Patents Assigned to Applied Biosystems
  • Axial Illumination for Capillary Electrophoresis
    Publication number: 20140009943
    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: May 16, 2013
    Publication date: January 9, 2014
    Applicant: Applied Biosystems, LLC
    Inventors: Richard REEL, Eric NORDMAN
  • Microfluidic size-exclusion devices, systems, and methods
    Patent number: 8623296
    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: Grant
    Filed: August 4, 2010
    Date of Patent: January 7, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Sean M. Desmond, Zbigniew T. Bryning, John Shigeura, Gary Lim, Adrian Fawcett, Jacob K. Freudenthal, Gary Bordenkircher
  • Peptide conjugates and fluorescence detection methods for intracellular caspase assay
    Patent number: 8623995
    Abstract: Polypeptides labelled with a donor and acceptor pair of dyes selected from a dibenzorhodamine dye and a diamino-benzophenoxazine dye are peptide conjugates which are useful for intracellular and bead-based assays with fluorescence detection. Peptide conjugates with a caspase-recognition site undergo cleavage into peptide fragments which may be detected, located, and quantitated by the changes in fluorescence. Intracellular cleavage of peptide conjugates is correlated with apoptosis.
    Type: Grant
    Filed: June 14, 2010
    Date of Patent: January 7, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Xiongwei Yan, Sheri Miraglia, Pau Miau Yuan
  • DNA sequencing system
    Patent number: 8625094
    Abstract: An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.
    Type: Grant
    Filed: September 14, 2012
    Date of Patent: January 7, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Mark Oldham, Eric Norman, Richard Reel, Janice Shigeura
  • Fluorescent polymeric materials containing lipid soluble rhodamine dyes
    Patent number: 8618161
    Abstract: Fluorescent polymeric materials are disclosed comprising a polymeric particle and one or more lipid soluble rhodamine dyes, comprising the following core structure: wherein R11 and R15 are each H or are each F or Cl; R12, R13, and R14 are each H or are each F or Cl; and wherein at least one of R3?, R3?, R6? and R6? is a (C4-C20) alkyl. The materials are especially useful in the preparation of multicolored microparticles, especially multicolored polystyrene microparticle, for use in the multiplexed analysis of a plurality of analytes in a single sample. When excited by a light source, the materials give off a unique emission based on the nature, concentration and ratio of the dyes therein. Methods of preparing and using said materials are also disclosed.
    Type: Grant
    Filed: February 14, 2011
    Date of Patent: December 31, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Joe Y. L. Lam, Steven M. Menchen, Ruiming Zou, Scott C. Benson
  • UV excitable fluorescent energy transfer dyes
    Patent number: 8604186
    Abstract: Novel energy transfer dyes which can be used with shorter wavelength light sources are provided. These dyes include a donor dye with an absorption maxima at a wavelength between about 250 to 450 nm and an acceptor dye which is capable of absorbing energy emitted from the donor dye. One of the energy transfer dyes has a donor dye which is a member of a class of dyes having a coumarin or pyrene ring structure and an acceptor dye which is capable of absorbing energy emitted from the donor dye, wherein the donor dye has an absorption maxima between about 250 and 450 nm and the acceptor dye has an emission maxima at a wavelength greater than about 500 nm.
    Type: Grant
    Filed: January 30, 2012
    Date of Patent: December 10, 2013
    Assignee: Applied Biosystems, LLC
    Inventor: Linda G. Lee
  • Systems and methods for multiple analyte detection
    Patent number: 8597590
    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: May 27, 2010
    Date of Patent: December 3, 2013
    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
  • Caps for sample wells and microcards for biological materials
    Patent number: 8591836
    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: April 8, 2008
    Date of Patent: November 26, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Steven J. Boege, Eugene F. Young, Donald R. Sandell
  • Multi-chromophoric quencher constructs for use in high sensitivity energy transfer probes
    Patent number: 8586718
    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. This can be accomplished by linking together, into a single molecule, two or more identical quenchers, by reacting the quenchers with a multivalent linker. The structure of the multi-chromophoric quencher can also be varied to quench a broader range of reporter emission wavelengths than previously possible. This can be accomplished by linking together, into a single molecule, two or more different quenchers, by reacting the quenchers with a multivalent linker.
    Type: Grant
    Filed: September 14, 2005
    Date of Patent: November 19, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Scott C. Benson, Steven M. Menchen, Krishna G. Upadhya
  • Computer algorithm for automatic allele determination from fluorometer genotyping device
    Patent number: 8571807
    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: Grant
    Filed: December 1, 2011
    Date of Patent: October 29, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Stephen Glanowski, Jeremy Heil, Emily S. Winn-Deen, Ivy A. McMullen
  • Systems and methods for isolating nucleic acids
    Patent number: 8568580
    Abstract: A system for collecting target nucleic acids from a sample can include at least one sample chamber configured to receive a sample containing target nucleic acids and other material, at least one collection chamber removably mountable relative to the at least one sample chamber and configured to collect target nucleic acids separated from the other material, a filter removably mountable relative to the at least one sample chamber and configured to be disposed between the at least one sample chamber and the at least one collection chamber when the at least one collection chamber is mounted relative to the at least one sample chamber.
    Type: Grant
    Filed: July 24, 2008
    Date of Patent: October 29, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Charles S. Vann, Maxim G. Brevnov, David W. Ruff, Kenneth J. Livak
  • Method and device for detecting the presence of a single target nucleic acid in a sample
    Patent number: 8563275
    Abstract: A method comprising subjecting one or more sample portion(s) to a single amplification step, thereby amplifying a single molecule in the sample portion to a detectable level, and, in some embodiments, then determining whether the sample portion contains at least one molecule of the target nucleic acid. In some embodiments, the sample portion is in a porous sample structure, or in a sample chamber which comprises means for minimizing diffusion of the sample portion, or in a sample chamber which is inside a microcapillary device, or in a sample retaining means.
    Type: Grant
    Filed: August 11, 2012
    Date of Patent: October 22, 2013
    Assignees: Applied Biosystems, LLC, The United States of America, as Represented by the Secretary, Department of Health and Human Services
    Inventors: James F. Brown, Jonathan E. Silver
  • Optical instrument including excitation source
    Patent number: 8557569
    Abstract: An optical instrument is provided for simultaneously illuminating two or more spaced-apart reaction regions with excitation beams generated by a light source. The light source can include an area light array of light emitting diodes, one or more solid state lasers, one or more micro-wire lasers, or a combination thereof. According to various embodiments, a Fresnel lens can be disposed along a beam bath between the light source and the reaction regions. Methods of analysis using the optical instrument are also provided.
    Type: Grant
    Filed: July 3, 2008
    Date of Patent: October 15, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Steven J. Boege, Howard G. King, Eugene F. Young, Johannes P. Sluis, Mark F. Oldham
  • Instrument for monitoring polymerase chain reaction of DNA
    Patent number: 8557566
    Abstract: An optical instrument monitors PCR replication of DNA in a reaction apparatus having a temperature cycled block with vials of reaction ingredients including dye that fluoresces in presence of double-stranded DNA. A beam splitter passes an excitation beam to the vials to fluoresce the dye. An emission beam from the dye is passed by the beam splitter to a CCD detector from which a processor computes DNA concentration. A reference strip with a plurality of reference emitters emit reference beams of different intensity, from which the processor selects an optimum emitter for compensating for drift. Exposure time is automatically adjusted for keeping within optimum dynamic ranges of the CCD and processor. A module of the beam splitter and associated optical filters is associated with selected dye, and is replaceable for different dyes.
    Type: Grant
    Filed: January 17, 2006
    Date of Patent: October 15, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Michael R. Gambini, Eugene F. Young, Edward J. Lakatos, Anthony L. Cerrone, Susan Atwood Stone, Judith K. Atwood
  • Method of loading sample into a microfluidic device
    Patent number: 8551698
    Abstract: A method comprising loading a sample into a microfluidic device which comprises plural sample chambers, subdividing the sample into a plurality of sample portions, such that respective sample portions are positioned in each of a plurality of the sample chambers, and subjecting the sample portions loaded into the respective sample chambers to at least a first amplification step. Each of the sample chambers has a respective volume such that if a sample portion positioned in the sample chamber comprises at least one molecule of a target nucleic acid, the target nucleic acid would attain a detectable concentration in the sample chamber after a single round of amplification.
    Type: Grant
    Filed: August 13, 2007
    Date of Patent: October 8, 2013
    Assignees: Applied Biosystems, LLC, The United States Department of Health and Human Services
    Inventors: James F. Brown, Jonathan E. Silver
  • Electrochemical polynucleotide detection comprising ligation
    Patent number: 8551697
    Abstract: Disclosed, for example, are methods comprising cleaving an uncleaved probe to form a cleaved oligonucleotide flap, forming a hybridization complex between the cleaved oligonucleotide flap, a bridging oligonucleotide, and a capture oligonucleotide that is immobilized on a surface, such that the oligonucleotide flap and the capture oligonucleotide are hybridized to immediately adjacent, complementary regions of the bridging oligonucleotide, ligating the oligonucleotide flap to the capture oligonucleotide to form an immobilized ligation product, and detecting the ligation product.
    Type: Grant
    Filed: December 11, 2006
    Date of Patent: October 8, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Vladimir I. Bashkirov, Konrad Faulstich
  • Methods, compositions, and kits for detecting protein aggregates
    Patent number: 8535878
    Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.
    Type: Grant
    Filed: May 2, 2007
    Date of Patent: September 17, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: David W. Ruff, Mark E. Shannon, Kenneth J. Livak, Karl J. Guegler, Kevin M. Hennessy
  • Method of making a paired tag library for nucleic acid sequencing
    Patent number: 8530197
    Abstract: The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.
    Type: Grant
    Filed: January 8, 2009
    Date of Patent: September 10, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Bin Li, Lei Xi, Swati S. Ranade, Yangzhou Wang
  • High potency siRNAS for reducing the expression of target genes
    Patent number: 8524680
    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: Grant
    Filed: August 31, 2009
    Date of Patent: September 3, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: David Brown, Lance P. Ford, Richard A. Jarvis, Vince Pallotta, Brittan L. Pasloske
  • siRNA sequence-independent modification formats for reducing off-target phenotypic effects in RNAi, and stabilized forms thereof
    Patent number: 8524681
    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: March 19, 2010
    Date of Patent: September 3, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Nitin Puri, Irudaya Charles, Susan Magdaleno, Alexander Vlassov, Chris Burnett