Patents Assigned to The Public Health Research Institute of the City of New
York
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Publication number: 20110129828Abstract: Nucleic acid detection probes that comprise a pair of complementary, fluorophore/quencher labeled oligonucleotides, one of which is shorter than the other, are able to detect single-stranded and double-stranded targets in hybridization reactions and amplification reactions with real-time detection. Double-stranded probes of equal length are useful in PCR amplification reactions with real-time detection.Type: ApplicationFiled: August 11, 2010Publication date: June 2, 2011Applicant: The Public Health Research Institute of the City of New York, Inc.Inventors: Qingge Li, Jixuan Liang, Guoyan Luan
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Patent number: 7799522Abstract: Double-stranded nucleic acid hybridization probes comprise a longer strand perfectly complementary to a preselected target sequence in an assay and a shorter second strand complementary to the longer strand. The strands are labeled with interactive labels such as a fluorophore and a quencher. The probes may be used in real-time amplification assays to distinguish among alleles.Type: GrantFiled: October 5, 2001Date of Patent: September 21, 2010Assignee: The Public Health Research Institute Of the City of New York, Inc.Inventors: Qingge Li, Jixuan Liang, Guoyan Luan
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Patent number: 7741031Abstract: A coding scheme for microcarriers suitable for use in distributed arrays includes labeling the carriers with quenched signaling hairpin molecules with any one of three to eight distinguishable fluorophores wherein the hairpins are of at least two types, most preferably three types, that open and fluoresce differentially as a chemical or physical condition, for example temperature, is changed. Mixtures of microcarriers having immobilized capture probes can be decoded by measuring fluorescence from said fluorophores under conditions under which only one type of hairpin is open, under which two types of hairpin are open, and so on. Mixtures of coded microcarriers with capture probes are used in assays for nucleic acids utilizing microarray methods.Type: GrantFiled: March 2, 2004Date of Patent: June 22, 2010Assignee: The Public Health Research Institute of the City of New YorkInventors: Fred R. Kramer, Sanjay Tyagi, Salvatore A. E. Marras, Hiyam Elhajj Trunfio
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Publication number: 20100120048Abstract: The invention provides assays that can detect multiple genetic variants of a gene (e.g., a mycobacterium gene) in a sample using a pool (using 2, 3, 4, or more) of oligonucletide hybridization probes.Type: ApplicationFiled: November 9, 2009Publication date: May 13, 2010Applicant: The Public Health Research Institute of the City of New York, Inc.Inventors: Sanjay Tyagi, Fred Kramer, David Alland
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Publication number: 20080213792Abstract: Kits for highly multiplexed homogeneous in vitro screening assays for numerous possible nucleic acid targets, any of which might be present in a sample, that utilize fluorescent hybridization probes that are combinatorially coded from a panel of fluorophores by subdividing each probe into portions and differently labeling each portion such that, when portions are combined, each probe has a unique code. The kits may include reagents and primers for target amplification and real-time detection.Type: ApplicationFiled: May 7, 2008Publication date: September 4, 2008Applicant: The Public Health Research Institute of the City of New York, Inc.Inventor: Fred R. Kramer
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Patent number: 7385043Abstract: Highly multiplexed homogeneous in vitro screening assays for numerous possible nucleic acid targets, any of which might be present in a sample, utilize fluorescent hybridization probes that are combinatorially coded from a panel of fluorophores by subdividing each probe into portions and differently labeling each portion such that, when portions are combined, each probe has a unique code. The assays may include target amplification and real-time detection. Probe sets and kits containing additional assay reagents may be used to perform the screening assays.Type: GrantFiled: April 30, 2003Date of Patent: June 10, 2008Assignee: The Public Health Research Institute of the City of New York, Inc.Inventor: Fred R. Kramer
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Patent number: 7313482Abstract: Nucleic acid hybridization under steady-state conditions is described by a kinetic model in which the intermediate state is assumed to be locally single stranded. An expression was derived that relates nucleic acid secondary structure to the rate of oligonucleotide-RNA hybridization. The model allows the calculation of a rate factor that is proportional to the rate constant for hybridization between complementary nucleic acids and is generally applicable to any RNA molecule with potential utility for rapid identification of sites for antisense attack of mRNA.Type: GrantFiled: May 15, 2002Date of Patent: December 25, 2007Assignee: The Public Health Research Institute of the city of New York, Inc.Inventors: Karl Drlica, Jian-Ying Wang
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Patent number: 7129087Abstract: Coalescence of cells or other membrane-bound entities is facilitated by anchoring an outwardly projecting first oligonucleotide in one member and an outwardly projecting second oligonucleotide, complementary to the first, in a second member and incubating under hybridizing conditions. Liposomes may be coalesced with cells to deliver hydrophilic agents thereto, such as DNA probes or drugs. Kits containing complementary oligonucleotides containing hydrophobic anchoring moieties may be used.Type: GrantFiled: October 11, 2001Date of Patent: October 31, 2006Assignee: The Public Health Research Institute of the City of New York, Inc.Inventors: Fred R. Kramer, Osama A. Alsmadi, Sanjay Tyagi
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Patent number: 7097810Abstract: Techniques for the delivery of metered amounts of liquid material include the use of a pin, such as an optical fiber. A sample of the liquid material may be placed on the tip of the pin for delivery to a target area, such as a specific location on a microarray, in a contactless manner. Light transmitted through the pin may be detected to facilitate accurate measuring of the pin's position.Type: GrantFiled: June 26, 2002Date of Patent: August 29, 2006Assignees: The Public Health Research Institute of the City of New York, Inc., New Jersey Institute of TechnologyInventors: Timothy Chang, Peter Tolias
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Patent number: 6815201Abstract: The invention features a protein which includes a gp120 V1/V2 domain of an HIV-1 strain and not a gp120 V3 domain of an HIV-1 strain, which protein does not substantially bind CD4. The gp120 V1/V2 domain of the protein displays an epitope which is recognized by an antibody which neutralizes at least one HIV-1 primary isolate with a ND90 of less than 100 &mgr;g/ml.Type: GrantFiled: January 2, 2002Date of Patent: November 9, 2004Assignee: The Public Health Research Institute of the City of New York, Inc.Inventor: Abraham Pinter
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Publication number: 20030162210Abstract: A method of sorting mixtures of nucleic acid strands comprising hybridizing the strands to an array of immobilized oligonucleotides, each of which includes a constant segment adjacent to a variable segment. The constant segment of the immobilized oligonucleotides can be made complementary to the ends of strands obtained by digesting a double-stranded nucleic acid with a restriction enzyme and restoring the restriction sites, thereby permitting the sorting of strands according to their variable sequences adjacent to their constant terminal restored restriction sites.Type: ApplicationFiled: December 31, 2002Publication date: August 28, 2003Applicant: PUBLIC HEALTH RESEARCH INSTITUTE OF THE CITY OF NEW YORK, INC., a New York CorporationInventors: Alexander B. Chetverin, Fred Russell Kramer
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Patent number: 6596281Abstract: Two genes for proteins of M. tuberculosis have been sequenced. The DNAs and their encoded polypeptides can be used for immunoassays and vaccines. Cocktails of at least three purified recombinant antigens, and cocktails of at least three DNAs encoding them can be used for improved assays and vaccines for bacterial pathogens and parasites.Type: GrantFiled: January 26, 2000Date of Patent: July 22, 2003Assignee: The Public Health Research Institute of the City of New York, Inc.Inventors: Maria L. Gennaro, Konstantin P. Lyashchenko, Claudia M. A. Manca
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Publication number: 20030105282Abstract: The invention features a protein which includes a gp120 V1/V2 domain of an HIV-1 strain and not a gp120 V3 domain of an HIV-1 strain, which protein does not substantially bind CD4. The gp120 V1/V2 domain of the protein displays an epitope which is recognized by an antibody which neutralizes at least one HIV-1 primary isolate with a ND90 of less than 100 &mgr;g/ml.Type: ApplicationFiled: January 2, 2002Publication date: June 5, 2003Applicant: The Public Health Research Institute of the City of New York, Inc., a New York corporationInventor: Abraham Pinter
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Patent number: 6461817Abstract: Non-competitive, quantitative amplification assay methods, including assays employing amplification by the polymerase chain reaction (PCR) process, for accurately measuring levels of target nucleic acid and sequences in samples and for ascertaining the relative amounts of cross-hybridizing alleles and mutants.Type: GrantFiled: October 20, 2000Date of Patent: October 8, 2002Assignee: The Public Health Research Institute of the City of New YorkInventors: David Alland, Fred R. Kramer, Amy Piatek, Sanjay Tyagi, Jacqueline Vet
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Patent number: 6406881Abstract: The invention is based on the discovery that, for many drugs (e.g., antiviral or antimicrobial drugs such as antifungal or antibacterial drugs, including bacteriocidal or bacteriostatic drugs) and many pathogen strains (e.g., viral, fungal, or bacterial pathogens), a concentration of drug can be identified at which drug-resistant mutant pathogen strains are not selected. This concentration is herein referred to as the “mutant prevention concentration” (MPC). Maintaining serum concentrations of the drug above the MPC throughout a course of treatment should severely restrict selection of drug-resistant mutants. Additionally, it is discovered that drug-resistant mutant pathogens are selected exclusively within a drug concentration window, termed the “mutant selection window” (MSW). A quantitative expression of this window, which we call the “window index” (WI), is defined as the ratio of the MPC to the MIC.Type: GrantFiled: July 9, 2001Date of Patent: June 18, 2002Assignee: The Public Health Research Institute of the City of New YorkInventors: Yuzhi Dong, Karl Drlica, Xilin Zhao
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Patent number: 6365729Abstract: For nucleic acid amplification including extension of primers by a DNA polymerase, high specificity primers are provided. The primers include a type of hairpin structure in which a single-stranded loop separates complementary 3′ and 5′ arms and in which the loop and the 3′ arm are complementary to the target nucleic acid. Amplification methods, assays and kits including such primers are included in the invention.Type: GrantFiled: July 12, 2001Date of Patent: April 2, 2002Assignee: The Public Health Research Institute of the city of New York, Inc.Inventors: Sanjay Tyagi, Fred R. Kramer, Robert Vartikian
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Publication number: 20020004220Abstract: The invention is based on the discovery that, for many drugs (e.g., antiviral or antimicrobial drugs such as antifungal or antibacterial drugs, including bacteriocidal or bacteriostatic drugs) and many pathogen strains (e.g., viral, fungal, or bacterial pathogens), a concentration of drug can be identified at which drug-resistant mutant pathogen strains are not selected. This concentration is herein referred to as the “mutant prevention concentration” (MPC). Maintaining serum concentrations of the drug above the MPC throughout a course of treatment should severely restrict selection of drug-resistant mutants. Additionally, it is discovered that drug-resistant mutant pathogens are selected exclusively within a drug concentration window, termed the “mutant selection window” (MSW). A quantitative expression of this window, which we call the “window index” (WI), is defined as the ratio of the MPC to the MIC.Type: ApplicationFiled: July 9, 2001Publication date: January 10, 2002Applicant: The Public Health Research Institute of the City of New York, Inc.Inventors: Yuzhi Dong, Karl Drlica, Xilin Zhao
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Patent number: 6322971Abstract: Ligation methods for manipulating nucleic acid stands and oligonucleotides utilizing hybridization arrays of immobilized oligonucleotides. The oligonucleotide arrays may be plain or sectioned, comprehensive or non-comprehensive. The immobilized oligonucleotides may in some cases be binary oligonucleotides having constant as well as variable segments. Some embodiments include amplification of ligated products.Type: GrantFiled: September 30, 1998Date of Patent: November 27, 2001Assignee: The Public Health Research Institute of the city of New York, Inc.Inventors: Alexander B. C{acute over (h)}etverin, Fred Russell Kramer
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Patent number: 6265181Abstract: The invention is based on the discovery that, for many drugs (e.g., antiviral or antimicrobial drugs such as antifungal or antibacterial drugs, including bacteriocidal or bacteriostatic drugs) and many pathogen strains (e.g., viral, fungal, or bacterial pathogens), a concentration of drug can be identified at which drug-resistant mutant pathogen strains are not selected. This concentration is herein referred to as the “mutant prevention concentration” (MPC). Maintaining serum concentrations of the drug above the MPC throughout a course of treatment should severely restrict selection of drug-resistant mutants. Additionally, it is discovered that drug-resistant mutant pathogens are selected exclusively within a drug concentration window, termed the “mutant selection window” (MSW). A quantitative expression of this window, which we call the “window index” (WI), is defined as the ratio of the MPC to the MIC.Type: GrantFiled: September 24, 1999Date of Patent: July 24, 2001Assignee: The Public Health Research Institute of the City of New York, Inc.Inventors: Yuzhi Dong, Karl Drlica, Xilin Zhao
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Patent number: 6150097Abstract: Nucleic acid hybridization probes having a first conformation when not interacting with a target and a second conformation when interacting with a target, and having the ability to bring a label pair into touching contact in one conformation but not the other, are labeled with a non-FRET pair of chromophores and generate a fluorescent or absorbance signal. Kits may include such probes, and assays, including multiplex assays, may utilize such probes.Type: GrantFiled: December 12, 1997Date of Patent: November 21, 2000Assignee: The Public Health Research Institute of the City of New York, Inc.Inventors: Sanjay Tyagi, Fred Russell Kramer