Patents by Inventor Rustem F. Ismagilov

Rustem F. Ismagilov 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: 12173363
    Abstract: Provided herein are methods and systems for absolute quantification of a target 16S rRNA and/or of a target prokaryotic taxon, based on amplifying and sequencing a same 16S rRNA recognition segment in which target 16S rRNA conserved regions flank 16S rRNA variable regions, conserved and variable among a plurality of sample 16S rRNAs and/or of a sample prokaryotic taxon of higher taxonomic rank with respect to the target taxon. In the methods and systems, absolute abundance of the a plurality of sample 16S rRNAs and/or of the sample prokaryotic taxon detected by the amplifying, is multiplied by the relative abundance of the target 16S rRNA and/or of a target prokaryotic taxon detected by the sequencing to provide the absolute quantification in accordance with method and systems of the disclosure.
    Type: Grant
    Filed: July 12, 2022
    Date of Patent: December 24, 2024
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Jacob T. Barlow, Said R. Bogatyrev
  • Patent number: 12173361
    Abstract: Provided herein are methods and systems and related composition, to provide a rodent model having a target microbiome profile formed by a target presence, a target proportion and/or a target total load of a target prokaryote of a target taxon, based on absolute quantification of the target prokaryote. Further provided are rodents obtained by the methods herein described and related use in testing methods performed in connection with physiological or pathological conditions in an individual preferably a human individual. Also provided herein is a tailcup device and related use to prevent coprophagia in rodents.
    Type: Grant
    Filed: January 13, 2021
    Date of Patent: December 24, 2024
    Inventors: Rustem F Ismagilov, Jacob T Barlow, Said R Bogatyrev
  • Patent number: 12157705
    Abstract: Provided herein are methods for making a freeze-cast material having a internal structure, the methods comprising steps of: determining the internal structure of the material, the internal structure having a plurality of pores, wherein: each of the plurality of pores has directionality; and the step of determining comprises: selecting a temperature gradient and a freezing front velocity to obtain the determined internal structure based on the selected temperature gradient and the selected freezing front velocity; directionally freezing a liquid formulation to form a frozen solid, the step of directionally freezing comprising: controlling the temperature gradient and the freezing front velocity to match the selected temperature gradient and the selected freezing front velocity during directionally freezing; wherein the liquid formulation comprises at least one solvent and at least one dispersed species; and subliming the at least one solvent out of the frozen solid to form the material.
    Type: Grant
    Filed: July 31, 2023
    Date of Patent: December 3, 2024
    Assignee: California Institute of Technology
    Inventors: Katherine T. Faber, Julia A. Kornfield, Noriaki Arai, Orland Bateman, Rustem F. Ismagilov
  • Publication number: 20240395397
    Abstract: An interactive modular device for instructing and assisting users on sample handling processes using features to guide a user through the processes in real time. The modules of the device include a processing module (e.g., pooling module), a sample-container module (e.g., tube module), a container-closure module (e.g., cap module), a sample-transfer module (e.g., pipette module), a scanning module (e.g., single barcode module), a multi-scanning module (e.g., multi-barcode module), a waste container module, and a display module. The features include mechanisms to determine presence and absence of items used for sample handling and visual, audible, and tactile indicators in real time.
    Type: Application
    Filed: May 17, 2024
    Publication date: November 28, 2024
    Inventors: Rustem F ISMAGILOV, Minkyo LEE, Si Hyung JIN, Matthew M COOPER, Roey LAZAROVITS
  • Patent number: 12122996
    Abstract: A device for allowing compartmentalized reactions with minimized cross-contamination between the compartments, utilizing a delivery of material by loading wells to pooling wells, such that the pooling wells can be additively provided with reactants while maintaining isolation between the pooling wells. The use of geometric properties is used to facilitate transmission of fluids/droplets without the need for hydrophilic surfaces.
    Type: Grant
    Filed: September 25, 2018
    Date of Patent: October 22, 2024
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Eugenia Khorosheva, Dmitriy V. Zhukov
  • Patent number: 12097475
    Abstract: The present invention provides microfluidic technology enabling rapid and economical manipulation of reactions on the femtoliter to microliter scale.
    Type: Grant
    Filed: January 12, 2024
    Date of Patent: September 24, 2024
    Assignee: The University of Chicago
    Inventors: Rustem F. Ismagilov, Bo Zheng, Cory John Gerdts
  • Publication number: 20240192707
    Abstract: The present invention provides microfluidic technology enabling rapid and economical manipulation of reactions on the femtoliter to microliter scale.
    Type: Application
    Filed: January 12, 2024
    Publication date: June 13, 2024
    Inventors: Rustem F. Ismagilov, Bo Zheng, Cory John Gerdts
  • Publication number: 20240160231
    Abstract: The present invention provides microfluidic technology enabling rapid and economical manipulation of reactions on the femtoliter to microliter scale.
    Type: Application
    Filed: December 22, 2023
    Publication date: May 16, 2024
    Inventors: Rustem F. Ismagilov, Bo Zheng, Cory John Gerdts
  • Publication number: 20240084360
    Abstract: Provided herein are methods and systems to selectively deplete a biological sample of host compartments and/or host nucleic acid while enriching the sample microbial compartments and/or related microbial nucleic acid. In addition, provided herein are compositions, methods and systems related to said host depletion and microbial enrichment methods and systems.
    Type: Application
    Filed: July 12, 2023
    Publication date: March 14, 2024
    Inventors: Rustem F. Ismagilov, Natalie Wu-Woods, Jacob T. Barlow, Anna E. Romano
  • Publication number: 20240034688
    Abstract: Provided herein are methods for making a freeze-cast material having a internal structure, the methods comprising steps of: determining the internal structure of the material, the internal structure having a plurality of pores, wherein: each of the plurality of pores has directionality; and the step of determining comprises: selecting a temperature gradient and a freezing front velocity to obtain the determined internal structure based on the selected temperature gradient and the selected freezing front velocity; directionally freezing a liquid formulation to form a frozen solid, the step of directionally freezing comprising: controlling the temperature gradient and the freezing front velocity to match the selected temperature gradient and the selected freezing front velocity during directionally freezing; wherein the liquid formulation comprises at least one solvent and at least one dispersed species; and subliming the at least one solvent out of the frozen solid to form the material.
    Type: Application
    Filed: July 31, 2023
    Publication date: February 1, 2024
    Applicant: California Institute of Technology
    Inventors: Katherine T. FABER, Julia A. KORNFIELD, Noriaki ARAI, Orland BATEMAN, Rustem F. ISMAGILOV
  • Publication number: 20240011021
    Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.
    Type: Application
    Filed: February 23, 2023
    Publication date: January 11, 2024
    Inventors: Rustem F. ISMAGILOV, Matthew S. CURTIS, Mary ARRASTIA, David A. SELCK, Mitchell GUTTMAN
  • Patent number: 11866695
    Abstract: Methods and systems and related compositions for separating through a solid matrix a mixture comprising a nucleic acid in a concentration of 1 ?M or less, together with a target compound having a water solubility equal to or greater than 0.001 g per 100 mL, which can be used for managing fluid flow, biochemical reactions and purification of the nucleic acid or other target analytes. The method comprises contacting the solid matrix with a target compound removing agent having a water solubility equal to or less than 0.05 g per 100 mL at 25° C. at 1 atm pressure with water having a solubility in the removing agent of less than 10 g per 100 mL at 25° C. at 1 atm pressure, the contacting performed to remove the target compound from the solid matrix.
    Type: Grant
    Filed: December 22, 2020
    Date of Patent: January 9, 2024
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Erik Jue, Daan Witters
  • Patent number: 11853087
    Abstract: The present invention provides microfluidic technology enabling rapid and economical manipulation of reactions on the femtoliter to microliter scale.
    Type: Grant
    Filed: August 3, 2020
    Date of Patent: December 26, 2023
    Assignee: The University of Chicago
    Inventors: Rustem F. Ismagilov, Bo Zheng, Cory John Gerdts
  • Patent number: 11827944
    Abstract: Provided herein is an antibiotic susceptibility test and related compositions, methods and systems based on detection of a nucleic acid from a target microorganism in a sample in the presence or absence of a lysis treatment of the sample.
    Type: Grant
    Filed: October 11, 2018
    Date of Patent: November 28, 2023
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Emily S. Savela, Nathan Schoepp, Eric J. Liaw
  • Patent number: 11760698
    Abstract: Provided herein are methods for making a freeze-cast material having a internal structure, the methods comprising steps of: determining the internal structure of the material, the internal structure having a plurality of pores, wherein: each of the plurality of pores has directionality; and the step of determining comprises: selecting a temperature gradient and a freezing front velocity to obtain the determined internal structure based on the selected temperature gradient and the selected freezing front velocity; directionally freezing a liquid formulation to form a frozen solid, the step of directionally freezing comprising: controlling the temperature gradient and the freezing front velocity to match the selected temperature gradient and the selected freezing front velocity during directionally freezing; wherein the liquid formulation comprises at least one solvent and at least one dispersed species; and subliming the at least one solvent out of the frozen solid to form the material.
    Type: Grant
    Filed: December 23, 2021
    Date of Patent: September 19, 2023
    Assignee: California Institute of Technology
    Inventors: Katherine T. Faber, Julia A. Kornfield, Noriaki Arai, Orland Bateman, Rustem F. Ismagilov
  • Publication number: 20230272466
    Abstract: Provided herein are methods and systems for absolute quantification of a target 16S rRNA and/or of a target prokaryotic taxon, based on amplifying and sequencing a same 16S rRNA recognition segment in which target 16S rRNA conserved regions flank 16S rRNA variable regions, conserved and variable among a plurality of sample 16S rRNAs and/or of a sample prokaryotic taxon of higher taxonomic rank with respect to the target taxon. In the methods and systems, absolute abundance of the a plurality of sample 16S rRNAs and/or of the sample prokaryotic taxon detected by the amplifying, is multiplied by the relative abundance of the target 16S rRNA and/or of a target prokaryotic taxon detected by the sequencing to provide the absolute quantification in accordance with method and systems of the disclosure.
    Type: Application
    Filed: July 12, 2022
    Publication date: August 31, 2023
    Inventors: Rustem F. ISMAGILOV, Jacob T. BARLOW, Said R. BOGATYREV
  • Publication number: 20230212661
    Abstract: The present invention relates to assays, including amplification assays, conducted in the presence of modulators. These assays can be used to detect the presence of particular nucleic acid sequences. In particular, these assays can allow for genotyping or other genetic analysis.
    Type: Application
    Filed: July 8, 2022
    Publication date: July 6, 2023
    Inventors: Rustem F. ISMAGILOV, Bing SUN, Jesus RODRIGUEZ MANZANO, Eugenia KHOROSHEVA, Matthew S. CURTIS
  • Publication number: 20230183818
    Abstract: Provided herein are RNA markers and compositions, methods and systems for the related identification and/or uses in methods for detection of antibiotic susceptibility and resistance in a microorganism, and in particular in N. gonorrhoeae.
    Type: Application
    Filed: August 1, 2019
    Publication date: June 15, 2023
    Inventors: Rustem F. ISMAGILOV, Nathan SCHOEPP, Tahmineh KHAZAEI, Jacob T. BARLOW
  • Patent number: 11661577
    Abstract: Provided herein are devices and methods that enable co-incubation of microorganisms. Also provided are methods of making such devices for co-incubation of microorganisms, and various applications of such devices.
    Type: Grant
    Filed: December 28, 2018
    Date of Patent: May 30, 2023
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: James Q. Boedicker, Rustem F. Ismagilov, Hyun Jung Kim
  • Patent number: 11624062
    Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.
    Type: Grant
    Filed: September 25, 2018
    Date of Patent: April 11, 2023
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Rustem F. Ismagilov, Matthew S. Curtis, Mary Arrastia, David A. Selck, Mitchell Guttman