Patents Examined by Christopher M. Gross
  • Patent number: 11591639
    Abstract: This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X?-A?-B?-Z?, wherein sequence A? is complementary to a genomic fragment and sequence B? is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.
    Type: Grant
    Filed: September 30, 2020
    Date of Patent: February 28, 2023
    Inventors: Carl Oscar Fredrik Dahl, Olof John Ericsson, Filip Karlsson, Fredrik Roos
  • Patent number: 11583575
    Abstract: The disclosure provides compositions comprising at least one assembly comprising a peptide and a major histocompatibility complex (MHC), wherein the peptide is an integral component of the MHC, wherein the peptide is attached to a surface at its C-terminus through a linker and wherein the peptide is synthesized on the surface. In certain embodiments, the compositions comprise a plurality of assemblies in a spatially-ordered array. The disclosure provides methods for making and using these compositions.
    Type: Grant
    Filed: September 5, 2017
    Date of Patent: February 21, 2023
    Assignees: Roche Sequencing Solutions, Inc., Hoffmann-La Roche Inc.
    Inventors: Christian Klein, Hanying Li, Victor Lyamichev, Ekkehard Moessner, Jigar Patel
  • Patent number: 11577249
    Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.
    Type: Grant
    Filed: April 21, 2021
    Date of Patent: February 14, 2023
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
  • Patent number: 11574705
    Abstract: A high-throughput hybridization and reading method for biochips uses probes with different marks to specifically connect single nucleotide loci by conducting connection between the probes and target genes at different temperatures, and performing hybridization at the same temperature after the probes are connected, thereby achieving hybridization detection for various loci in a single chip. The method enables fast detection for multiple loci as required by personalized medicine. The detection is high-throughput and systematized and provides highly visualized and highly accurate results. The method allows detection for different loci at different hybridization temperatures to be done simultaneously. The method features highly uniform and repeatable detection, making biochips more efficient and utility in terms of detection. Besides, the chip is easy to prepare and use, thus having a good promotional value.
    Type: Grant
    Filed: November 6, 2018
    Date of Patent: February 7, 2023
    Assignee: First Bioscience Ltd
    Inventors: Zhiyuan Zhu, Libo Chen
  • Patent number: 11560560
    Abstract: Provided herein are compositions and methods to identify a binding element (e.g., peptide, peptoid, or protein) that can be bound by an immunoreceptor (e.g., antibody). The binding element can be provided in a target binding unit comprising two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule comprising an antigen binding domain of an antibody. The present disclosure provides various methods to construct the spacer. The identified binding elements can be further used to manufacture an array which can be used to profile antibodies obtained from a blood sample.
    Type: Grant
    Filed: September 24, 2020
    Date of Patent: January 24, 2023
    Assignee: RootPath Genomics, Inc.
    Inventors: Xi Chen, Ely Porter
  • Patent number: 11555184
    Abstract: The present disclosure methods for identifying binding partners using cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of peptides that bind to targets of interest. The engineered peptides are preferably expressed in the cells under conditions that provide both secretion and display of the engineered peptides on the cell surfaces, thus providing access of the engineered peptides to identify potential binding pairs. The cell libraries cab be engineered using an automated editing system that provides for one or more targeted edits per cell.
    Type: Grant
    Filed: August 9, 2020
    Date of Patent: January 17, 2023
    Assignee: Inscripta, Inc.
    Inventors: Stephen Federowicz, Deanna Church, Michael Graige
  • Patent number: 11549945
    Abstract: Provided herein are nucleic acid-cleaving catalytic nucleic acid probes, biosensors and lateral flow biosensor devices and methods and kits of using the probes, biosensors and lateral flow biosensor devices for detecting an analyte present on or generated from a microorganism in a test sample, including Helicobacter pylori and methods for determining whether a subject has a Helicobacter pylori infection.
    Type: Grant
    Filed: May 15, 2020
    Date of Patent: January 10, 2023
    Assignee: McMaster University
    Inventors: John D. Brennan, Yingfu Li, Monsur Ali, Carlos Filipe, Michael Gregory Wolfe
  • Patent number: 11542633
    Abstract: The present disclosure provides shuttle vectors for editing exogenous polynucleotides in heterologous live cells, as well as automated methods, modules, and multi-module cell editing instruments and systems for performing the editing methods.
    Type: Grant
    Filed: April 25, 2022
    Date of Patent: January 3, 2023
    Assignee: Inscripta, Inc.
    Inventors: Richard Fox, Daniel Held
  • Patent number: 11535844
    Abstract: The present invention relates to genomic analysis. In particular, the present invention provides methods and compositions for mapping genomic interactions.
    Type: Grant
    Filed: August 29, 2018
    Date of Patent: December 27, 2022
    Inventors: Job Dekker, Josee Dostie
  • Patent number: 11529603
    Abstract: An elongate solid phase body suitable for performing solid phase synthesis. The solid phase body includes a plurality of enclosures formed of a material of a chemically inert mesh and, within each enclosure, a plurality of solid phase beads.
    Type: Grant
    Filed: November 20, 2017
    Date of Patent: December 20, 2022
    Assignee: Swedish Biomimetics 3000 LTD
    Inventor: Andrew Prewer
  • Patent number: 11519913
    Abstract: Methods are disclosed herein for identifying a compound of use in treating a condition treatable by metformin. The methods include determining if the test compound binds a subunit of the mitochondrial electron transport complex IV, and/or alters the function of the mitochondrial electron transport complex IV. Methods for treating a subject with a condition treatable by metformin, are also disclosed. In some embodiments, the condition is type II diabetes.
    Type: Grant
    Filed: June 21, 2017
    Date of Patent: December 6, 2022
    Assignee: University of Pittsburgh—Of the Commonwealth System of Higher Education
    Inventors: Nathan A. Yates, Steven James Mullett, Harris B. Bell-Temin
  • Patent number: 11512347
    Abstract: Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Additionally, devices described herein for de novo synthesis of oligonucleic acids encoding information related to the original source information may have a flexible material for oligonucleic acids extension.
    Type: Grant
    Filed: September 21, 2016
    Date of Patent: November 29, 2022
    Assignee: Twist Bioscience Corporation
    Inventor: Bill James Peck
  • Patent number: 11513126
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Grant
    Filed: October 31, 2018
    Date of Patent: November 29, 2022
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 11512339
    Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.
    Type: Grant
    Filed: December 20, 2017
    Date of Patent: November 29, 2022
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
  • Patent number: 11506670
    Abstract: The present invention relates to a method for identifying endogenous first responder protein-cysteines. Methods for screening candidate compounds suitable for regulating NF-kB signaling and the DNA damage response pathway are also disclosed.
    Type: Grant
    Filed: February 23, 2018
    Date of Patent: November 22, 2022
    Inventors: Yimon Aye, Marcus J. C. Long, Yi Zhao
  • Patent number: 11498952
    Abstract: The present disclosure presents a general approach to engineering existing protein-protein interactions through domain addition and evolution. The disclosure teaches the creation of novel fusion proteins that include knottin peptides where a portion of the knottin peptide is replaced with a sequence that has been created for binding to a particular target. Such fusion proteins can also be bispecific or multi specific in that they can bind to and/or inhibit two or more receptors or receptor ligands. Knottins may be fused with an existing ligand (or receptor) as a general platform tor increasing the affinity of a ligand-receptor interaction or for creating a multi specific protein. In addition, the fusion proteins may comprise a knottin peptide fused to another protein where the other protein facilitates proper expression and folding of the knottin.
    Type: Grant
    Filed: October 8, 2020
    Date of Patent: November 15, 2022
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Jennifer R. Cochran, Douglas S. Jones, Mihalis S. Kariolis, Ping-Chuan Tsai
  • Patent number: 11498072
    Abstract: The present invention relates to systems and methods for the arrangement of droplets in pre-determined locations. Many applications require the collection of time-resolved data. Examples include the screening of cells based on their growth characteristics or the observation of enzymatic reactions. The present invention provides a tool and related techniques which addresses this need, and which can be used in many other situations. The invention provides, in one aspect, a tool that allows for stable storage and indexing of individual droplets. The invention can interface not only with microfluidic/microscale equipment, but with macroscopic equipment to allow for the easy injection of liquids and extraction of sample droplets, etc.
    Type: Grant
    Filed: October 1, 2020
    Date of Patent: November 15, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: David A. Weitz, Christian Boehm, Amy Rowat, Sarah Koester, Jeremy Agresti
  • Patent number: 11499150
    Abstract: Use of the surface presentation level of binders (e.g., antibodies, receptors) on cultured higher eukaryotic cells in vitro as a predictive indicator of developability characteristics, e.g., solubility, of the binders. Display libraries of higher eukaryotic cells, e.g., mammalian cells, adapted for use in screening surface-displayed binders for developability and affinity of target binding. High-throughput screening of display libraries with in-built selection for developability including binder solubility, capability to be formulated at high concentrations, low propensity for non-specific binding, and half-life. Enrichment of populations of binders for developability characteristics and/or other qualities such as target binding and affinity, by controlling cell surface presentation of binders from an inducible promoter operably linked to binder-encoding DNA.
    Type: Grant
    Filed: December 5, 2018
    Date of Patent: November 15, 2022
    Assignee: Iontas Limited
    Inventors: John McCafferty, Rajika Perera, Michael Richard Dyson, Kothai Parthiban, Johanna Liinamaria Syrjanen
  • Patent number: 11493503
    Abstract: The present application provides a method of quantifying an amount of a derivatized peptide displayed on a phage by phage display, the method comprising: providing a phage containing a target peptide thereon; reacting the phage containing the target peptide with a first reagent to derivatize the target peptide to form a derivatized peptide, reacting the derivatized peptide with a capture agent comprising a detection marker, thereby incorporating the detection marker within the derivatized peptide; and determining an amount of the detection marker, thereby quantifying the amount of the derivatized peptide dis-played on the phage. A kit comprising a capture agent compris-ing a detection marker for quantifying the phage displayed derivatized peptides is also provided.
    Type: Grant
    Filed: March 22, 2018
    Date of Patent: November 8, 2022
    Assignee: 48Hour Discovery Inc.
    Inventors: Ratmir Derda, Simon Ng, Seyed Mohammadreza Jafari
  • Patent number: 11486881
    Abstract: Methods and devices for identifying agents that block binding or activation of peripheral membrane proteins are disclosed.
    Type: Grant
    Filed: November 8, 2018
    Date of Patent: November 1, 2022
    Inventors: Joshua S. Salafsky, Carl Benton Moree, III