Patents Examined by Narayan Bhat
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Patent number: 10081832Abstract: The present invention relates to methods for the design and/or production of a probe or primer that is capable of hybridizing to a plurality of sites in a sample comprising nucleic acid. Furthermore, the present invention provides methods for detecting and amplifying nucleic acid using such a probe or primer, for example, for identification of a strain, species or genera. Probe or primer sequences are determined by reference to codon usage bias of a target nucleic acid. In addition, the present invention provides methods for determining codon distribution and/or base pair distance between codons in a nucleic acid.Type: GrantFiled: December 9, 2010Date of Patent: September 25, 2018Assignee: Ezygene PTY Ltd.Inventors: Murali Nayudu, Andrew Franklin, Yafei Zhang, Mark John Gibbs, Terry John Murphy, Adrian John Gibbs, Sheba Khan, Christian Samundsett
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Patent number: 10072287Abstract: The present invention provides methods for targeted sequencing of polynucleotide. In one aspect, the present invention provides a method of sequencing a target polynucleotide with fewer probes. In another aspect, the present invention provides a method of sequencing a target polynucleotide with longer reads. Locus-specific, ligation-assisted sequencing/genotyping method and ligation-captured sequencing method are also provided in the present invention. The methods of the present invention allow low-cost, high-throughput and accurate sequencing of nucleic acids.Type: GrantFiled: September 10, 2010Date of Patent: September 11, 2018Assignee: Centrillion Technology Holdings CorporationInventors: Wei Zhou, Rui Mei, Hajime Matsuzaki
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Patent number: 10071377Abstract: The disclosure provides devices, systems and methods for the generation of encapsulated reagents and the partitioning of encapsulated reagents for use in subsequent analyses and/or processing, such as in the field of biological analyzes and characterization.Type: GrantFiled: August 28, 2017Date of Patent: September 11, 2018Assignee: 10X GENOMICS, INC.Inventors: Rajiv Bharadwaj, Kevin Ness, Debkishore Mitra, Donald Masquelier, Anthony Makarewicz, Christopher Hindson, Benjamin Hindson, Serge Saxonov
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Patent number: 10066260Abstract: A method of forming a polymer matrix array includes applying an aqueous solution into wells of a well array. The aqueous solution includes polymer precursors. The method further includes applying an immiscible fluid over the well array to isolate the aqueous solution within the wells of the well array and polymerizing the polymer precursors isolated in the wells of the well array to form the polymer matrix array. An apparatus includes a sensor array, a well array corresponding to the sensor array, and an array of polymer matrices disposed in the well array.Type: GrantFiled: March 13, 2014Date of Patent: September 4, 2018Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: David Light, Wolfgang Hinz, Ronald L. Cicero, Christina E. Inman, Paul M. Kenney, Alexander Mastroianni, Roman Rozhkov, Yufang Wang, Jeremy Gray, Marc Glazer, Dmitriy Gremyachinskiy
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Patent number: 10047392Abstract: Described herein are systems for analysis of biopolymers and complexes containing biopolymers based on optical measurement of ion flux through pores. Also described are methods of using such devices for analysis of biopolymers and complexes containing biopolymers, including methods of determining the nucleotide sequences of polynucleotides.Type: GrantFiled: February 23, 2015Date of Patent: August 14, 2018Assignee: Northeastern UniversityInventors: Andrey Ivankin, Joseph Larkin, Robert Henley, Meni Wanunu
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Patent number: 10041121Abstract: A method and kit for detecting a genetic variant associated with a disease or disorder, including incompatibility with a pharmaceutical. The method and kit using a first nano-particle coupled to at least one morpholino nucleic acid probe comprising a target complimentary region base sequence that is a perfect match to a genetic variant sequence.Type: GrantFiled: September 17, 2014Date of Patent: August 7, 2018Assignee: Agency for Science, Technology and ResearchInventors: Yanbing Zu, Jackie Y. Ying
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Patent number: 10041109Abstract: Disclosed is a method of facilitating detection of a nucleic acid target sequence. The method may include utilizing a toehold-mediated DNA strand displacement apparatus comprising a portion complementary to the nucleic acid target sequence. The method may further include utilizing a RNA toehold switch comprising a RNA sequence. Further, the toehold portion of the RNA sequence may be complementary to a portion of the toehold-mediated DNA strand displacement apparatus. The method may further include combining the toehold-mediated DNA strand displacement apparatus and the RNA toehold switch in an assay, such that the two are never in direct physical contact with each other. Accordingly, a sample containing the nucleic acid target sequence on the substrate may displace a nucleic acid strand from the toehold-mediated DNA strand displacement apparatus and bind a portion of it to the RNA toehold switch resulting in expression of the reporter protein.Type: GrantFiled: April 15, 2016Date of Patent: August 7, 2018Inventor: Monica Isgut
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Patent number: 10041108Abstract: This disclosure provides methods for generating super-resolution patterns of molecules on substrates. In one aspect, disclosed herein is a method comprising contacting a plurality of transiently binding nucleic acid probes to their respective targets wherein the targets are immobilized on a substrate, detecting a binding event in a select region or set of select regions within a diffraction limited region of the substrate, and irradiating the diffraction limited region of the substrate, wherein the probes comprise a photocrosslinker. In one embodiment, the photocrosslinker is 3-cyanovinylcarbazole.Type: GrantFiled: December 15, 2014Date of Patent: August 7, 2018Assignee: President and Fellows of Harvard CollegeInventors: Robert Barish, Peng Yin
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Patent number: 10036056Abstract: The present invention relates to catalytic nucleic acid molecule signal amplification combined with surface plasmon properties of gold nanoparticles to achieve simple and sensitive colorimetric detection of biological targets. The assays of the present invention have about 50 pM sensitivity without the need for purification steps, can detect multiple targets in parallel, and is easily adaptable to new targets. The methods of the present invention are capable of rapid detection of genetic targets for gonorrhea, syphilis, malaria, and hepatitis B infections.Type: GrantFiled: June 12, 2013Date of Patent: July 31, 2018Assignee: THE GOVERNING COUNCIL OF THE UNIVERSITY OF TORONTOInventors: Warren Che Wor Chan, Kyrylo Zagorovsky
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Patent number: 10031133Abstract: Implementations herein relates to a biological sample signal amplification method using terahertz metamaterials and gold nanoparticles. A plurality of biological sample solutions and a plurality of gold nanoparticles-labeled avidin solutions are dropped on surfaces of metamaterials and dried at room temperature. Terahertz time-domain signals of sample points and reference sample points on the surfaces of metamaterials are acquired, transmission or reflectance of the sample points and the reference sample points are calculated using terahertz time-domain signals, and the frequency shift of transmission or reflection peaks are calculated according to the lowest point of transmission or reflectance. The effect of local electric field enhancement of metamaterials is used for sample signal amplification, gold nanoparticles are used to change a distribution of electric fields, and a sample signal is further enhanced by gold nanoparticles modification.Type: GrantFiled: July 17, 2015Date of Patent: July 24, 2018Assignee: ZHEJIANG UNIVERSITYInventors: Yibin Ying, Wendao Xu, Lijuan Xie
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Patent number: 10030253Abstract: A method for synthesizing long DNA constructs from oligonucleotide precursors directly within a microfluidic device uses several oligonucleotides at once. A precursor mix containing at least two oligonucleotide precursors with at least partial base complementarity is introduced into an input of a microfluidic chip and at least one cycle of at least one gene synthesis protocol is applied to fabricate a DNA construct containing the sequence of at least two oligonucleotide precursors. A method for the synthesis of a modified DNA construct includes electroporating at least one oligonucleotide encoding for at least one point mutation and having homology with at least one DNA region of a target cell into the target cell and incorporating the oligonucleotide into the target cell DNA through the action of recombination protein beta or a recombination protein beta functional homolog.Type: GrantFiled: October 30, 2014Date of Patent: July 24, 2018Assignee: Massachusetts Institute of TechnologyInventors: David Kong, Peter A. Carr, Joseph M. Jacobson
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Patent number: 10030240Abstract: In order to conduct gene expression analysis of a number of genes in a number of cells, it has been necessary to separate cells, extract genes therefrom, amplify nucleic acids, and perform sequence analysis. However, separation of cells imposes damages on the cells, and it requires the use of an expensive system. Gene expression analysis in each cell can be carried out with high accuracy by arranging a pair of structures comprising a cell trapping section and a nucleic acid trapping section in a vertical direction to extract individual genes in relevant cells, synthesizing cDNA in the nucleic acid trapping section, amplifying nucleic acids, and analyzing the sequences using a next-generation sequencer.Type: GrantFiled: March 12, 2013Date of Patent: July 24, 2018Assignee: Hitachi, Ltd.Inventors: Masataka Shirai, Hideki Kambara, Kiyomi Taniguchi, Maiko Tanabe
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Patent number: 10023895Abstract: A system for automated microorganism identification and antibiotic susceptibility testing comprising a reagent cartridge, a reagent stage, a cassette, a cassette, stage, a pipettor assembly, an optical detection system, and a controller is disclosed. The system is designed to dynamically adjust motor idle torque to control heat load and employs a fast focus process for determining the true focus position of an individual microorganism. The system also may quantify the relative abundance of viable microorganisms in a sample using dynamic dilution, and facilitate growth of microorganisms in customized media for rapid, accurate antimicrobial susceptibility testing.Type: GrantFiled: March 30, 2016Date of Patent: July 17, 2018Assignee: Accelerate Diagnostics, Inc.Inventors: William L. Richards, Austin Ashby, Matthew Ketterer, Kevin Marshall, Josh Harrison, Matthew Mette, Paul Richards, Wayne Showalter, Jasmin Cote, Phillip C. Halbert, Solene Bourgeois, Steven W. Metzger, Ken Hance, Meghan Mensack, Carlos Michel, Elke Allers, Dulini Gamage, Landon Prisbrey, Oleg Gusyatin, Alena Shamsheyeva, Ben Turng, Andrew Ghusson, Kurt Reinhardt
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Patent number: 10023859Abstract: The present invention provides a novel method to fabricate silica nanostructures on thin polymer films based on silica deposition and self-wrinkling induced by thermal shrinkage. These micro- and nano-scale structures have vastly enlarged the specific area of silica, thus the silica nanomembranes can be used for solid phase extraction of nucleic acids. The inventive silica nanomembranes are suitable for nucleic acid purification and isolation and demonstrated better performance than commercial particles in terms of DNA recovery yield and integrity. In addition, the silica nanomembranes have extremely high nucleic acid capacity due to its significantly enlarged specific surface area of silica. Methods of use and devices comprising the silica nanomembranes are also provided.Type: GrantFiled: December 19, 2016Date of Patent: July 17, 2018Assignee: The Johns Hopkins UniversityInventors: Tza-Huei Wang, Yi Zhang
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Patent number: 10018627Abstract: A technique for efficiently sealing many substances, such as beads, nucleic acid, protein, virus, cells, and lipid membrane complex, into an array is provided. The present invention provides a method for sealing a substance, including: (i) a step of introducing a first solvent containing a substance on a substrate on which a plurality of receptacles capable of storing the substance are formed separated from each other by a side wall; and (ii) a step of introducing a second solvent having a greater specific gravity than that of the first solvent onto the first solvent, the step (ii) being carried out after the step (i).Type: GrantFiled: October 14, 2014Date of Patent: July 10, 2018Assignee: JAPAN SCIENCE AND TECHNOLOGY AGENCYInventors: Hiroyuki Noji, Lisa Yamauchi
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Patent number: 10012631Abstract: The present invention is intended to provide a novel fluorescence sensor for target analysis, a kit for target analysis, and a target analysis method using the same. The fluorescence sensor for target analysis according to the present invention includes a nucleic acid molecule that includes a G-quartet-forming nucleic acid region (D) that forms a G-quartet and a binding nucleic acid region (A) that binds to a target. In the absence of a target, formation of a G-quartet in the G-quartet-forming nucleic acid region (D) is inhibited. In the presence of a target, the target comes into contact with the binding nucleic acid region (A), the G-quartet is formed in the G-quartet-forming nucleic acid region (D) due to the contact, the G-quartet-forming region (D) and porphyrin forms a complex, and the complex generates fluorescence.Type: GrantFiled: June 27, 2014Date of Patent: July 3, 2018Assignee: NEC Solution Innovators, Ltd.Inventors: Naoto Kaneko, Ikuo Shiratori, Katsunori Horii, Jou Akitomi, Iwao Waga
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Patent number: 10006909Abstract: Disclosed herein are formulations, substrates, and arrays. Also disclosed herein are methods for manufacturing and using the formulations, substrates, and arrays. Also disclosed are methods for identifying peptide sequences useful for diagnosis and treatment of disorders, and methods for using the peptide sequences for diagnosis and treatment of disorders, e.g., celiac disorder. In certain embodiments, substrates and arrays comprise a porous layer for synthesis and attachment of polymers or biomolecules.Type: GrantFiled: September 30, 2013Date of Patent: June 26, 2018Assignee: Vibrant Holdings, LLCInventors: John J. Rajasekaran, Vasanth Jayaraman, Tianhao Wang, Kang Bei, Hari Krishnan Krishnamurthy
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Patent number: 10000804Abstract: Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as wen as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.Type: GrantFiled: March 7, 2016Date of Patent: June 19, 2018Assignee: BioNano Genomics, Inc.Inventors: Han Cao, Parikshit A. Deshpande, Michael D. Austin, Michael Boyce-Jacino
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Patent number: 9983134Abstract: In accordance with preferred embodiments of the present invention, a method for imaging tissue, for example, includes the steps of mounting the tissue on a computer controlled stage of a microscope, determining volumetric imaging parameters, directing at least two photons into a region of interest, scanning the region of interest across a portion of the tissue, imaging a plurality of layers of the tissue in a plurality of volumes of the tissue in the region of interest, sectioning the portion of the tissue, capturing the sectioned tissue, and imaging a second plurality of layers of the tissue in a second plurality of volumes of the tissue in the region of interest, and capturing each sectioned tissue, detecting a fluorescence image of the tissue due to said excitation light; and processing three-dimensional data that is collected to create a three-dimensional image of the region of interest.Type: GrantFiled: June 10, 2014Date of Patent: May 29, 2018Inventor: Timothy Ragan
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Patent number: 9981239Abstract: Devices and methods for de novo synthesis of large and highly accurate libraries of oligonucleic acids are provided herein. Devices include structures having a main channel and microchannels, where the microchannels have a high surface area to volume ratio. Devices disclosed herein provide for de novo synthesis of oligonucleic acids having a low error rate.Type: GrantFiled: April 21, 2016Date of Patent: May 29, 2018Assignee: TWIST BIOSCIENCE CORPORATIONInventors: William Banyai, Bill James Peck, Andres Fernandez, Siyuan Chen, Pierre Indermuhle, Eugene P. Marsh