Direct Analysis Of A Library Member, Per Se, By A Physical Method (e.g., Spectroscopy, Etc.) Patents (Class 506/6)
  • Patent number: 10787704
    Abstract: The present disclosure provides a method for sequencing nucleic acids. The method can include polymerase catalyzed incorporation of nucleotides into a nascent nucleic acid strand against a nucleic acid template, wherein the polymerase is attached to a charge sensor that detects nucleotide incorporation events. One or more non-natural nucleotide types that each produce a unique signatures at the charge sensor can be used to uniquely identify different nucleotides in the template nucleic acid.
    Type: Grant
    Filed: May 11, 2016
    Date of Patent: September 29, 2020
    Assignees: ILLUMINA, INC., THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Kevin L Gunderson, Jingwei Bai, Cheng-Yao Chen, Jeffrey G Mandell, Sergio Peisajovich, Philip G Collins, Gregory A Weiss, Boyan Boyanov
  • Patent number: 10458995
    Abstract: Provided herein are methods, kits, and compositions for use in the diagnosis and treatment of diseases. Peptoids recognized by Alzheimers disease specific antibodies are identified.
    Type: Grant
    Filed: March 21, 2017
    Date of Patent: October 29, 2019
    Inventor: Muralidhar Reddy Moola
  • Patent number: 10441668
    Abstract: Various embodiments are described herein for a system and a method for identifying a region of interest in tissue using mass spectrometry. An agent administration component can be provided to administer an exogenous agent to the tissue. A sampling unit can also be provided to acquire a sample from the tissue. The sample can then be provided to a high sensitivity analysis platform, such as a mass analyzer, to analyze the sample and determine a distribution of the exogenous agent or a by-product of the exogenous agent within the tissue based on the analysis. The analysis platform can then identify the region of interest based on the distribution of the exogenous agent or the distribution of the by-product.
    Type: Grant
    Filed: December 8, 2015
    Date of Patent: October 15, 2019
    Assignee: University Health Network
    Inventors: Arash Zarrine-Afsar, David Anthony Jaffray
  • Patent number: 10228326
    Abstract: At least an embodiment addresses the problem of providing a SPR (surface plasmon resonance) or SPFS (surface plasmon-field enhanced fluorescence spectroscopy) immunoassay, which enables the measurement of whole blood, undergoes little fluctuations in measurement values, and can measure whole blood, serum and plasma in a single apparatus. At least an embodiment solves the above-mentioned problem by a SPR or SPFS immunoassay, which is an immunoassay utilizing SPR or SPFS, including an absorbance measurement step of measuring an absorbance of a sample, a mode setting step of setting a mode that corresponds to the result of the absorbance measured in the absorbance measurement step, and one or multiple step(s) for which treatment condition(s) has/have been set in accordance with the mode set in the mode setting step.
    Type: Grant
    Filed: September 10, 2013
    Date of Patent: March 12, 2019
    Assignee: KONICA MINOLTA, INC.
    Inventors: Makiko Ootani, Takatoshi Kaya
  • Patent number: 10031135
    Abstract: Viruses and other bioagents are of high medical and biodefense concern and their detection at concentrations well below the threshold necessary to cause health hazards continues to be a challenge with respect to sensitivity, specificity, and selectivity. Ideally, assays for accurate and real time detection of viral agents and other bioagents would not necessitate any pre-processing of the analyte, which would make them applicable for example to bodily fluids (blood, sputum) and man-made as well as naturally occurring bodies of water (pools, rivers). We describe herein a robust biosensor that combines the sensitivity of surface acoustic waves (SAW) generated at a frequency of 325 MHz with the specificity provided by antibodies and other ligands for the detection of viral agents.
    Type: Grant
    Filed: February 4, 2014
    Date of Patent: July 24, 2018
    Assignees: STC.UNM, SANDIA CORPORATION
    Inventors: Richard S. Larson, Brian Hjelle, Pam R. Hall, David C. Brown, Marco Bisoffi, Susan M. Brozik, Darren W. Branch, Thayne L. Edwards, David Wheeler
  • Patent number: 9988623
    Abstract: Provided herein are methods for a novel bead-based next-generation “X-aptamer” selection scheme that extends aptamer technology to include X-modified bases, thus resulting in X-aptamers, at any position along the sequence because the aptamers are chemically synthesized via a split-pool scheme on individual beads. Also provides are application to a wide range of commonly used DNA modifications, including, but not limited to, monothioate and dithioate backbone substitutions. This new class of aptamer allows chemical modifications introduced to any of the bases in the aptamer sequence as well as the phosphate backbones and can be extended to other carbohydrate-based systems.
    Type: Grant
    Filed: October 10, 2013
    Date of Patent: June 5, 2018
    Assignees: AM Biotechnologies, LLC, Board of Regents of the University of Texas System
    Inventors: David G Gorenstein, Weiguo He, David E Volk, Miguel-Angel Elizondo-Riojas, Ross Durland, Johnnie Engelhardt
  • Patent number: 9983191
    Abstract: Disclosed herein are methods and compositions for detection of target small molecules in a mixed sample by performing a competition assay between the target and a surrogate and subsequently detecting the complex types in a nanopore device. Disclosed herein are competition assays for detection of small molecules using a nanopore. Target molecules of a sufficient size (>20 kDa) when passed through a solid-state nanopore cause a change in the current impedance, translocation time, or other measurable parameter. In the event the target molecule is not sufficiently big, and thus does not cause a noticeable change, an additional molecule/reagent can be used to aid in detection. This detection reagent would bind to the small molecule or to the “capture ligand-molecule complex” (e.g. peptide detection is aided by a monoclonal antibody (mAb) that recognizes a peptide/aptamer complex).
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: May 29, 2018
    Assignee: Two Pore Guys, Inc.
    Inventor: Trevor J. Morin
  • Patent number: 9404150
    Abstract: Provided herein are products and processes for the amplification, detection and sequencing of short-stranded nucleic acid in the presence of a high background of long-stranded genomic material (e.g., host or maternal nucleic acids). The methods rely on the use of inside and outside primers introduced at varying concentrations, as well as universal amplification reactions that preferentially amplify short, low copy number nucleic acid.
    Type: Grant
    Filed: August 28, 2008
    Date of Patent: August 2, 2016
    Assignee: SEQUENOM, INC.
    Inventors: Min Seob Lee, Yanfeng Yang
  • Patent number: 9202680
    Abstract: Disclosed herein are systems and methods for mass spectrometry using laserspray ionization (LSI). LSI can create multiply-charged ions at atmospheric pressure for analysis and allows for analysis of high molecular weight molecules including molecules over 4000 Daltons. The analysis can be solvent-based or solvent-free. Solvent-free analysis following LSI allows for improved spatial resolution beneficial in surface and/or tissue imaging.
    Type: Grant
    Filed: June 3, 2010
    Date of Patent: December 1, 2015
    Assignee: Wayne State University
    Inventor: Sarah Trimpin
  • Patent number: 9150897
    Abstract: The present invention provides a new method for recombinantly expressing a protein of interest, such as the human BRCA2 protein, BLM protein, CtIP protein, or EXOI protein, by expressing the protein in the form of a fusion protein comprising two maltose-binding protein (MBP) or glutathione-S-transferase (GST) tags. The expression cassette useful for this method and the fusion protein produced by this method are also described.
    Type: Grant
    Filed: August 5, 2011
    Date of Patent: October 6, 2015
    Assignee: The Regents of the University of California
    Inventors: Stephen Kowalczykowski, Ryan Jensen
  • Patent number: 9134228
    Abstract: The present invention relates to a method of measuring polysorbates, such as polysorbate 80, using Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR).
    Type: Grant
    Filed: May 21, 2013
    Date of Patent: September 15, 2015
    Assignee: GlaxoSmithKline Biologicals, S.A.
    Inventors: Benedicte Gbaguidi, Olivier C Germay, Sonia Lardau
  • Publication number: 20150141271
    Abstract: A method for analyzing water toxicity, the method including: exposure experiment, sample collection, transcriptome detection, metabolome detection, screening of differentially expressed genes, screening of differentially expressed metabolites, and identification of commonly changed biological pathways in both the transcriptome and the metabolome.
    Type: Application
    Filed: September 3, 2014
    Publication date: May 21, 2015
    Inventors: Yan ZHANG, Hongqiang REN, Bing WU, Xuxiang ZHANG
  • Publication number: 20150133306
    Abstract: The invention provides a method for preparing a compound or a product having one or more characteristics that meet or exceed a user specification, the process comprising the step of selecting a first combination of chemical inputs, optionally together with physical inputs, and supplying those inputs to a reaction space, thereby to generate a first product; analysing one or more characteristics of the product generated; comparing the one or more characteristics against a user specification; using a genetic algorithm selecting a second combination of chemical inputs, optionally together with physical inputs, wherein the second combination differs from the first combination, and supplying those inputs to the reaction space, thereby to generate a second product; analysing one or more characteristics of the second product generated; comparing the one or more characteristics generated against the user specification; repeating the selecting and analysing steps for further individual combinations of chemical and/or p
    Type: Application
    Filed: May 24, 2013
    Publication date: May 14, 2015
    Inventor: Leroy Cronin
  • Publication number: 20150094213
    Abstract: A method of comparative ligand mapping to identify peptide ligands presented by MHC positive cells that distinguish an infected/transfected cell from an uninfected/non-transfected cell is disclosed.
    Type: Application
    Filed: November 10, 2014
    Publication date: April 2, 2015
    Inventors: WILLIAM H. HILDEBRAND, HEATHER D. HICKMAN
  • Publication number: 20150094214
    Abstract: Techniques for characterizing a molecule are described herein. In one example, a portion of the molecule is trapped in a nanopore, a variable voltage is applied across the nanopore until the trapped portion of molecule is moved within the nanopore, and the molecule is characterized based on the electrical stimulus required to affect movement of at least a portion of the trapped portion of the molecule within the nanopore.
    Type: Application
    Filed: October 14, 2014
    Publication date: April 2, 2015
    Inventors: Roger J.A. Chen, Randy Davis
  • Publication number: 20150080234
    Abstract: The present disclosure provides technologies for achieving cell patterning, as well as patterned cell arrays achieved with such technologies. Provided apparatus and methods are useful in a variety of contexts and provide particular advantages with respect to assessing living cell arrays and/or their responsiveness to stimuli, including identifying and/or characterizing complex cellular responses.
    Type: Application
    Filed: September 16, 2014
    Publication date: March 19, 2015
    Inventors: John Christopher Love, Ayca Yalcin Ozkumur, Brittany Anne Thomas
  • Patent number: 8980637
    Abstract: A method for the parallel identification of one or more metabolite species within a biological sample is provided. The method comprises producing a first spectrum by subjecting the sample to a nuclear magnetic resonance analysis, the first spectrum containing individual spectral peaks representative of the one or more metabolite species contained within the sample; producing a second spectrum by subjecting the sample to a mass spectrometry analysis, the spectrum containing individual spectral peaks representative of the one or more metabolite species contained within the sample; subjecting each of the individual spectral peaks to a statistical pattern recognition analysis to identify the one or more metabolite species contained within the sample; and identifying the one or more metabolite species contained within the sample by analyzing the individual spectral peaks of the mass and nuclear magnetic resonance spectra.
    Type: Grant
    Filed: October 3, 2008
    Date of Patent: March 17, 2015
    Assignee: Purdue Research Foundation
    Inventors: Daniel M. Raftery, Zhengzheng Pan, Haiwei Gu
  • Patent number: 8969287
    Abstract: Disclosed here is a method for measuring the kinetics (i.e., the molecular flux rates-synthesis and breakdown or removal rates) of a plurality of proteins or organic metabolites in living systems. The methods may be accomplished in a high-throughput, large-scale automated manner, by using existing mass spectrometric profiling techniques and art well known in the fields of static proteomics and static organeomics, without the need for additional biochemical preparative steps or analytic/instrumental devices.
    Type: Grant
    Filed: June 19, 2013
    Date of Patent: March 3, 2015
    Assignee: The Regents of the University of California
    Inventor: Marc K. Hellerstein
  • Patent number: 8969251
    Abstract: A method for assaying phenotypic similarity or dissimilarity between organisms is disclosed in which a composite sample of admixed first and second samples is provided. The first, standard sample contains average concentrations of compounds of molecular mass less than about 1000 AMU present in the organism species. The second, assay sample contains compounds of having a similar molecular mass present in the organism whose phenotype is to be assayed. The constituents of both samples are (i) in a liquid medium and (ii) each compound of a sample has the same, first and second respective amounts of first and second stable isotopes of a first atom. The composite sample is mass spectroscopically analyzed for analytes, with the ratio of first to second isotope being determined for each analyte, along with a composite sample median ratio. The ratios for each analyte are compared to the median, with outlying ratios indicating dissimilarity.
    Type: Grant
    Filed: October 2, 2008
    Date of Patent: March 3, 2015
    Assignee: Methabolic Analyses, Inc.
    Inventor: Christopher William Ward Beecher
  • Publication number: 20150045238
    Abstract: The present invention provides a method for assessing the presence and risk of developing type 2 diabetes, cancer of all sites, or cardiovascular disease in a subject by detecting sequence variation in one or more genes such as carboxypeptidase E (CPE) and insulin degradation enzyme (IDE). A kit, array, and device useful for such a method are also provided. In addition, the present invention provides a method for treating type 2 diabetes, cancer of all sites, or cardiovascular disease in patients who have been tested and shown to have the pertinent genetic variations.
    Type: Application
    Filed: January 28, 2013
    Publication date: February 12, 2015
    Applicant: The Chinese University of Hong Kong
    Inventors: Juliana Chung-Ngor Chan, Wing-Yee So, Ronald Ching-Wan Ma
  • Publication number: 20140378323
    Abstract: The invention relates to an additive which can be added to buffers used in nucleotide detection processes and improved methods of nucleic acid sequencing using this additive. In particular the invention relates to use of the additive to improve the efficiency of fluorescence-based multiple cycle nucleic acid sequencing reactions.
    Type: Application
    Filed: June 3, 2014
    Publication date: December 25, 2014
    Applicant: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Milan Fedurco, Anthony Romieu, Gerardo Turcatti
  • Publication number: 20140364324
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes compositions and methods of nucleic acid sequencing using a single polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid attached proximal to a nanopore, and nucleotide analogs in solution comprising charge blockade label that are attached to the polyphosphate portion of the nucleotide analog such that the charge blockade labels are cleaved when the nucleotide analog is incorporated into a growing nucleic acid and the charge blockade label is detected by the nanopore to determine the presence and identity of the incorporated nucleotide and thereby determine the sequence of a template nucleic acid.
    Type: Application
    Filed: June 27, 2014
    Publication date: December 11, 2014
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jeffrey Wegener
  • Publication number: 20140357501
    Abstract: A peptide is cleaved at various bonding sites into oligopeptides or similar fragments by digestion using proteinase K (S3). The obtained fragments are separated according to their kinds by reversed-phase chromatography and fractionated (S4), and each fragment is subjected to mass spectrometry to determine its mass (S6). For each peptide fragment, an amino-acid composition is calculated from the measured mass, and amino-acid sequence candidates are deduced from that composition. The amino-acid sequence candidates of the other peptide fragments are searched for a fragment having an overlapping portion available for combining two peptide fragments to obtain amino-acid sequence candidates of the original peptide (S7). The masses of the amino-acid sequence candidates are compared with a measured mass derived from a result of mass spectrometry of the original peptide to select a correct sequence (S6 and S8).
    Type: Application
    Filed: March 14, 2014
    Publication date: December 4, 2014
    Applicant: SHIMADZU CORPORATION
    Inventors: Akiyasu Yoshizawa, Takayuki Yoshimori, Yuki Ohta
  • Publication number: 20140357502
    Abstract: In a first location of a mass spectrometer, a plurality of ionized molecules of an ion source are selected that have mass-to-charge ratios within a mass-to-charge ratio window width. The plurality of selected ionized molecules are transmitted from a first to a second location. Reagent ions are transmitted to the second location to reduce a charge state of one or more of the plurality of selected ionized molecules. A mass analyzer is used to analyze the plurality of reduced ionized molecules and produce a mass spectrum. A compound is identified from a peak of the spectrum that has a mass-to-charge ratio less than or equal to the highest mass-to-charge ratio in the window width if the noise is multiply charged and greater than the highest mass-to-charge ratio in the window width if the noise is singly charged.
    Type: Application
    Filed: November 28, 2012
    Publication date: December 4, 2014
    Inventors: John Lawrence Campbell, Yves Le Blanc, Alexandre V. Loboda, Igor Chernushevich
  • Publication number: 20140329699
    Abstract: The present disclosure relates to systems and methods for high efficiency electronic sequencing of nucleic acids and molecular detection. In an example embodiment of the instant disclosure, the NanoNeedle may be utilized to detect a change in impedance resulting from the modulation of the counter ion concentration or Debye length associated with a biomolecule of interest, such as DNA or protein, for an application of interest, such as DNA sequencing, DNA hybridization, or protein detection.
    Type: Application
    Filed: December 3, 2012
    Publication date: November 6, 2014
    Inventor: Hesaam Esfandyarpour
  • Publication number: 20140287936
    Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.
    Type: Application
    Filed: December 13, 2013
    Publication date: September 25, 2014
    Applicants: CORNELL RESEARCH FOUNDATION, INC., METABOLON, INC.
    Inventors: Rima Kaddurah-Daouk, Bruce S. Kristal
  • Patent number: 8822917
    Abstract: In order to provide an analysis method that is capable of determining a glycan structure with high detection sensitivity, a method of the present invention includes the steps of: carrying out triple quadrupole mass spectrometry at various values of CID energy; creating an energy-resolved profile including yield curves representing relationships between (i) a value of the CID energy and (ii) measured amounts of specific types of product ions; preparing a reference profile, and identifying a glycan structure of a test material by comparing the energy-resolved profile with the reference profile.
    Type: Grant
    Filed: January 6, 2014
    Date of Patent: September 2, 2014
    Assignees: Riken, Shimadzu Corporation
    Inventors: Koji Ueda, Atsuhiko Toyama
  • Publication number: 20140243217
    Abstract: The present disclosure provides methods an compositions for the detection of plant exposure to plant pathogens. The methods relate to determining the identity of peptides isolated from the surface of plant starch granules.
    Type: Application
    Filed: November 4, 2011
    Publication date: August 28, 2014
    Inventor: Illimar Altosaar
  • Publication number: 20140235463
    Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.
    Type: Application
    Filed: January 21, 2014
    Publication date: August 21, 2014
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Jonathan ROTHBERG, Todd REARICK
  • Patent number: 8791053
    Abstract: The invention relates to a spatially encoded polymer matrix in the form of a bead or a granule for combinatorial solid phase synthesis, assaying, functional proteomics and diagnostic use. Compositions of such beads or granules are also provided. Each beaded polymer matrix of the composition comprises a plurality of spatially immobilized particles. The spatial immobilization of the particles confers on each beaded polymer matrix a “fingerprint” which enables identification of unique beads in a population of beads. The unique identification of individual beads makes it possible to perform combinatorial chemistry strategies while logging individual chemical transformation. Also provided are methods for detection of relative positions in space of particles, methods for generating matrices, methods for distance matrix determination, methods for identifying individual matrices and devices for recording and storing images of matrices.
    Type: Grant
    Filed: September 26, 2003
    Date of Patent: July 29, 2014
    Assignee: MPM-Holding APS
    Inventors: Soren Flygenring Christensen, Jens Hog Truelsen, Morten Meldal, Roice Michael, Ib Johannsen
  • Publication number: 20140206555
    Abstract: Nanochannel arrays that enable high-throughput macromolecular analysis are disclosed. Also disclosed are methods of preparing nanochannel arrays and nanofluidic chips. Methods of analyzing macromolecules, such as entire strands of genomic DNA, are also disclosed, as well as systems for carrying out these methods.
    Type: Application
    Filed: March 24, 2014
    Publication date: July 24, 2014
    Applicant: THE TRUSTEES OF PRINCETON UNIVERSITY
    Inventors: Robert H. Austin, Zhaoning Yu, Jonas O. Tegenfeldt, Stephen Y. Chou, Han Cao
  • Patent number: 8778842
    Abstract: The present invention provides copolymers that facilitate nucleic acid analysis, compositions that comprise such copolymers, and methods for making or using such copolymers.
    Type: Grant
    Filed: February 6, 2006
    Date of Patent: July 15, 2014
    Assignee: QIAGEN GmbH
    Inventors: Ralf Himmelreich, Roland Fabis, Christoph Erbacher, Sabine Werner, Bernd Springer
  • Publication number: 20140194301
    Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.
    Type: Application
    Filed: March 12, 2014
    Publication date: July 10, 2014
    Applicant: Life Technologies Corporation
    Inventor: Mark J. MILGREW
  • Publication number: 20140194302
    Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.
    Type: Application
    Filed: March 12, 2014
    Publication date: July 10, 2014
    Applicant: Life Technologies Corporation
    Inventor: Mark J. MILGREW
  • Publication number: 20140194303
    Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.
    Type: Application
    Filed: March 12, 2014
    Publication date: July 10, 2014
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventor: Mark J. MILGREW
  • Patent number: 8765419
    Abstract: The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.
    Type: Grant
    Filed: April 29, 2013
    Date of Patent: July 1, 2014
    Assignee: Illumina, Inc.
    Inventors: Bernard Hirschbein, Filiz Gorpe-Yasar
  • Patent number: 8759007
    Abstract: The present invention provides a method for detecting modified LDL, abnormal cells or bacteria using an intermolecular interaction analysis method, in which a region involved in ligand recognition by a receptor is expressed, without modification or as a biotinylated protein, in cells or in a test tube, and thereafter, the expressed region or the expressed biotinylated protein is immobilized via avidin or streptavidin to a solid phase while the orientation thereof is maintained, and the immobilized protein is utilized; and a kit for detecting the modified LDL or the like.
    Type: Grant
    Filed: December 11, 2009
    Date of Patent: June 24, 2014
    Assignee: National Food Research Institute
    Inventors: Sachiko Machida, Kiyoshi Hayashi, Ken Tokuyasu, Yoshikiyo Sakakibara, Shigeru Matsunaga
  • Publication number: 20140171331
    Abstract: An analytical assembly within a unified device structure for integration into an analytical system. The analytical assembly is scalable and includes a plurality of analytical devices, each of which includes a reaction cell, an optical sensor, and at least one optical element positioned in optical communication with both the reaction cell and the sensor and which delivers optical signals from the cell to the sensor. Additional elements are optionally integrated into the analytical assembly. Methods for forming and operating the analytical system are also disclosed.
    Type: Application
    Filed: December 16, 2013
    Publication date: June 19, 2014
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Nathaniel Joseph McCaffrey, Stephen Turner, Ravi Saxena, Scott Edward Helgesen
  • Patent number: 8754012
    Abstract: The present invention relates to methods of screening for expression of a soluble candidate protein within an expression library of candidate proteins. The method involves fusing each candidate protein in the library to a peptide substrate and identifying cells that express soluble candidate protein by detecting enzymatic modification of the peptide substrate.
    Type: Grant
    Filed: September 5, 2005
    Date of Patent: June 17, 2014
    Assignee: European Molecular Biology Laboratory
    Inventor: Darren James Hart
  • Patent number: 8653448
    Abstract: In order to provide an analysis method that is capable of determining a glycan structure with high detection sensitivity, a method of the present invention includes the steps of: carrying out triple quadrupole mass spectrometry at various values of CID energy; creating an energy-resolved profile including yield curves representing relationships between (i) a value of the CID energy and (ii) measured amounts of specific types of product ions; preparing a reference profile, and identifying a glycan structure of a test material by comparing the energy-resolved profile with the reference profile.
    Type: Grant
    Filed: July 16, 2013
    Date of Patent: February 18, 2014
    Assignees: Riken, Shimadzu Corporation
    Inventors: Koji Ueda, Atsuhiko Toyama
  • Patent number: 8633139
    Abstract: The invention provides methods of making designed and constructed protein (e.g., antibody) libraries and libraries resulting from the same.
    Type: Grant
    Filed: December 19, 2008
    Date of Patent: January 21, 2014
    Assignee: Abbvie Biotherapeutics Inc.
    Inventors: Robert DuBridge, David Powers
  • Publication number: 20130336929
    Abstract: Disclosed herein are methods for identifying compounds for the treatment of viral infection, including RNA viral infection and uses of the compounds as pharmaceutical compositions. The identified compounds modulate the RIG-I pathway in vertebrate cells.
    Type: Application
    Filed: February 23, 2012
    Publication date: December 19, 2013
    Inventors: Shawn P. Iadonato, Kristin Bedard
  • Patent number: 8592347
    Abstract: The present invention relates to screening methods and, in particular, to methods of screening anti-ligands libraries for identifying anti-ligands specific for differentially and/or infrequently expressed ligands. The method comprises the steps of providing a library of anti-ligands; providing a first subtractor ligand; providing a second target ligand; determining the amount of the first and second target ligands using one or more equations derived from the universal law of mass action; providing the determined amount of a first subtractor ligand; providing the determined amount of a second target ligand; providing separation means capable of use to isolate anti-ligand bound to the second target ligand from anti-ligand bound to the first subtractor ligand; exposing the library of to the first and second target ligands to permit binding of anti-ligands to ligands; and using the separation means to isolate the anti-ligand bound to second target ligand.
    Type: Grant
    Filed: September 3, 2003
    Date of Patent: November 26, 2013
    Assignee: BioInvent Internatioal AB
    Inventor: Björn Frendéus
  • Publication number: 20130310265
    Abstract: This invention is directed to the discovery of improved methods of preparing cyclic peptides, cyclic peptide esters, cyclic peptide amidines, and libraries of these compounds. The invention also includes uses of these compounds and libraries for screens as drugs and binders of biologics.
    Type: Application
    Filed: March 14, 2013
    Publication date: November 21, 2013
    Applicant: NORTH CAROLINA STATE UNIVERSITY
    Inventors: STEFANO MENEGATTI, RUBEN CARBONELL, AMITH D. NAIK, KEVIN BLACKBURN
  • Publication number: 20130296176
    Abstract: The invention discloses methods and apparatus for characterizing trace nucleic acids that are biomarkers for disease. The methods and apparatus provide increased sensitivity to such trace nucleic acids, and allow analysis of nucleic acids present in a sample at only 0.01% of the wild-type sequences. The methods and apparatus are also designed for straightforward multiplexing, thus allowing pooling of clinical samples.
    Type: Application
    Filed: May 3, 2013
    Publication date: November 7, 2013
    Inventors: Andrea Marziali, Matthew Wiggin, Gosuke Shibahara, Valentina Semenovna Vysotskaia
  • Patent number: 8575070
    Abstract: The present invention provides the means for producing libraries of peptide structures for drug screening applications that are capable of folding or assuming their native conformations independently of artificial scaffolds or flanking sequences in the proteins from which they are derived. The libraries can be highly diverse such that they are representative of the repertoire of protein structures existing in nature. The libraries can also be non-redundant or normalized such that the bias towards specific structures existing in source data sets and/or in nature is/are removed. In a particularly preferred embodiment, the present invention provides 30,000 independent fold structures produced by this method. The present invention also provides computer-readable media and systems comprising structural data in relation to the peptide libraries, and methods for displaying and screening the libraries.
    Type: Grant
    Filed: February 7, 2007
    Date of Patent: November 5, 2013
    Assignee: Phylogica Limited
    Inventors: Paul Michael Watt, Roland Dunbrack
  • Publication number: 20130267676
    Abstract: The present invention provides a fibronectin type III (Fn3) molecule, wherein the Fn3 contains a stabilizing mutation. The present invention also provides Fn3 polypeptide monobodies, nucleic acid molecules encoding monobodies, and variegated nucleic acid libraries encoding such monobodies. Also provided are methods of preparing a Fn3 polypeptide monobody, and kits to perform the methods.
    Type: Application
    Filed: August 2, 2012
    Publication date: October 10, 2013
    Inventor: Shohei Koide
  • Patent number: 8551920
    Abstract: The disclosure features methods for identifying antibodies that bind to a carbohydrate moiety. Libraries coding for antibodies that bind to a carbohydrate moiety are provided. The libraries can be provided by modifying a pre-existing nucleic acid library. Antibodies that bind to a carbohydrate moiety are described.
    Type: Grant
    Filed: February 1, 2006
    Date of Patent: October 8, 2013
    Assignee: Morpho Sys AG
    Inventors: Rene Hoet, Sonia Schoonbroodt, Robert C. Ladner
  • Publication number: 20130231255
    Abstract: Methods and compositions related to high mannose glycans are described.
    Type: Application
    Filed: April 7, 2011
    Publication date: September 5, 2013
    Applicant: MOMENTA PHARMACEUTICALS, INC.
    Inventors: Brian Edward Collins, Jay Duffner, Carlos J. Bosques, Dorota A. Bulik, James Myette, James Meador
  • Publication number: 20130225423
    Abstract: The present invention provides a method for enrichment and isolation of endogenous transcription factors and their complexes. Also, this invention provides corresponding tandem arrays of concatenated transcription factor response elements (catTFRE). The method employs the property of transcription factors binding to sequence-specific DNA elements during regulation of gene expression. The catTFREs are designed and synthesized as concatenate dual copies of DNA response elements for various transcription factors. The DNA sequence of synthesized catTFRE is cloned to a target vector. Biotinylated catTFRE with 200 bp arms is prepared by PCR strategy. For enrichment and isolation of endogenous transcription factors and their complexes, the biotinylated catTFRE is immobilized to streptavidin-coated magnetic beads and then incubated with nuclear extract. Thereby endogenous transcription factors and their complexes are isolated from nuclear extract.
    Type: Application
    Filed: December 28, 2012
    Publication date: August 29, 2013
    Applicants: Baylor College of Medicine, Institute of Radiation Medicine, China Academy of Military Medical Sciences
    Inventors: Institute of Radiation Medicine, China Academy of Military Medical Sciences, Baylor College of Medicine