the one or more sources of systematic variation. By compensating for the systematic variation in this manner, the genotype for the sample is readily determined based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model.
    Type: Grant
    Filed: August 31, 2009
    Date of Patent: January 22, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Mark R. Pratt, David P. Holden
  • METHODS AND KITS FOR MULTIPLEX AMPLIFICATION OF SHORT TANDEM REPEAT LOCI
    Publication number: 20130012406
    Abstract: Methods and materials are disclosed for use in simultaneously amplifying at least 11 specific STR loci of genomic DNA in a single multiplex reaction, as are methods and materials for use in the analysis of the products of such reactions. Included in the present invention are materials and methods for the simultaneous amplification of 16 specific loci in a single multiplex reaction, comprising the 10 AmpFlSTR® SGMplus® STR loci, the Amelogenin locus, and 5 new STR loci, including methods and materials for the analysis of these loci.
    Type: Application
    Filed: June 21, 2012
    Publication date: January 10, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Lori K. HENNESSY, Robert Green
  • Polypeptides having nucleic acid binding activity
    Patent number: 8349600
    Abstract: Polypeptides having nucleic acid binding activity are provided. Methods of stabilizing a nucleic acid duplex are provided. Methods of promoting the annealing of complementary nucleic acid strands are provided. Methods of increasing the processivity of a DNA polymerase are provided. Methods of enhancing the activity of a nucleic acid modification enzyme are provided. Fusion proteins are provided. Methods of using fusion proteins are provided. Kits are provided.
    Type: Grant
    Filed: January 6, 2006
    Date of Patent: January 8, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Patrick K. Martin, David A. Simpson
  • EXPRESSION SIGNATURE IN PERIPHERAL BLOOD FOR DETECTION OF AORTIC ANEURYSM
    Publication number: 20130006342
    Abstract: We hypothesized that gene expression patterns in peripheral blood cells may correlate with TAA disease status, and carried out a comprehensive gene expression survey on peripheral blood cells obtained from TAA patients and normal individuals. A distinct gene expression profile in peripheral blood cells can classify TAA patients from normal individuals. The genes provided by the present teachings define a set of diagnostic markers, thus providing a blood-based gene expression test to facilitate early detection of TAA disease. Methods of distinguishing ascending from descending TAA are also provided, as are methods of distinguishing familial from sporadic TAA.
    Type: Application
    Filed: September 12, 2012
    Publication date: January 3, 2013
    Applicant: Applied BioSystems, LLC
    Inventors: Yulei WANG, Catalin Barbacioru, Raymond R. Samaha, John A. Elefteriades
  • Preparation and isolation of 5? capped MRNA
    Patent number: 8344118
    Abstract: The synthesis of capped/tagged RNA, methods of use and kits providing same are contemplated. Tagged RNA permits isolation of RNA transcripts in vitro. The ability to isolate and purify capped RNA results in improved transcription and translation and provides a tool for identifying RNA-protein interactions. Such capped RNA finds use in therapeutic applications, diagnosis and prognosis and in the treatment of cancers and HIV.
    Type: Grant
    Filed: December 13, 2011
    Date of Patent: January 1, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Anilkumar Kore, Shanmugasundaram Muthian, Irudaya Charles
  • Sample distribution devices and methods
    Patent number: 8337777
    Abstract: A device and methods for sample distribution through a channel in which an expandable valve provides a mechanism to regulate flow through the channel. The valve may be configured to exert a force on a membrane layer so as to substantially block a portion of the channel to retain the sample in a desired location and prevent flow past the valve mechanism between the channel and a chamber.
    Type: Grant
    Filed: June 25, 2007
    Date of Patent: December 25, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: James C. Nurse, Douglas P. Greiner, Nigel P. Beard
  • Reagents, methods, and libraries for bead-based sequencing
    Patent number: 8329404
    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 immobilized beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages.
    Type: Grant
    Filed: March 2, 2012
    Date of Patent: December 11, 2012
    Assignee: Applied Biosystems LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Polyelectrolyte-Coated Size-Exclusion Ion-Exchange Particles
    Publication number: 20120305838
    Abstract: A polyelectrolyte-coated particle, devices for using the particle, methods for using the particle for separating PCR reaction products and/or DNA sequencing reaction products, and compositions for coating the particle are provided.
    Type: Application
    Filed: June 5, 2012
    Publication date: December 6, 2012
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Michael P. Harrold, Aldrich N.K. Lau, Ben F. Johnson, Gilbert P. Amparo, Frank W. Mercer
  • Multiplex amplification of polynucleotides
    Patent number: 8323897
    Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.
    Type: Grant
    Filed: November 26, 2003
    Date of Patent: December 4, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Mark R. Andersen, David W. Ruff
  • METHODS FOR PLACING, ACCEPTING, AND FILLING ORDERS FOR PRODUCTS AND SERVICES
    Publication number: 20120303472
    Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.
    Type: Application
    Filed: April 27, 2012
    Publication date: November 29, 2012
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Ryan T. KOEHLER, Kenneth J. LIVAK, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Janet S. ZIEGLE, Julie WILLIAMS, Dawn MADDEN, Dennis A. GILBERT, Charles R. SCAFE, Hadar I. Isaac, Yu N. WANG, Eugene G. SPIER, Xiaoqing YOU, Lily XU, Jeremy HEIL, Stephen GLANOWSKI, John SCOTT, Emily S. WINN-DEEN, Ivy MCMULLEN, Lini WU, Harold Carey GIRE, Michael W. HUNKAPILLER, Susan EDDINS, Leila G. SMITH
  • nucleic acid polymerases
    Patent number: 8318469
    Abstract: The invention provides nucleic acids and polypeptides for nucleic acid polymerases from a thermophilic organism, Thermus brockianus. The invention also provides methods for using these nucleic acids and polypeptides.
    Type: Grant
    Filed: December 13, 2005
    Date of Patent: November 27, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: James E. Rozzelle, Elena V. Bolchakova
  • POLYELECTROLYTE-COATED SIZE-EXCLUSION ION-EXCHANGE PARTICLES
    Publication number: 20120292244
    Abstract: A polyelectrolyte-coated particle, devices for using the particle, methods for using the particle for separating PCR reaction products and/or DNA sequencing reaction products, and compositions for coating the particle are provided.
    Type: Application
    Filed: June 4, 2012
    Publication date: November 22, 2012
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Michael P. Harrold, Aldrich N.K. Lau
  • Dissolvable valve in a fluid processing device
    Patent number: 8312890
    Abstract: A fluid processing device, system, and method for processing a fluid, are provided. The device includes a substrate, a plurality of fluid retainment regions formed in or on the substrate, and a barrier at least partially separating two or more of the fluid retainment regions, wherein the barrier can include a solvent-dissolvable, LCST-free material.
    Type: Grant
    Filed: October 18, 2005
    Date of Patent: November 20, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Aldrich N. K. Lau