Patents Assigned to Vilnius University
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Patent number: 11860076Abstract: The present invention relates to methods and systems for isolation of species in semi-permeable capsules and processing of encapsulated species through series of steps and/or reactions. To produce capsules, first aqueous two-phase system (ATPS) droplets are generated using microfluidics system and then the hydrogel shell layer is hardened by inducing polymerization. As exemplified in this invention to achieve concentric ATPS droplet formation density-matched PEGDA and Dextran polymer solutions can be used. Once a capsule is formed, its composition can be changed by adding new reagents or replacing out old ones (e.g. by resuspending capsules in desired aqueous solution). The hydrogel shell of semi-permeable capsules can be dissolved at selected step during multi-step procedures in order to release the encapsulated species. The present invention exemplifies the isolation of individual cells within capsules and using the encapsulated cells for genotypic and phenotypic analysis.Type: GrantFiled: July 21, 2020Date of Patent: January 2, 2024Assignees: Vilnius University, Droplet GenomicsInventors: Linas Mazutis, Greta Stonyte, Karolis Leonavicius, Ausra Zelvyte
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Patent number: 11850589Abstract: A system and method are provided for harvesting target biological substances. The system includes a substrate and a first and second channel formed in the substrate. The channels longitudinally extending substantially parallel to each other. A series of gaps extend from the first channel to the second channel to create a fluid communication path passing between a series of columns with the columns being longitudinally separated by a predetermined separation distance. The system also includes a first source configured to selectively introduce into the first channel a first biological composition at a first channel flow rate and a second source configured to selectively introduce into the second channel a second biological composition at a second channel flow rate. The sources are configured to create a differential between the first and second channel flow rates to generate physiological shear rates along the second channel that are bounded within a predetermined range.Type: GrantFiled: June 24, 2022Date of Patent: December 26, 2023Assignees: The Brigham and Women's Hospital, Inc., Boston, MA;, President and Fellows of Harvard College, Vilnius UniversityInventors: Joseph Italiano, Linas Mazutis, Jonathan N. Thon, David A. Weitz
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Publication number: 20230272394Abstract: Isolation or in vitro assembly of the Cas9-crRNA complex of the Streptococcus thermophilus CRISPR3/Cas system and use for cleavage of DNA bearing a nucleotide sequence complementary to the crRNA and a proto-spacer adjacent motif. Methods for site-specific modification of a target DNA molecule in vitro or in vivo using an RNA-guided DNA endonuclease comprising RNA sequences and at least one of an RuvC active site motif and an HNH active site motif; for conversion of Cas9 polypeptide into a nickase cleaving one strand of double-stranded DNA by inactivating one of the active sites (RuvC or HNH) in the polypeptide by at least one point mutation; for assembly of active polypeptide-polyribonucleotides complex in vivo or in vitro; and for re-programming a Cas9-crRNA complex specificity in vitro and using a cassette containing a single repeat-spacer-repeat unit.Type: ApplicationFiled: December 13, 2022Publication date: August 31, 2023Applicant: VILNIUS UNIVERSITYInventors: Virginijus SIKSNYS, Giedrius GASIUNAS, Tautvydas KARVELIS, Arvydas LUBYS, Lolita ZALIAUSKIENE, Monika GASIUNIENE, Anja SMITH
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Publication number: 20230123754Abstract: Isolation or in vitro assembly of the Cas9-crRNA complex of the Streptococcus thermophilus CRISPR3/Cas system and use for cleavage of DNA bearing a nucleotide sequence complementary to the crRNA and a proto-spacer adjacent motif. Methods for site-specific modification of a target DNA molecule using an RNA-guided DNA endonuclease comprising at least one RNA sequence and at least one of an RuvC active site motif and an HNH active site motif; for conversion of Cas9 polypeptide into a nickase cleaving one strand of double-stranded DNA by inactivating one of the active sites (RuvC or HNH) in the polypeptide by at least one point mutation; for assembly of active polypeptide-polyribonucleotides complex in vivo or in vitro; and for re-programming a Cas9-crRNA complex specificity in vitro or using a cassette containing a single repeat-spacer-repeat unit.Type: ApplicationFiled: July 5, 2022Publication date: April 20, 2023Applicant: Vilnius UniversityInventors: Virginijus {hacek over (S)}iksnys, Giedrius Gasiunas, Tautvydas Karvelis
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Patent number: 11584772Abstract: Disclosed are W-position modified cytidine nucleotides of formula (I). Provided herein are methods of chemical synthesis of AP-modified cytidine nucleoside triphosphates and their applications as well as uses of the cytidine analogues for the synthesis of modified nucleic acids. The nucleic acid molecule includes DNA, RNA or a combination of DNA/RNA. One of many applications of modified cytidine nucleotides described herein is enzyme selection, when an enzyme of interest bears an activity of an esterase, amidase, oxidoreductase, lyase, ligase or other enzymatic activity, formula (I) wherein the substituants are as defined in the appended claims.Type: GrantFiled: September 12, 2018Date of Patent: February 21, 2023Assignee: VILNIUS UNIVERSITYInventors: Rolandas Meskys, Jevgenija Jakubovska, Daiva Tauraite
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Patent number: 11566214Abstract: Systems and methods generating physiologic models that can produce functional biological substances are provided. In some aspects, a system includes a substrate and a first and second channel formed therein. The channels extend longitudinally and are substantially parallel to each other. A series of apertures extend between the first channel and second channel to create a fluid communication path passing through columns separating the channels that extends further along the longitudinal dimension than other dimensions. The system also includes a first source configured to selectively introduce into the first channel a first biological composition at a first channel flow rate and a second source configured to selectively introduce into the second channel a second biological composition at a second channel flow rate, wherein the first channel flow rate and the second channel flow rate create a differential configured to generate physiological shear rates within a predetermined range in the channels.Type: GrantFiled: February 17, 2020Date of Patent: January 31, 2023Assignees: BRIGHAM AND WOMEN'S HOSPITAL, INC., PRESIDENT AND FELLOWS OF HARVARD COLLEGE, VILNIUS UNIVERSITYInventors: Jonathan N. Thon, Joseph E. Italiano, Linas Mazutis, David A. Weitz
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Patent number: 11555187Abstract: Isolation or in vitro assembly of the Cas9-crRNA complex of the Streptococcus thermophilus CRISPR3/Cas system and use for cleavage of DNA bearing a nucleotide sequence complementary to the crRNA and a proto-spacer adjacent motif. Methods for site-specific modification of a target DNA molecule in vitro or in vivo using an RNA-guided DNA endonuclease comprising RNA sequences and at least one of an RuvC active site motif and an HNH active site motif; for conversion of Cas9 polypeptide into a nickase cleaving one strand of double-stranded DNA by inactivating one of the active sites (RuvC or HNH) in the polypeptide by at least one point mutation; for assembly of active polypeptide-polyribonucleotides complex in vivo or in vitro; and for re-programming a Cas9-crRNA complex specificity in vitro and using a cassette containing a single repeat-spacer-repeat unit.Type: GrantFiled: December 7, 2017Date of Patent: January 17, 2023Assignee: Vilnius UniversityInventors: Virginijus {hacek over (S)}ik{hacek over (s)}nys, Giedrius Gasiunas, Tautvydas Karvelis, Arvydas Lubys, Lolita Zaliauskiene, Monika Gasiuniene, Anja Smith
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Patent number: 11396016Abstract: A system and method are provided for harvesting target biological substances. The system includes a substrate and a first and second channel formed in the substrate. The channels longitudinally extending substantially parallel to each other. A series of gaps extend from the first channel to the second channel to create a fluid communication path passing between a series of columns with the columns being longitudinally separated by a predetermined separation distance. The system also includes a first source configured to selectively introduce into the first channel a first biological composition at a first channel flow rate and a second source configured to selectively introduce into the second channel a second biological composition at a second channel flow rate. The sources are configured to create a differential between the first and second channel flow rates to generate physiological shear rates along the second channel that are bounded within a predetermined range.Type: GrantFiled: June 17, 2020Date of Patent: July 26, 2022Assignees: The Brigham and Women's Hospital, Inc., President and Fellows of Harvard College, Vilnius UniversityInventors: Joseph Italiano, Linas Mazutis, Jonathan Thon, David A. Weitz
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Patent number: 11326196Abstract: Disclosed is a system and method for production of DNA particles and use thereof. The DNA particles can be produced by amplification of nucleic acid molecule(s). Alternatively, DNA particles can be prepared by condensing multiple DNA molecules. The DNA condensation into a particle is mainly triggered by pyrophosphate and positively charged cations (e.g. magnesium). DNA particles can be applied for numerous biological applications but not limited to directed evolution, proteomics, drug delivery and imaging. DNA particles can be used to synthesize proteins using in vitro transcription/translation reaction.Type: GrantFiled: January 10, 2017Date of Patent: May 10, 2022Assignees: VILNIUS UNIVERSITY, ETH 7LIRICHInventors: Linas Mazutis, Greta Stonyte, Vaidotas Kiseliovas, Rapolas Zilionis, Arvydas Janulaitis, Robertas Galinis, Sabine Studer, Donald Hilvert
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Patent number: 11312682Abstract: Disclosed are novel compounds—benzenesulfonamides of general formulas (I) and (II) The compounds can be used in biomedicine as active ingredients in pharmaceutical formulations, because they inhibit enzymes which participate in disease progression. Also disclosed are method of treatment using such compounds.Type: GrantFiled: September 1, 2015Date of Patent: April 26, 2022Assignee: VILNIUS UNIVERSITYInventors: Daumantas Matulis, Edita Capkauskaite, Andrius Zaksauskas, Vaida Morkunaite
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Patent number: 11274317Abstract: Methods and compositions using a CRISPR-Cas Type IIIA resulting in RNA gene knockdown and knockout in an animal.Type: GrantFiled: August 31, 2017Date of Patent: March 15, 2022Assignee: VILNIUS UNIVERSITYInventors: Thomas Fricke, Matthias Bochtler, Gintautas Tamulaitis, Miglé Kazlauskiene, Virginijus {hacek over (S)}ik{hacek over (s)}nys
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Publication number: 20210379555Abstract: The present invention generally relates to microfluidics and labeled nucleic acids. For example, certain aspects are generally directed to systems and methods for labeling nucleic acids within microfluidic droplets. In one set of embodiments, the nucleic acids may include “barcodes” or unique sequences that can be used to distinguish nucleic acids in a droplet from those in another droplet, for instance, even after the nucleic acids are pooled together. In some cases, the unique sequences may be incorporated into individual droplets using particles and attached to nucleic acids contained within the droplets (for example, released from lysed cells). In some cases, the barcodes may be used to distinguish tens, hundreds, or even thousands of nucleic acids, e.g., arising from different cells or other sources.Type: ApplicationFiled: May 18, 2021Publication date: December 9, 2021Applicants: President and Fellows of Harvard College, Vilnius UniversityInventors: David A. Weitz, Allon Moshe Klein, Ilke Akartuna, Linas Mazutis, Marc W. Kirschner
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Patent number: 11052368Abstract: The present invention generally relates to microfluidics and labeled nucleic acids. For example, certain aspects are generally directed to systems and methods for labeling nucleic acids within microfluidic droplets. In one set of embodiments, the nucleic acids may include “barcodes” or unique sequences that can be used to distinguish nucleic acids in a droplet from those in another droplet, for instance, even after the nucleic acids are pooled together. In some cases, the unique sequences may be incorporated into individual droplets using particles and attached to nucleic acids contained within the droplets (for example, released from lysed cells). In some cases, the barcodes may be used to distinguish tens, hundreds, or even thousands of nucleic acids, e.g., arising from different cells or other sources.Type: GrantFiled: May 29, 2018Date of Patent: July 6, 2021Assignees: Vilnius University, President and Fellows of Harvard CollegeInventors: David A. Weitz, Allon Moshe Klein, Ilke Akartuna, Linas Mazutis, Marc W. Kirschner
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Publication number: 20210147909Abstract: Methods and compositions are provided for the identification, detection, characterization, and/or utilization of double strand breaks in a target polynucleotide; the identification, detection, characterization, and/or utilization of cutting sites for double-strand-break-inducing agents; and the identification, detection, characterization, and/or utilization of double-strand-break-inducing agents.Type: ApplicationFiled: May 10, 2019Publication date: May 20, 2021Applicants: PIONEER HI-BRED INTERNATIONAL, INC., VILNIUS UNIVERSITYInventors: STEPHANE DESCHAMPS, VIRGINIJUS SIKSNYS, JOSHUA K YOUNG, MINDAUGAS ZAREMBA
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Patent number: 11008605Abstract: Provided is a method for modifying a ssRNA at the 3? end, the method including contacting the strand with a ssRNA 2?-O-methyltransferase in the presence of a co-factor, under conditions which allow for the transfer by the ssRNA 2?-O-methyltransferase of a part of the co-factor onto the 3? end of the ssRNA to form a modified ssRNA, wherein the ssRNA bears 2?-OH group at 3? terminal nucleotide and wherein the part of the co-factor transferred includes a reporter group or a functional group.Type: GrantFiled: March 18, 2016Date of Patent: May 18, 2021Assignee: Vilnius UniversityInventors: Saulius Klimasauskas, Giedrius Vilkaitis, Milda Mickute
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Patent number: 10844378Abstract: Isolation or in vitro assembly of the Cas9-crRNA complex of the Streptococcus thermophilus CRISPR3/Cas system and use for cleavage of DNA bearing a nucleotide sequence complementary to the crRNA and a proto-spacer adjacent motif. Methods for site-specific modification of a target DNA molecule using an RNA-guided DNA endonuclease comprising at least one RNA sequence and at least one of an RuvC active site motif and an HNH active site motif; for conversion of Cas9 polypeptide into a nickase cleaving one strand of double-stranded DNA by inactivating one of the active sites (RuvC or HNH) in the polypeptide by at least one point mutation; for assembly of active polypeptide-polyribonucleotides complex in vivo or in vitro; and for re-programming a Cas9-crRNA complex specificity in vitro or using a cassette containing a single repeat-spacer-repeat unit.Type: GrantFiled: October 1, 2018Date of Patent: November 24, 2020Assignee: Vilnius UniversityInventors: Virginijus {hacek over (S)}ik{hacek over (s)}nys, Giedrius Gasiūnas, Tautvydas Karvelis
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Patent number: 10710073Abstract: A system and method are provided for harvesting target biological substances. The system includes a substrate and a first and second channel formed in the substrate. The channels longitudinally extending substantially parallel to each other. A series of gaps extend from the first channel to the second channel to create a fluid communication path passing between a series of columns with the columns being longitudinally separated by a predetermined separation distance. The system also includes a first source configured to selectively introduce into the first channel a first biological composition at a first channel flow rate and a second source configured to selectively introduce into the second channel a second biological composition at a second channel flow rate. The sources are configured to create a differential between the first and second channel flow rates to generate physiological shear rates along the second channel that are bounded within a predetermined range.Type: GrantFiled: May 24, 2019Date of Patent: July 14, 2020Assignees: Brigham and Women's Hospital, Inc., President and Fellows of Harvard College, Vilnius UniversityInventors: Joseph Italiano, Linas Mazutis, Jonathan N. Thon, David A. Weitz
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Patent number: 10596541Abstract: The present invention generally relates to microfluidics and labeled nucleic acids. For example, certain aspects are generally directed to systems and methods for labeling nucleic acids within microfluidic droplets. In one set of embodiments, the nucleic acids may include “barcodes” or unique sequences that can be used to distinguish nucleic acids in a droplet from those in another droplet, for instance, even after the nucleic acids are pooled together. In some cases, the unique sequences may be incorporated into individual droplets using particles and attached to nucleic acids contained within the droplets (for example, released from lysed cells). In some cases, the barcodes may be used to distinguish tens, hundreds, or even thousands of nucleic acids, e.g., arising from different cells or other sources.Type: GrantFiled: October 3, 2017Date of Patent: March 24, 2020Assignees: President and Fellows of Harvard College, Vilnius UniversityInventors: David A. Weitz, Allon Moshe Klein, Ilke Akartuna, Linas Mazutis, Marc W. Kirschner
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Patent number: 10590373Abstract: Systems and methods generating physiologic models that can produce functional biological substances are provided. In some aspects, a system includes a substrate and a first and second channel formed therein. The channels extend longitudinally and are substantially parallel to each other. A series of apertures extend between the first channel and second channel to create a fluid communication path passing through columns separating the channels that extends further along the longitudinal dimension than other dimensions. The system also includes a first source configured to selectively introduce into the first channel a first biological composition at a first channel flow rate and a second source configured to selectively introduce into the second channel a second biological composition at a second channel flow rate, wherein the first channel flow rate and the second channel flow rate create a differential configured to generate physiological shear rates within a predetermined range in the channels.Type: GrantFiled: March 30, 2015Date of Patent: March 17, 2020Assignees: BRIGHAM AND WOMEN'S HOSPITAL, INC., PRESIDENT AND FELLOWS OF HARVARD COLLEGE, VILNIUS UNIVERSITYInventors: Jonathan N. Thon, Joseph E. Italiano, Linas Mazutis, David A. Weitz
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Patent number: 10385336Abstract: A Type III-A CRISPR-Cas (StCsm) complex of Streptococcus thermophilus comprising crRNA, Csm4, and Csm3 and use for cleavage of RNA bearing a nucleotide sequence complementary to the crRNA, in vitro or in vivo. Methods for site-specific cleavage/shredding of a target RNA molecule using an RNA-guided RNA endonuclease comprising a minimal complex of crRNA, Csm4, and Csm3, and methods of RNA knock-down and RNA knock-out are disclosed.Type: GrantFiled: March 3, 2017Date of Patent: August 20, 2019Assignee: VILNIUS UNIVERSITYInventors: Virginijus Siksnys, Migle Kazlauskiene, Gintautas Tamulaitis