Patents by Inventor Tyler Lopez
Tyler Lopez 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: 12163163Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: GrantFiled: January 27, 2023Date of Patent: December 10, 2024Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Jendrik Boothby-Hentschel, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger, Mark Ambroso
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Patent number: 12139727Abstract: Provided herein are engineered variants of archaeal, prokaryotic, and eukaryotic polymerases that exhibit enhanced thermostability, enhanced incorporation of 3? modified nucleotides, and improved uracil-tolerance, in polymerase-catalyzed nucleotide extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases, forming binding complexes and forming ternary complexes, and uses for conducting nucleic acid sequencing reactions.Type: GrantFiled: March 25, 2022Date of Patent: November 12, 2024Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger
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Patent number: 12091657Abstract: Provided herein are compositions and methods for the incorporation of unnatural nucleotides using mutant polymerases, such as reverse transcriptases. Further provided herein are methods of detection and sequencing of polynucleotide sequences. In some aspects, the compositions and methods are used enhance the efficiency and speed of detecting nucleotide bases. The methods and compositions described herein may further reduce time, cost, or scale of devices for next generation sequencing platforms.Type: GrantFiled: December 11, 2020Date of Patent: September 17, 2024Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Matthew Kellinger, Molly He, Tyler Lopez
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Publication number: 20240287482Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: April 30, 2024Publication date: August 29, 2024Inventors: Jendrik HENTSCHEL, Tyler LOPEZ, Michael KLEIN, Virginia SAADE, Matthew KELLINGER, Mark AMBROSO
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Publication number: 20240270554Abstract: An aerial lift that is interlocked with a fall-protection safety apparatus and may be further interlocked with at least one additional safety apparatus. The aerial lift is equipped with a monitoring system that is configured to detect whether a connector of a safety line of the fall-protection apparatus appears to be connected to a safety harness of a user of the aerial lift.Type: ApplicationFiled: June 22, 2022Publication date: August 15, 2024Inventors: Jonathan J. Lepp, Christopher J. Reineke, Kristin M. Mikes, Donaldo J. Medeiros, Jeffrey T. Keacher, Aline H. Hinkle, Christopher M. Higgins, Heidi A. Lopez-Hidalgo, Tyler B. Henn, Lauren K. Carlson, Michael T. Weiss
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Publication number: 20240191278Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: ApplicationFiled: November 15, 2023Publication date: June 13, 2024Inventors: Sinan ARSLAN, Junhua ZHAO, Molly HE, Samantha SNOW, William LIGHT, Matthew KELLINGER, Michael PREVITE, Michael KIM, Hua YU, Yu-Hsien HWANG-FU, Marco TJIOE, Andrew BODDICKER, Mark AMBROSO, Tyler LOPEZ, Michael KLEIN, Virginia SAADE
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Patent number: 12006518Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: GrantFiled: January 27, 2023Date of Patent: June 11, 2024Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Jendrik Hentschel, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger, Mark Ambroso
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Publication number: 20240117428Abstract: The present disclosure provides nucleotide conjugates each configured to include a core attached to multiple nucleotide-arms, where the nucleotide-arms are modular and comprise (i) a core attachment moiety, (ii) a spacer, (iii) a linker, and (iv) a nucleotide unit. The nucleotide unit of each nucleotide-arm can bind a polymerase which is complexed with a nucleic acid template and nucleic acid primer. The nucleotide unit can bind the 3? end of the primer at a position that is opposite a complementary nucleotide in the template strand. Under suitable conditions, the nucleotide unit of the nucleotide conjugates binds the primer strand but does not undergo polymerase-catalyzed incorporation. The binding event can be detected, and the specific base of the nucleotide unit can be identified. The nucleotide conjugates described herein are useful for nucleic acid sequencing methods, particularly for massively parallel sequencing methods employed for next gen sequencing platforms.Type: ApplicationFiled: August 2, 2023Publication date: April 11, 2024Inventors: MICHAEL PREVITE, MARK AMBROSO, TYLER LOPEZ, MICHAEL KLEIN, VIRGINIA SAADE, MATTHEW KELLINGER
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Patent number: 11859241Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: February 8, 2023Date of Patent: January 2, 2024Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker, Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade
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Patent number: 11788075Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: GrantFiled: January 27, 2023Date of Patent: October 17, 2023Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Jendrik Hentschel, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger, Mark Ambroso
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Publication number: 20230323450Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: March 9, 2023Publication date: October 12, 2023Inventors: Sinan Arslan, Molly Min HE, Matthew KELLINGER, Jake LEVIEUX, Michael PREVITE, Junhua ZHAO, Su ZHANG, Tyler LOPEZ
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Publication number: 20230265402Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: January 27, 2023Publication date: August 24, 2023Inventors: Jendrik HENTSHCEL, Tyler LOPEZ, Michael KLEIN, Virginia SAADE, Matthew KELLINGER, Mark AMBROSO
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Publication number: 20230265400Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: January 27, 2023Publication date: August 24, 2023Inventors: Jendrik HENTSHCEL, Tyler LOPEZ, Michael KLEIN, Virginia SAADE, Matthew KELLINGER, Mark AMBROSO
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Publication number: 20230265401Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3? modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: January 27, 2023Publication date: August 24, 2023Inventors: Jendrik HENTSHCEL, Tyler LOPEZ, Michael KLEIN, Virginia SAADE, Matthew KELLINGER, Mark AMBROSO
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Publication number: 20230203564Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: ApplicationFiled: February 8, 2023Publication date: June 29, 2023Inventors: Sinan ARSLAN, Junhua ZHAO, Molly HE, Samantha SNOW, William LIGHT, Matthew KELLINGER, Michael PREVITE, Michael KIM, Hua YU, Yu-Hsien HWANG-FU, Marco TJIOE, Andrew BODDICKER, Mark AMBROSO, Tyler LOPEZ, Michael KLEIN, Virginia SAADE
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Publication number: 20230074615Abstract: Certain embodiments provide an isolated anti-matrix metalloproteinase-9 (MMP-9) antibody or fragment thereof, as well as methods of use thereof.Type: ApplicationFiled: May 21, 2020Publication date: March 9, 2023Applicants: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, DUKE UNIVERSITYInventors: Xin GE, Tyler LOPEZ, Ru-Rong JI
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Publication number: 20220403351Abstract: Provided herein are engineered variants of archaeal, prokaryotic, and eukaryotic polymerases that exhibit enhanced thermostability, enhanced incorporation of 3? modified nucleotides, and improved uracil-tolerance, in polymerase-catalyzed nucleotide extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases, forming binding complexes and forming ternary complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: March 25, 2022Publication date: December 22, 2022Inventors: Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger
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Publication number: 20220403352Abstract: Provided herein are engineered variants of archaeal, prokaryotic, and eukaryotic polymerases that exhibit enhanced thermostability, enhanced incorporation of 3? modified nucleotides, and improved uracil-tolerance, in polymerase-catalyzed nucleotide extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases, forming binding complexes and forming ternary complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: March 25, 2022Publication date: December 22, 2022Inventors: Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger
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Publication number: 20220403353Abstract: Provided herein are engineered variants of archaeal, prokaryotic, and eukaryotic polymerases that exhibit enhanced thermostability, enhanced incorporation of 3? modified nucleotides, and improved uracil-tolerance, in polymerase-catalyzed nucleotide extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases, forming binding complexes and forming ternary complexes, and uses for conducting nucleic acid sequencing reactions.Type: ApplicationFiled: March 25, 2022Publication date: December 22, 2022Inventors: Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade, Matthew Kellinger
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Publication number: 20220186310Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: October 26, 2021Publication date: June 16, 2022Inventors: Sinan Arslan, Molly Min HE, Matthew KELLINGER, Jake LEVIEUX, Michael PREVITE, Junhua ZHAO, Su ZHANG, Tyler LOPEZ