Patents Examined by Gary Benzion
  • Patent number: 8323899
    Abstract: Magnetic particles for nucleic acid isolation are coated with silica and separated from impurities and nanoparticulates using a multi-step fractionation process. In each cycle of the fractionation process, the particles are stirred, sedimented, and resuspended, resulting in a decline in pH of the suspended particles. Repeating the fractionation process until the resuspended particles have dropped to a target pH in the range of about 9 to 10.5, and their zeta potential is more negative than about ?40 mV, results in a purified population of particles with a high and reproducible binding capacity for nucleic acids. The silica-treated magnetic beads produced by the method offer improved sensitivity and consistency for recovery of nucleic acids in a sample.
    Type: Grant
    Filed: February 1, 2008
    Date of Patent: December 4, 2012
    Assignee: Siemens Healthcare Diagnostics Inc.
    Inventors: David Sherman, Karlheinz Hildenbrand
  • 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
  • Patent number: 8313903
    Abstract: The invention is directed to binary oligonucleotide probes for nucleic analysis, which probes can be made of DNA or RNA that recognize nucleic acid analytes (both DNA and RNA) with unprecedented high selectivity under mild conditions and are highly sensitive to single nucleotide mismatches (SNP single nucleotide polymorphisms) without PCR amplification. In one group, the binary probes indicate that they have hybridized to a particular nucleic analyte by binding to a molecular beacon that gives off a fluorescent signal. A second group of binary probes bind to a dye such as malachite green, where upon hybridization to analyte the fluorescence of the dye increases dramatically and is easily detected and measured. The new binary probes require only about five minutes at room temperature to generate a detectable signal.
    Type: Grant
    Filed: April 1, 2007
    Date of Patent: November 20, 2012
    Assignee: The Trustees of Columbia University in the City of New York
    Inventor: Dmitry Kolpashchikov
  • Patent number: 8313931
    Abstract: Methods for amplifying and detecting nucleic acids are described, as well as sets of 5? labeled oligonucleotides.
    Type: Grant
    Filed: September 26, 2008
    Date of Patent: November 20, 2012
    Assignee: 3M Innovative Properties Company
    Inventor: Jesse D. Miller
  • Patent number: 8313930
    Abstract: The invention relates to kits and methods for assessing skin health for a human and the human's susceptibility to skin disorders. The methods involve assessing occurrence in the human's genome of one or more polymorphisms (e.g., single nucleotide polymorphisms) that occur in one or more genes associated disclosed herein and that are associated with a disorder in humans. Preferred assessment and scoring methods are disclosed, as are kits for performing the methods.
    Type: Grant
    Filed: March 30, 2007
    Date of Patent: November 20, 2012
    Assignee: Genelink, Inc.
    Inventors: John R. DePhillipo, Robert P. Ricciardi
  • Patent number: 8304214
    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: Grant
    Filed: November 21, 2007
    Date of Patent: November 6, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: John C. Gerdes, Elaine A. Best, Jeffrey M. Marmaro
  • Patent number: 8298794
    Abstract: The invention relates to nucleic acid and amino acid sequences for sorghum CAD alleles and truncated CAD polypeptides. Sorghum plants having such truncations or combinations thereof, methods of genotyping sorghum plants for CAD truncations, and methods for breeding sorghum plants having truncated CAD sequences or combinations thereof are described.
    Type: Grant
    Filed: October 8, 2009
    Date of Patent: October 30, 2012
    Assignee: Ceres, Inc.
    Inventor: Timothy Swaller
  • Patent number: 8293501
    Abstract: Methods and compositions for performing low background multiplex nucleic acid amplification reactions are provided. Aspects of the invention include contacting a nucleic acid sample with two or more primer pairs for two or more target nucleic acids under template dependent primer extension reaction conditions, e.g., polymerase chain reaction (PCR) conditions. The resultant amplified composition is then contacted with target nucleic acid circularizing reagents, and product circularized target nucleic acids are then selected, e.g., for further amplification. Also provided are systems and kits that find use in practicing embodiments of the inventions.
    Type: Grant
    Filed: September 11, 2007
    Date of Patent: October 23, 2012
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Johan Erik Simon Fredriksson, Carl Oscar Fredrik Dahl
  • Patent number: 8288103
    Abstract: The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously.
    Type: Grant
    Filed: May 28, 2010
    Date of Patent: October 16, 2012
    Assignee: Illumina, Inc.
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Patent number: 8288128
    Abstract: The present invention relates to a method and apparatus for monitoring a real-time quantification of multiple target molecules during their binding on capture molecules of a micro-array. The method comprises the steps of: placing, in a chamber (14), a support (15) having fixed upon its surface a micro-array comprising at least 5 capture molecules (20) being immobilized in specifically localized areas (21) of said support; introducing said labeled target molecules solution (13) into the chamber; incubating said labeled target molecules under stable and controlled temperature conditions to allow the binding between said target and capture molecules; directing an excitation light (2) from a light source (1) on the surface of the micro-array; measuring the electromagnetic light emission (7) from the bound target molecules in response to said excitation light in presence of the solution containing the target molecules wherein the surface of emission for a localized area is comprised between about 0.
    Type: Grant
    Filed: November 18, 2004
    Date of Patent: October 16, 2012
    Assignee: Eppendorf Array Technologies S.A.
    Inventors: José Remacle, Isabelle Alexandre, Sylvain Margaine, Dieter Husar
  • Patent number: 8268551
    Abstract: Techniques and systems for using nonlinear four wave mixing to optically measure microarrays with sample cells of biological or chemical materials. Examples of suitable microarrays include but are not limited to DNA microchips and capillary electrophoresis microarrays.
    Type: Grant
    Filed: January 27, 2004
    Date of Patent: September 18, 2012
    Assignee: San Diego State University Foundation
    Inventor: William G. Tong
  • Patent number: 8263331
    Abstract: A device and a method are disclosed for the detection and/or for the quantification of an analyte. In at least one embodiment, the device includes a basic matrix and magnetized nanoparticles, which are arranged in moveable fashion in or at the basic matrix and to which catcher molecules that bind specifically to the analyte are anchored. Further, the mobility of the nanoparticle in the basic matrix can be influenced by a binding of the analyte to be detected to the catcher molecules and can be read out magnetically.
    Type: Grant
    Filed: January 22, 2007
    Date of Patent: September 11, 2012
    Assignee: Siemens Aktiengesellschaft
    Inventors: Joachim Bangert, Ludwig Bär, Thomas Ehben, Hans-Dieter Feucht, Christian Zilch
  • Patent number: 8258273
    Abstract: The invention is directed to an isolated genomic polynucleotide fragment that encodes human soluble (cytosolic) aminopeptidase P, vectors and hosts containing the fragment and fragments hybridizing to noncoding regions as well as antisense oligonucleotides to these fragments. The invention is further directed to methods of using these fragments to obtain human soluble aminopeptidase P and to diagnose, treat, prevent and/or ameliorate a pathological disorder.
    Type: Grant
    Filed: June 3, 2007
    Date of Patent: September 4, 2012
    Inventor: James W Ryan
  • Patent number: 8247197
    Abstract: An aptamer-probe complex for detecting the presence of a target molecule is disclosed. The complex of the present invention contains an aptamer moiety which is able to bind to an indicator protein and change the properties of the indicator protein, and a probe moiety which is able to bind to a target molecule, wherein the aptamer moiety and the probe moiety are combined in such a manner that the binding mode between the aptamer moiety and the indicator protein changes when the probe moiety binds to the target molecule. A target molecule can be detected with combination of an aptamer which binds to a certain protein, and a probe which binds to the target molecule, utilizing the properties of that protein as an indicator.
    Type: Grant
    Filed: September 1, 2010
    Date of Patent: August 21, 2012
    Assignee: Techno Medica Co., Ltd.
    Inventors: Koji Sode, Kazunori Ikebukuro
  • Patent number: 8247196
    Abstract: The present invention relates to a method and apparatus for monitoring on a micro-array a PCR amplification of a nucleotide molecule being present in a solution.
    Type: Grant
    Filed: November 18, 2005
    Date of Patent: August 21, 2012
    Assignee: Eppendorf Array Technologies S.A.
    Inventors: Jose Remacle, Isabelle Alexandre, Sylvain Margaine, Dieter Husar
  • Patent number: 8241898
    Abstract: Methods and compositions are provided for the isolation, culture and use of highly regenerative somatic mammalian cells. The cells are very small, and have an undefined nuclear structure. The cells may be isolated from fetal or adult tissues, and are found in tissue including, without limitation, fetal dermal tissue, blood, and bone marrow. The cells are characterized as expressing one or more markers selected from E-cadherin, integrin ?1, CXCR4, CD90 and CD34, and may be selected on the basis of such expression patterns.
    Type: Grant
    Filed: December 10, 2008
    Date of Patent: August 14, 2012
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Wuyi Kong, Shaowei Li, Peter Lorenz
  • Patent number: 8236496
    Abstract: The present invention relates to the use of gene activity markers for classification of patients suffering from infectious and non-infectious multiple organ failure, respectively. The present invention in particular relates to gene activity markers for classification of patients as “not infected without multiple organ failure” or as “not suffering from infectious multiple organ failure” or as “suffering from infectious multiple organ failure”, the gene activity markers being polynucleotides selected from the group consisting of: SEQ ID I.1, SEQ ID I.2, SEQ ID I.3, SEQ ID I.4, SEQ ID I.5, SEQ ID I.6, SEQ ID I.7, SEQ ID I.8 and SEQ ID I.9 or partial sequences thereof.
    Type: Grant
    Filed: March 16, 2006
    Date of Patent: August 7, 2012
    Assignee: SIRS-Lab GmbH
    Inventors: Stefan Russwurm, Konrad Reinhart
  • Patent number: 8236938
    Abstract: Disclosed herein are assays for detecting the presence of a lysine-increasing transgenic event based on the DNA sequence of the exogenous DNA construct inserted into the maize genome and of genomic sequences flanking the insertion site. Also provided are transgenic plants having a novel exogenous DNA construct that expresses a dihydrodipicolinic acid synthase, the activity of which results in increased lysine in a plant or plant product.
    Type: Grant
    Filed: November 9, 2009
    Date of Patent: August 7, 2012
    Assignee: Monsanto Technology LLC
    Inventors: Mark A. Dizigan, Rebecca A. Kelly, Dale A. Voyles, Michael Hans Luethy, Thomas M. Malvar, Kathleen P. Malloy
  • Patent number: 8222003
    Abstract: This invention provides compositions and methods for HCV typing, e.g., genotyping and/or subtyping. The compositions and methods of the invention can be used to assign an HCV isolate to one of at least five HCV genotypes (for example, selected from genotypes 1, 2, 3, 4, 5 or 6), or assign an HCV isolate to one of at least six subtypes (for example, selected from subtypes 1a/b/c, 2a/c, 2b, 3a, 4a, 5a or 6a), where the methods of the invention use only a single typing probe to make the HCV type assignment.
    Type: Grant
    Filed: November 11, 2008
    Date of Patent: July 17, 2012
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Amar P Gupta, Stephen Gordon Will
  • Patent number: 8206953
    Abstract: Disclosed is a single stranded primer-promoter-selector construct comprising (in 3? to 5? orientation) a primer subsequence annealing to the target, a T7 or other promoter subsequence (the template strand), and a selector subsequence. The primer can be extended by template mediated elongation, including reverse transcription, or ligation to another oligonucleotide. The promoter sequence is oriented to direct the in-vitro transcription (IVT) opposite to that of primer extension, where the selector subsequence serves as a template for IVT. The selector is associated with the target subsequence of interest and it, and the amplified product are unique subsequences, dissimilar to other sequence present in the sample. The construct's is useful for determination of the presence and relative abundance of designated subsequences in the sample, multiplex gene expression analysis, multiplex allele counting, determination of polymorphic/mutation site, and loss of heterozygosity.
    Type: Grant
    Filed: September 21, 2006
    Date of Patent: June 26, 2012
    Assignee: BioArray Solutions, Ltd.
    Inventors: Nataliya Korzheva, Michael Seul