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).
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Patent number: 11946056Abstract: 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: GrantFiled: June 23, 2021Date of Patent: April 2, 2024Assignees: ELIGO BIOSCIENCE, INSTITUT PASTEURInventors: Antoine Decrulle, Jesus Fernandez Rodriguez, Xavier Duportet, David Bikard
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Patent number: 11918631Abstract: 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: GrantFiled: May 20, 2016Date of Patent: March 5, 2024Assignee: THE ROCKEFELLER UNIVERSITYInventors: David Bikard, Luciano Marraffini
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Patent number: 11905516Abstract: 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: GrantFiled: February 2, 2018Date of Patent: February 20, 2024Assignees: ELIGO BIOSCIENCE, INSTITUT PASTEURInventors: Antoine Decrulle, Jesus Fernandez Rodriguez, Xavier Duportet, David Bikard
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Patent number: 11725183Abstract: The present invention relates to an in vitro method of culturing a segmented filamentous bacterium strain, comprising co-culturing said segmented filamentous bacterium strain with a eukaryotic host cell, wherein the culture is performed at an O2 level inferior to 5% in a rich tissue culture liquid medium containing bacterial medium components including iron. The present invention also relates to methods for genetically modifying a segmented filamentous bacterium strain comprising a step a culturing the strain in vitro.Type: GrantFiled: August 22, 2019Date of Patent: August 15, 2023Assignees: INSTITUT PASTEUR, FONDATION IMAGINE, ASSISTANCE PUBLIQUE—HOPITAUX DE PARIS, UNIVERSITE PARIS CITE, INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE (INSERM)Inventors: Gerard Eberl, David Bikard, Pamela Schnupf, Nadine Cerf Bensussan, Valerie Gaboriau-Routhiau, Philippe Sansonetti
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Patent number: 11497797Abstract: 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: GrantFiled: March 29, 2022Date of Patent: November 15, 2022Assignee: The Rockfeller UniversityInventors: David Bikard, Luciano Marraffini
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Patent number: 11491210Abstract: 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: GrantFiled: March 29, 2022Date of Patent: November 8, 2022Assignee: The Rockefeller UniversityInventors: David Bikard, Luciano Marraffini
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Patent number: 11491209Abstract: 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: GrantFiled: March 29, 2022Date of Patent: November 8, 2022Assignee: The Rockefeller UniversityInventors: David Bikard, Luciano Marraffini
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Publication number: 20220347271Abstract: 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: ApplicationFiled: June 3, 2022Publication date: November 3, 2022Inventors: David BIKARD, Lun CUI, Xavier DUPORTET, Jesus FERNANDEZ RODRIGUEZ
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Patent number: 11452765Abstract: 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: GrantFiled: January 21, 2022Date of Patent: September 27, 2022Assignee: The Rockefeller UniversityInventors: David Bikard, Luciano Marraffini
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Publication number: 20220218795Abstract: 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: ApplicationFiled: March 29, 2022Publication date: July 14, 2022Inventors: David Bikard, Luciano Marraffini
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Publication number: 20220218797Abstract: 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: ApplicationFiled: March 29, 2022Publication date: July 14, 2022Inventors: David Bikard, Luciano Marraffini
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Publication number: 20220218796Abstract: 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: ApplicationFiled: March 29, 2022Publication date: July 14, 2022Inventors: David Bikard, Luciano Marraffini
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Patent number: 11377645Abstract: 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: GrantFiled: December 18, 2017Date of Patent: July 5, 2022Assignee: The Rockefeller UniversityInventors: Luciano Marraffini, Robert Heller, David Bikard
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Patent number: 11357831Abstract: 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: GrantFiled: November 1, 2019Date of Patent: June 14, 2022Assignees: INSTITUT PASTEUR, ELIGO BIOSCIENCEInventors: David Bikard, Lun Cui, Xavier Duportet, Jesus Fernandez Rodriguez
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Publication number: 20220143154Abstract: 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: ApplicationFiled: January 21, 2022Publication date: May 12, 2022Inventors: David Bikard, Luciano Marraffini
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Publication number: 20210380993Abstract: 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: ApplicationFiled: June 23, 2021Publication date: December 9, 2021Applicants: Eligo Bioscience, Institut PasteurInventors: Antoine Decrulle, Jesus Fernandez Rodriguez, Xavier Duportet, David Bikard
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Publication number: 20210322525Abstract: 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: ApplicationFiled: May 18, 2020Publication date: October 21, 2021Inventors: David Bikard, Luciano Marraffini
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Patent number: 11135273Abstract: 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: GrantFiled: May 18, 2020Date of Patent: October 5, 2021Assignee: THE ROCKEFELLER UNIVERSITYInventors: David Bikard, Luciano Marraffini
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Patent number: 11078490Abstract: 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: GrantFiled: September 10, 2020Date of Patent: August 3, 2021Assignees: Eligo Bioscience, Institut PasteurInventors: Antoine Decrulle, Jesus Fernandez Rodriguez, Xavier Duportet, David Bikard
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Publication number: 20210193259Abstract: 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 lateType: ApplicationFiled: November 16, 2018Publication date: June 24, 2021Applicant: INSTITUT PASTEURInventors: David BIKARD, Sébastien BAUR, Alexander HAWKINS-HOOKER