Patents Assigned to Applied Biosystems, LLC.
  • Patent number: 9914123
    Abstract: A cover for a biological sample well tray, comprising a cap for sealing a sample well. The cap comprises a well lens for focusing light into the sample well and collecting light from the sample. In another aspect, the cap comprises an elongate portion configured to permit incoming light to pass into the sample well and out of the sample well. Various other aspects comprise a microcard for biological material, and an apparatus for a plurality of sample well strips. A method for testing a biological sample is also provided.
    Type: Grant
    Filed: November 2, 2015
    Date of Patent: March 13, 2018
    Assignee: Applied Biosystems, LLC
    Inventors: Eugene F. Young, Steven J. Boege, Donald R. Sandell
  • Patent number: 9914125
    Abstract: The invention relates to a device for carrying out chemical or biological reactions, having a reaction vessel receiving element for receiving a microtiter plate with several reaction vessels, where the reaction vessel receiving element has several recesses arranged in a regular pattern to receive the respective reaction vessels, a treating device for heating the reaction vessel receiving element, and a cooling device for cooling the reaction vessel receiving element. The reaction vessel receiving element is divided into several segments so that the individual segments are thermally decoupled from one another, and each segment is assigned a heating device which can be actuated independently of the others. By means of the segmentation of the reaction vessel receiving element, it is possible for zones to be set and held at different temperatures.
    Type: Grant
    Filed: September 30, 2013
    Date of Patent: March 13, 2018
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Wolfgang Heimberg, Thomas Herrmann, Matthias Knulle, Markus Schurf, Tilmann Wagner
  • Publication number: 20180057516
    Abstract: The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.
    Type: Application
    Filed: September 1, 2017
    Publication date: March 1, 2018
    Applicant: Applied Biosystems, LLC
    Inventors: Scott C. Benson, Ruiming N. Zou, Krishna G. Upadhya, Paul M. Kenney, Jonathan M. Cassel
  • Patent number: 9889448
    Abstract: A thermal cycling device for performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray. The thermal cycling device includes a sample block assembly, an optical detection system, and a sample well tray holder configured to hold the sample well tray. The sample block assembly is adapted for movement between a first position permitting the translation of the sample well tray into alignment with sample block assembly, and a second position, upward relative to the first position, where the sample block assembly contacts the sample well tray. A method of performing nucleic acid amplification on a plurality of biological samples positioned in a sample well tray in a thermal cycling device is also provided.
    Type: Grant
    Filed: March 2, 2015
    Date of Patent: February 13, 2018
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventor: Donald R. Sandell
  • Patent number: 9855558
    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 30, 2013
    Date of Patent: January 2, 2018
    Assignee: APPLIED BIOSYSTEM, LLC
    Inventors: Hon Siu Shin, Hock Lai Khoo
  • Publication number: 20170356877
    Abstract: The invention relates generally to polymers and copolymers comprising N-vinylamide-type monomers, their preparation, and compositions, such as electrophoresis separation media, containing the same; to supports, such as capillaries, containing these polymers; and methods for separating a mixture of biomolecules, especially polynucleotides, using capillary electrophoresis. Separation media comprising such polymers yield advantageous performance in the analysis and separation of biomolecules by capillary electrophoresis.
    Type: Application
    Filed: May 15, 2017
    Publication date: December 14, 2017
    Applicant: Applied Biosystems, LLC
    Inventor: Aldrich N.K. Lau
  • Patent number: 9834816
    Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.
    Type: Grant
    Filed: March 6, 2017
    Date of Patent: December 5, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventor: R. Scott Kuersten
  • Patent number: 9822395
    Abstract: Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5? end tag and 3? end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence.
    Type: Grant
    Filed: March 21, 2016
    Date of Patent: November 21, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Douglas Smith, Joel Malek, Kevin McKernan
  • Patent number: 9822405
    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: June 26, 2015
    Date of Patent: November 21, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Mark Andersen, David Ruff
  • Patent number: 9783560
    Abstract: The present disclosure provides reagents that can be used to label synthetic oligonucleotides with rhodamine dyes or dye networks that contain rhodamine dyes.
    Type: Grant
    Filed: May 1, 2015
    Date of Patent: October 10, 2017
    Assignee: Applied Biosystems, LLC
    Inventors: Scott C. Benson, Ruiming N. Zou, Krishna G. Upadhya, Paul M. Kenney, Jonathan M. Cassel
  • Patent number: 9784563
    Abstract: Systems and methods are provided that comprise calibration techniques and associated systems that identify the two-dimensional position, or other alignment or positioning, of sample wells or other calibration objects located in a sample well plate, or other surface or area of interest. In some embodiments, calibration of the plate and/or positioning and/or alignment with respect to detection optics can be performed in multiple stages for two or more dimensions.
    Type: Grant
    Filed: September 3, 2010
    Date of Patent: October 10, 2017
    Assignee: Applied Biosystems, LLC
    Inventors: Alan R. Stanford, David C. Woo, John David Morgenthaler
  • Patent number: 9776187
    Abstract: An instrument for performing highly accurate PCR employing an assembly, a heated cover, and an internal computer, is provided. The assembly is made up of a sample block, a number of Peltier thermal electric devices, and a heat sink, clamped together. A control algorithm manipulates the current supplied to thermoelectric coolers such that the dynamic thermal performance of a block can be controlled so that pre-defined thermal profiles of sample temperature can be executed. The sample temperature is calculated instead of measured using a design specific model and equations. The control software includes calibration diagnostics which permit variation in the performance of thermoelectric coolers from instrument to instrument to be compensated for such that all instruments perform identically. The block/heat sink assembly can be changed to another of the same or different design.
    Type: Grant
    Filed: August 22, 2008
    Date of Patent: October 3, 2017
    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
  • Publication number: 20170276609
    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: Application
    Filed: April 6, 2017
    Publication date: September 28, 2017
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Austin B. TOMANEY, Mark F. OLDHAM
  • Patent number: 9771583
    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: Grant
    Filed: February 4, 2016
    Date of Patent: September 26, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Nitin Puri, Irudaya Charles, Susan Magdaleno, Alexander Vlassov, Christopher Burnett
  • Publication number: 20170269031
    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: March 7, 2017
    Publication date: September 21, 2017
    Applicant: Applied Biosystems, LLC
    Inventors: Karl O. Voss, Aldrich N.K. Lau
  • Patent number: 9765405
    Abstract: This invention is related to novel PNA probes, probe sets, methods and kits pertaining to the detection of one or more species of Candida yeast. Non-limiting examples of probing nucleobase sequences that can be used for the probes of this invention can be selected from the group consisting of: AGA-GAG-CAG-CAT-GCA (Seq. Id. No. 1), AGA-GAG-CAA-CAT-GCA (Seq. Id. No. 2), ACA-GCA-GAA-GCC-GTG (Seq. Id. No. 3), CAT-AAA-TGG-CTA-CCA-GA (Seq. Id. No. 4), CAT-AAA-TGG-CTA-CCC-AG (Seq. Id. No. 5), ACT-TGG-AGT-CGA-TAG (Seq. Id. No. 6), CCA-AGG-CTT-ATA-CTC-GC (Seq. Id. No. 7), CCC-CTG-AAT-CGG-GAT (Seq. Id. No. 8), GAC-GCC-AAA-GAC-GCC (Seq. Id. No. 9), ATC-GTC-AGA-GGC-TAT-AA (Seq. Id. No. 10), TAG-CCA-GAA-GAA-AGG (Seq. Id. No. 11), CAT-AAA-TGG-CTA-GCC-AG (Seq. Id. No. 12), CTC-CGA-TGT-GAC-TGC-G (Seq. Id. No. 13), TCC-CAG-ACT-GCT-CGG (Seq. Id. No. 14), TCC-AAG-AGG-TCG-AGA (Seq. Id. No. 15), GCC-AAG-CCA-CAA-GGA (Seq. Id. No. 16), GCC-GCC-AAG-CCA-CA (Seq. Id. No. 17), GGA-CTT-GGG-GTT-AG (Seq. Id. No.
    Type: Grant
    Filed: December 15, 2014
    Date of Patent: September 19, 2017
    Assignee: Applied Biosystems, LLC
    Inventors: Jens J. Hyldig-Nielsen, Henrik Stender, Kenneth M. Oliveira, Susan Rigby
  • Patent number: 9745336
    Abstract: The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof.
    Type: Grant
    Filed: March 28, 2014
    Date of Patent: August 29, 2017
    Assignee: Applied Biosystems, LLC
    Inventors: Ronald Graham, Ruiming Zou, Krishna Upadhya, Scott Benson
  • Patent number: 9719925
    Abstract: An apparatus and method are provided for differentiating multiple detectable signals by excitation wavelength. The apparatus can include a light source that can emit respective excitation light wavelengths or wavelength ranges towards a sample in a sample retaining region, for example, in a well. The sample can contain two or more detectable markers, for example, fluorescent dyes, each of which can be capable of generating increased detectable emissions when excited in the presence of a target component. The detectable markers can have excitation wavelength ranges and/or emission wavelength ranges that overlap with the ranges of the other detectable markers. A detector can be arranged for detecting an emission wavelength or wavelength range emitted from a first marker within the overlapping wavelength range of at least one of the other markers.
    Type: Grant
    Filed: June 16, 2015
    Date of Patent: August 1, 2017
    Assignee: Applied Biosystems, LLC
    Inventors: Howard G. King, Steven J. Boege, Eugene F. Young, Mark F. Oldham
  • Patent number: 9714444
    Abstract: Systems and methods for multiple analyte detection include a system for distribution of a biological sample that includes a substrate, wherein the substrate includes a plurality of sample chambers, a sample introduction channel for each sample chamber, and a venting channel for each sample chamber. The system may further include a preloaded reagent contained in each sample chamber and configured for nucleic acid analysis of a biological sample that enters the substrate and a sealing instrument configured to be placed in contact with the substrate to seal each sample chamber so as to substantially prevent sample contained in each sample chamber from flowing out of each sample chamber. The substrate can be constructed of detection-compatible and assay-compatible materials.
    Type: Grant
    Filed: December 2, 2013
    Date of Patent: July 25, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Min Yue, David M. Liu, Joy Roy, Yuh-Min Chiang, Joon Mo Yang, Dennis Lehto, Charles S. Vann, Nigel P. Beard, Ian A. Harding, John R. Van Camp, Alexander Dromaretsky, Sergey V. Ermakov, Mark F. Oldham, Maryam Shariati, Umberto Ulmanella
  • Patent number: RE46683
    Abstract: Disclosed are methods and kits applicable to sequencing methods, such as Sanger dideoxy sequencing methods. The methods and kits disclosed utilize a cationically charged nucleic acid terminator in combination with a discriminatory polymerase.
    Type: Grant
    Filed: September 30, 2014
    Date of Patent: January 23, 2018
    Assignee: Applied Biosystems, LLC
    Inventors: Barnett Rosenblum, Steven Menchen, Shaheer Khan, Paul Kenney