Patents Assigned to Applied Biosystems, LLC.
  • Signal noise reduction for imaging in biological analysis
    Patent number: 8482730
    Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
    Type: Grant
    Filed: August 24, 2012
    Date of Patent: July 9, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Austin Tomaney, Mark Oldham
  • Detection of nucleic acid amplification
    Publication number: 20130164748
    Abstract: Methods for detecting a target polynucleotide sequences are provided that utilize a probe having a target-complementary segment and a detectable tag. By cleaving the detectable tab and associating the tag with a tag complement coupled to an electrode, an electrochemical signal can be detected that is related to the presence of the tag:tag complement complex.
    Type: Application
    Filed: October 24, 2012
    Publication date: June 27, 2013
    Applicant: APPLIED BIOSYSTEMS LLC
    Inventor: APPLIED BIOSYSTEMS LLC
  • POLYPEPTIDES HAVING NUCLEIC ACID BINDING ACTIVITY
    Publication number: 20130164817
    Abstract: Polynucleotides 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: Application
    Filed: September 14, 2012
    Publication date: June 27, 2013
    Applicant: APPLIED BIOSYSTEMS LLC
    Inventors: Patrick K. MARTIN, David A. Simpson
  • Electrowetting dispensing devices and related methods
    Patent number: 8470149
    Abstract: A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.
    Type: Grant
    Filed: December 5, 2011
    Date of Patent: June 25, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Charles S. Vann, Debjyoti Banerjee, Timothy G. Geiser, James C. Nurse, Nigel P. Beard
  • Compositions, methods, and kits for amplifying nucleic acids
    Patent number: 8470531
    Abstract: The present teachings are directed to compositions, methods, and kits for amplifying target nucleic acids while reducing non-specific fluorescence and undesired amplification products, sometimes referred to as secondary amplification products or spurious side-products. The enzyme inhibitors disclosed herein comprise a nucleotide sequence and at least one quencher. Complexes comprising an enzyme inhibitor associated with an enzyme, wherein at least one enzymatic activity of the enzyme is inhibited, are also provided. Methods for amplifying a target nucleic acid while reducing undesired amplification products are disclosed, as are methods for reducing non-specific fluorescence. Kits for expediting the performance of certain disclosed methods are also provided.
    Type: Grant
    Filed: December 8, 2009
    Date of Patent: June 25, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Shoulian Dong, Junko Stevens, Danny Lee
  • GRAFT COPOLYMERS, THEIR PREPARATION AND USE IN CAPILLARY ELECTROPHORESIS
    Publication number: 20130153421
    Abstract: The invention relates to graft copolymers, their preparation, and compositions, such as electrophoresis separation media, containing the same; also to ultra-high molecular weight poly(N,N-dimethylacrylamide) (“poly(DMA)”) polymers, their preparation, and compositions, such as electrophoresis separation media, containing the same; and more particularly to supports, such as capillaries, containing these polymers and methods for separating biomolecules, especially polynucleotides, using capillary electrophoresis. The graft copolymers can be prepared by, e.g., grafting polyacrylamide units onto a poly(DMA) backbone. Separation media comprising such graft copolymers or ultra-high molecular weight poly(DMA) polymers yield superior performance in the analysis and separation of biomolecules by capillary electrophoresis.
    Type: Application
    Filed: September 13, 2012
    Publication date: June 20, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Aldrich N.K. LAU
  • Method for direct amplification from crude nucleic acid samples
    Patent number: 8460934
    Abstract: The present teachings relate to improved methods, kits, and reaction mixtures for amplifying nucleic acids. In some embodiments a novel direct buffer formulation is provided which allows for the direct amplification of the nucleic acids in a crude sample with minimal sample purification.
    Type: Grant
    Filed: April 3, 2012
    Date of Patent: June 11, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Chien-Wei Chang, Lori Hennessy, Dennis Wang
  • System and methods for indel identification using short read sequencing
    Patent number: 8463555
    Abstract: Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.
    Type: Grant
    Filed: April 18, 2012
    Date of Patent: June 11, 2013
    Assignee: Applied Biosystems, LLC
    Inventor: Zheng Zhang
  • DEVICE FOR AMPLIFYING TARGET NUCLEIC ACID
    Publication number: 20130143218
    Abstract: A device for amplifying a target nucleic acid in a sample containing one or more target nucleic acids may include a substrate assembly comprising a flow channel and an inlet, wherein the inlet is in flow communication with the flow channel and is configured to introduce sample containing one or more target nucleic acids into the flow channel. The device may further include a plurality of moieties disposed at inner surface regions of the flow channel along at least a portion of a length of the flow channel, each of the plurality of moieties being sufficient to respectively hybridize to the one or more target nucleic acids in the sample to facilitate amplification of the one or more target nucleic acids when hybridized. The device is further configured to retain amplified product of the one or more hybridized target nucleic acids at discrete locations proximate the inner surface regions after amplification.
    Type: Application
    Filed: February 12, 2013
    Publication date: June 6, 2013
    Applicants: HEALTH AND HUMAN SERVICES, UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECR, APPLIED BIOSYSTEMS, LLC
    Inventors: APPLIED BIOSYSTEMS, LLC, HEALTH AND HUMAN SERVICES, UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECR
  • METHODS FOR MULTIPLEXING AMPLIFICATION REACTIONS
    Publication number: 20130143754
    Abstract: A two-step multiplex amplification reaction includes a first step which truncates the standard initial multiplex amplification round to “boost” the sample copy number by only a 100-1000 fold increase in the target. Following the first step the product is divided into optimized secondary single amplification reactions, each containing one of the primer sets that were used previously in the first or multiplexed booster step. The booster step can occur using an aqueous target nucleic acid or using a solid phase archived nucleic acid. In particular, nucleic acid sequences that uniquely identify E. Coli were identified using the multiplex amplification method.
    Type: Application
    Filed: September 14, 2012
    Publication date: June 6, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: John C. GERDES, Elaine Best, Jeffery M. Marmaro
  • CRUDE BIOLOGICAL DERIVATIVES COMPETENT FOR NUCLEIC ACID DETECTION
    Publication number: 20130143275
    Abstract: The invention relates to methods for the detection of a specific sequence of RNA in a cell or tissue sample. The invention also relates to methods to enzymatically manipulate the RNA in a crude cell lysate in a number of applications.
    Type: Application
    Filed: September 14, 2012
    Publication date: June 6, 2013
    Applicant: Applied Biosystems, LLC
    Inventors: Brittan L. PASLOSKE, Quoc Hoang
  • OPTICAL INSTRUMENT COMPRISING MULTI-NOTCH BEAM SPLITTER
    Publication number: 20130143310
    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: Application
    Filed: January 23, 2013
    Publication date: June 6, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Applied Biosystems, LLC
  • Method of automated calibration and diagnosis of laboratory instruments
    Patent number: 8452562
    Abstract: Method and system providing an automated workflow for installing and/or calibrating laboratory equipment. The workflow empowers an end user to perform installation and calibration thereby reducing the costs associated with such activities. The automated workflow taught herein, can greatly reduce the incidence of calibration error by providing for verification of certain events during the calibration process.
    Type: Grant
    Filed: January 27, 2012
    Date of Patent: May 28, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Bruce E. DeSimas, Leslie A. Dow
  • Axial illumination for capillary electrophoresis
    Patent number: 8446588
    Abstract: System and method for fluorescent light excitation and detection from samples to enhance the numerical aperture and/or reduce the cross-talk of the fluorescent light.
    Type: Grant
    Filed: May 7, 2012
    Date of Patent: May 21, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Richard Reel, Eric Nordman
  • Multiplex compositions and methods for quantification of human nuclear DNA and human male DNA and detection of PCR inhibitors
    Patent number: 8445657
    Abstract: The invention relates to a method for simultaneous quantification of human nuclear DNA and human male DNA in a biological sample while also detecting the presence of PCR inhibitors in a single reaction. The multiplex quantification method also provides a ratio of human nuclear and male DNA present in a biological sample. Such sample characterization is useful for achieving efficient and accurate results in downstream molecular techniques such as genotyping.
    Type: Grant
    Filed: August 26, 2011
    Date of Patent: May 21, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Jaiprakash Shewale, Manohar Furtado, Pius Brzoska, Maura Barbisin, Rixun Fang, Michael Malicdem, Cristin O'Shea
  • Pasting edge heater
    Patent number: 8440454
    Abstract: An apparatus and method for thermal cycling including a pasting edge heater. The pasting edge heater can provide substantial temperature uniformity throughout the retaining elements during thermal cycling by a thermoelectric module.
    Type: Grant
    Filed: April 27, 2011
    Date of Patent: May 14, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Hon Siu Shin, Hock Lai Khoo
  • Systems and Methods for Calibration Using Dye Signal Amplification
    Publication number: 20130115611
    Abstract: The present teachings relate to a method of generating calibration information during a real-time polymerase chain reaction (RT-PCR) or other amplification reaction. A sample well plate or other support can contain one or more dyes or other reference materials that are subjected to the same RT-PCR thermal cycles or other conditions used to conduct amplification or other reactions on a biological sample. A set of maxima values and a set of minimum values, and/or other calibration information useful for adjusting emission data for sample dyes can be recorded, for example, for 10 cycles, 20 cycles, or each cycle of a complete RT-PCR run. Such testing of dye response under realistic operating conditions can enable more accurate characterization of plate, dye, filter, or instrument response and therefore more accurate calibration corrections and other and/or adjustments.
    Type: Application
    Filed: November 9, 2012
    Publication date: May 9, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Applied Biosystems, LLC
  • METHOD AND COMPOSITION FOR NUCLEIC ACID AMPLIFICATION
    Publication number: 20130109023
    Abstract: The present teachings provide methods, compositions, and kits for nucleic acid amplification. In some embodiments of the present teachings, amplification reactions are performed with at least one high stability primer. In some embodiments, the present teachings provide a method comprising a high stability primer for amplification of a nucleic acid sequence in a sample comprising a target nucleic acid sequence and a PCR inhibitor.
    Type: Application
    Filed: August 24, 2012
    Publication date: May 2, 2013
    Applicant: APPLIED BIOSYSTEMS LLC
    Inventors: Julio J. Mulero, Lori K. Hennessy
  • HIGH SPEED, HIGH RESOLUTION COMPOSITIONS, METHODS AND KITS FOR CAPILLARY ELECTROPHORESIS
    Publication number: 20130105314
    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: Application
    Filed: September 12, 2012
    Publication date: May 2, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Karl O. VOSS, Aldrich N. LAU
  • HIGH SPEED, HIGH RESOLUTION COMPOSITIONS, METHODS AND KITS FOR CAPILLARY ELECTROPHORESIS
    Publication number: 20130105315
    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: Application
    Filed: September 13, 2012
    Publication date: May 2, 2013
    Applicant: APPLIED BIOSYSTEMS, LLC.
    Inventors: Karl O. VOSS, Aldrich N.K. Lau