Patents Assigned to Applied Biosystems, LLC.
  • Sample Preparation for in Situ Nucleic Acid Analysis, Methods and Compositions Therefor
    Publication number: 20140127692
    Abstract: Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.
    Type: Application
    Filed: December 20, 2013
    Publication date: May 8, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: RICHARD FEKETE, ANNALEE NGUYEN
  • Method of Automated Calibration and Diagnosis of Laboratory Instruments
    Publication number: 20140122006
    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: Application
    Filed: September 10, 2013
    Publication date: May 1, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Bruce E. DeSimas, Leslie A. Dow
  • Method to quantify siRNAs, miRNAs and polymorphic miRNAs
    Patent number: 8710208
    Abstract: The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3? end of a target polynucleotide, using a ligase that can ligate the 3? end of RNA to the 5? end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleotides that vary by as little as one nucleotide.
    Type: Grant
    Filed: April 26, 2012
    Date of Patent: April 29, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Ruoying Tan, Caifu Chen, Karl J. Guegler
  • DETECTION AND MIXING IN A CONDUIT IN INTEGRATED BIOANALYSIS SYSTEMS
    Publication number: 20140113298
    Abstract: Apparatuses and methods in which detection is integrated with various liquid processing and environmental control functions to create integrated bioanalysis systems are disclosed. Though the various integrated bioanalysis systems are useful for any number of analysis formats, they are adaptable to high-throughput processing of samples.
    Type: Application
    Filed: September 13, 2013
    Publication date: April 24, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Charles S. Vann
  • Multi-Chromophoric Quencher Constructs for Use in High Sensitivity Energy Transfer Probes
    Publication number: 20140114048
    Abstract: Dark quencher constructs, termed “multi-chromophoric quenchers” are described herein that comprise at least two dark quenching moieties, which can be the same or different, linked together by at least one multivalent linking moiety. The structure of the multi-chromophoric quenchers can be varied to selectively enhance quenching within a specific range of reporter emission wavelengths, to quench a broader range of reporter emission wavelengths than previously possible, or can combine both concepts. Multiple types of quenching moieties can be employed to increase the absorption range and a multiple number of each type of quenching moiety can be used to increase the total absorptivity within the absorption range. The multi-chromophoric quenchers can be tethered to probes for biomolecules, insoluble supports and/or fluorescent dyes for use in a wide variety of biomolecular assays.
    Type: Application
    Filed: October 15, 2013
    Publication date: April 24, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Scott BENSON, Steven MENCHEN, Krishna UPADHYA
  • Nanowire-based system for analysis of nucleic acids
    Patent number: 8703497
    Abstract: A system and method for analyzing nucleic acids is presented herein. The system can include a nanowire assembly including a plurality of nanowires. In some embodiments, at least two nanowires can be coupled to a different probe corresponding to a different sequence version of a polymorphism. The system can include a reagent delivery system capable of delivering a template polymorphic nucleotide, an extension nucleic acid, and an enzyme to the nanowire assembly. The system can include an electrical detector configured to measure an electrical characteristic of the nanowire assembly and/or a controller in communication with the reagent delivery system. In some embodiments, the electrical detector can be configured to collect data corresponding to changes in the electrical characteristic in response to contact with the template polymorphic nucleotide, the extension nucleic acid, and the enzyme.
    Type: Grant
    Filed: June 4, 2012
    Date of Patent: April 22, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Hongye Sun, Steven Fung, Sam Woo
  • Microfluidic Size-Exclusion Devices, Systems, and Methods
    Publication number: 20140106364
    Abstract: Microfluidic devices, assemblies, and systems are provided, as are methods of manipulating micro-sized samples of fluids. Microfluidic devices having a plurality of specialized processing features are also provided.
    Type: Application
    Filed: December 20, 2013
    Publication date: April 17, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Sean M. Desmond, Zbigniew T. Bryning, John S. Shigeura, Gary Lim, Adrian Fawcett, Jacob K. Freudenthal, Gary Bordenkircher
  • Methods And Kits For Multiplex Amplification Of Short Tandem Repeat Loci
    Publication number: 20140106353
    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: October 14, 2013
    Publication date: April 17, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Lori Hennessy, Robert Green
  • Surface Tension Controlled Valves
    Publication number: 20140102571
    Abstract: The present teachings relate to surface tension controlled valves used for handling biological fluids. The valves controlled by optically actuating an electrowetting circuit.
    Type: Application
    Filed: October 11, 2013
    Publication date: April 17, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Sergey V. Ermakov
  • Automatic Threshold Setting and Baseline Determination for Real-Time PCR
    Publication number: 20140106978
    Abstract: The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated.
    Type: Application
    Filed: October 7, 2013
    Publication date: April 17, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC.
    Inventors: David C. Woo, Clinton Lewis, Nasser M. Abbasi
  • Computer Algorithm for Automatic Allele Determination from Fluorometer Genotyping Device
    Publication number: 20140108411
    Abstract: The present invention provides methods and systems for an automated method of identifying allele values from data files derived from processed fluorophore emissions detected during the observation of fluorophore labeled nucleotide probes used in analyzing polymorphic DNA are provided. These methods are used in the rapid and efficient distinguishing of targeted polymorphic DNA sites without control samples.
    Type: Application
    Filed: October 9, 2013
    Publication date: April 17, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Stephen A. Glanowski, Jeremy Heil, Emily S. Winn-Deen, Ivy A. McMullen
  • Sequencing system with memory
    Patent number: 8697004
    Abstract: The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, per, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory.
    Type: Grant
    Filed: May 19, 2010
    Date of Patent: April 15, 2014
    Assignee: Applied Biosystems, LLC
    Inventor: Jeffery D. Frazier
  • Sample Substrate Having a Divided Sample Chamber and Method of Loading Thereof
    Publication number: 20140096625
    Abstract: A sample substrate configured for samples of biological material is provided. The sample substrate has a dual chambered sample well separated by a wall that may be punctured or otherwise breached to allow mixing of material contained in the two initially separate chambers. The chambers are connected by channels to fluid reservoirs, wherein the channels can be staked to prevent further fluid flow into and out of the chambers. Methods of loading a sample substrate are also provided.
    Type: Application
    Filed: December 11, 2013
    Publication date: April 10, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: Donald R. SANDELL
  • HIGH POTENCY SIRNAS FOR REDUCING THE EXPRESSION OF TARGET GENES
    Publication number: 20140099715
    Abstract: The present invention provides improved methods of attenuating gene expression through the phenomenon of RNA interference. The invention provides methods of synthesis of double stranded RNAs (dsRNAs) of increased potency for use as small interfering RNA (siRNA). Surprisingly and unexpectedly, siRNAs made by the methods of the invention are significantly more potent than previously available siRNAs.
    Type: Application
    Filed: August 21, 2013
    Publication date: April 10, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: David Brown, Lance P. Ford, Vince Pallotta, Brittan L. Pasloske, Richard A. Jarvis
  • High Speed, High Resolution Compositions, Methods and Kits for Capillary Electrophoresis
    Publication number: 20140090980
    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: August 23, 2013
    Publication date: April 3, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Karl O. VOSS, Aldrich N.K. LAU
  • Method of Automated Calibration and Diagnosis of Laboratory Instruments
    Publication number: 20140095099
    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: Application
    Filed: April 30, 2013
    Publication date: April 3, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventor: APPLIED BIOSYSTEMS, LLC
  • Axial Illumination for Capillary Electrophoresis
    Publication number: 20140091233
    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: Application
    Filed: September 20, 2013
    Publication date: April 3, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Richard REEL, Eric Nordman
  • Devices and Methods for Flow Control in Microfluidic Structures
    Publication number: 20140090716
    Abstract: An apparatus for controlling flow in a fluid flow path can include a chamber containing an expandable material, the expandable material being configured to expand out of the chamber into a portion of the fluid flow path so as to at least partially block the fluid flow path. The apparatus also can include at least one structure providing flow communication between the chamber and the fluid flow path. The at least one structure can be configured to pass the expandable material from the chamber to the portion of the fluid flow path during expansion so as to control a rate at which the expandable material expands into the portion of the fluid flow path.
    Type: Application
    Filed: September 19, 2013
    Publication date: April 3, 2014
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: James C. Nurse, John R. Van Camp
  • SiRNA Sequence-Independent Modification Formats for Reducing Off-Target Phenotypic Effects in RNAi, and Stabilized Forms Thereof
    Publication number: 20140094501
    Abstract: Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.
    Type: Application
    Filed: August 23, 2013
    Publication date: April 3, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Nitin PURI, Irudaya CHARLES, Susan MAGDALENO, Alexander VLASSOV, Christopher BURNETT
  • Thermal cycler for PCR
    Patent number: 8685717
    Abstract: An apparatus comprising an assembly and a cover. The assembly comprises a sample block configured to receive a microtiter tray having a plurality of vials, each vial comprising a cap having a surface and a perimeter. The cover comprises a platen, vertically and horizontally displaceable in relationship to the sample block, the platen having a plurality of recesses. Each recess corresponds to a respective vial and is shaped and arranged to clear the surface of its respective cap when the cover is displaced onto the sample block. The cover includes a skirt in contact with and surrounding a perimeter of the platen. The skirt is configured for mating with a perimeter of a microtiter tray when a microtiter tray is received in the sample block, and also configured such that the cover contacts a microtiter tray when a microtiter tray is received in the sample block.
    Type: Grant
    Filed: January 17, 2007
    Date of Patent: April 1, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: John G. Atwood, Adrian Fawcett, Keith S. Ferrara, Paul M. Hetherington, Richard W. Noreiks, Douglas E. Olsen, John R. Widomski, Charles M. Wittmer