Patents by Inventor David Bikard

David Bikard has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 11497797
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: November 15, 2022
    Assignee: The Rockfeller University
    Inventors: David Bikard, Luciano Marraffini
  • Patent number: 11491209
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: November 8, 2022
    Assignee: The Rockefeller University
    Inventors: David Bikard, Luciano Marraffini
  • Patent number: 11491210
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: November 8, 2022
    Assignee: The Rockefeller University
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20220347271
    Abstract: The invention relates to the improvement of endonuclease-based antimicrobials by blocking DNA repair of double-strand break(s) (DSB(s)) in prokaryotic cells. In this respect, the invention especially concerns a method involving blocking DNA repair after a nucleic acid has been submitted to DSB, in particular by a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated programmable double-strand endonuclease. The invention particularly relates to the use of an exogenous molecule that inhibits DNA repair, preferably a protein that binds to the ends of the double-stranded break to block DSB repair. The invention also relates to vectors, particularly phagemids and plasmids, comprising nucleic acids encoding nucleases and Gam proteins, and a pharmaceutical composition and a product containing these vectors and their application.
    Type: Application
    Filed: June 3, 2022
    Publication date: November 3, 2022
    Inventors: David BIKARD, Lun CUI, Xavier DUPORTET, Jesus FERNANDEZ RODRIGUEZ
  • Patent number: 11452765
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Grant
    Filed: January 21, 2022
    Date of Patent: September 27, 2022
    Assignee: The Rockefeller University
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20220218795
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: March 29, 2022
    Publication date: July 14, 2022
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20220218796
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: March 29, 2022
    Publication date: July 14, 2022
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20220218797
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: March 29, 2022
    Publication date: July 14, 2022
    Inventors: David Bikard, Luciano Marraffini
  • Patent number: 11377645
    Abstract: Provided are Cas9 enzymes that have mutations that enhance their properties, relative to un-mutated Cas9. The altered Cas9 enzymes exhibit i) an increased rate of spacer acquisition, or ii) increased cleavage efficiency of targets with NAG PAMs, or a combination of i) and ii). The altered Cas9 enzymes comprise an amino acid substitution of 1473 and K500 in a Streptococcus pyogenes or similar Cas9 enzyme. Also provided are polynucleotides, including expression vectors that encode the Cas9 enzymes, cells that contain the polynucleotides, and methods of making and using such cells. The disclosure includes tagging, or labelling bacteria, and for enhancing phage acquired immunity in bacteria, such as those used in industrial processes, including the food and beverage industry, such as the dairy industry. The food products are also included.
    Type: Grant
    Filed: December 18, 2017
    Date of Patent: July 5, 2022
    Assignee: The Rockefeller University
    Inventors: Luciano Marraffini, Robert Heller, David Bikard
  • Patent number: 11357831
    Abstract: The invention relates to the improvement of endonuclease-based antimicrobials by blocking DNA repair of double-strand break(s) (DSB(s)) in prokaryotic cells. In this respect, the invention especially concerns a method involving blocking DNA repair after a nucleic acid has been submitted to DSB, in particular by a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated programmable double-strand endonuclease. The invention particularly relates to the use of an exogenous molecule that inhibits DNA repair, preferably a protein that binds to the ends of the double-stranded break to block DSB repair. The invention also relates to vectors, particularly phagemids and plasmids, comprising nucleic acids encoding nucleases and Gam proteins, and a pharmaceutical composition and a product containing these vectors and their application.
    Type: Grant
    Filed: November 1, 2019
    Date of Patent: June 14, 2022
    Assignees: INSTITUT PASTEUR, ELIGO BIOSCIENCE
    Inventors: David Bikard, Lun Cui, Xavier Duportet, Jesus Fernandez Rodriguez
  • Publication number: 20220143154
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: January 21, 2022
    Publication date: May 12, 2022
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20210380993
    Abstract: The present invention relates to a vector, preferably included in a delivery vehicle, comprising no more than 100, preferably no more than 10, restriction sites recognized by the restriction enzymes encoded by each bacterium of a group of bacteria of interest. The invention also relates to the use of said vector, preferably included in a delivery vehicle, as a drug, especially in the treatment of a disease in a patient in need thereof.
    Type: Application
    Filed: June 23, 2021
    Publication date: December 9, 2021
    Applicants: Eligo Bioscience, Institut Pasteur
    Inventors: Antoine Decrulle, Jesus Fernandez Rodriguez, Xavier Duportet, David Bikard
  • Publication number: 20210322525
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: May 18, 2020
    Publication date: October 21, 2021
    Inventors: David Bikard, Luciano Marraffini
  • Patent number: 11135273
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Grant
    Filed: May 18, 2020
    Date of Patent: October 5, 2021
    Assignee: THE ROCKEFELLER UNIVERSITY
    Inventors: David Bikard, Luciano Marraffini
  • Patent number: 11078490
    Abstract: The present invention relates to a vector, preferably included in a delivery vehicle, comprising no more than 100, preferably no more than 10, restriction sites recognized by the restriction enzymes encoded by each bacterium of a group of bacteria of interest. The invention also relates to the use of said vector, preferably included in a delivery vehicle, as a drug, especially in the treatment of a disease in a patient in need thereof.
    Type: Grant
    Filed: September 10, 2020
    Date of Patent: August 3, 2021
    Assignees: Eligo Bioscience, Institut Pasteur
    Inventors: Antoine Decrulle, Jesus Fernandez Rodriguez, Xavier Duportet, David Bikard
  • Publication number: 20210193259
    Abstract: The invention relates to a method for generating protein sequences in an autoregressive neural network comprising an encoder and a decoder, the decoder comprising an autoregressive module, the method comprising: obtaining a latent code and inputting the latent code into the autoregressive module; obtaining probabilities from the autoregressive module, the obtained probabilities representing probabilities for amino acids to be selected at locations of the sequence; and generating an ordered sequence of amino acids from the obtained probabilities, wherein the autoregressive module is such that, for a location of the sequence, the probabilities associated with amino acids to be selected for the location in the sequence are determined as a function of probabilities of amino acids to be selected for previous locations in the sequence and wherein the autoregressive neural network has been trained end-to-end with the encoder, the encoder making it possible to encode protein sequences in a latent space as late
    Type: Application
    Filed: November 16, 2018
    Publication date: June 24, 2021
    Applicant: INSTITUT PASTEUR
    Inventors: David BIKARD, S├ębastien BAUR, Alexander HAWKINS-HOOKER
  • Publication number: 20210162022
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: February 5, 2021
    Publication date: June 3, 2021
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20210060140
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: November 3, 2020
    Publication date: March 4, 2021
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20210060141
    Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
    Type: Application
    Filed: November 3, 2020
    Publication date: March 4, 2021
    Inventors: David Bikard, Luciano Marraffini
  • Publication number: 20200399645
    Abstract: The present invention relates to a vector, preferably included in a delivery vehicle, comprising no more than 100, preferably no more than 10, restriction sites recognized by the restriction enzymes encoded by each bacterium of a group of bacteria of interest. The invention also relates to the use of said vector, preferably included in a delivery vehicle, as a drug, especially in the treatment of a disease in a patient in need thereof.
    Type: Application
    Filed: September 10, 2020
    Publication date: December 24, 2020
    Inventors: Antoine DECRULLE, Jesus FERNANDEZ RODRIGUEZ, Xavier DUPORTET, David BIKARD