Patents Assigned to The Public Health Research Institute of the City of New York, Inc.
  • Publication number: 20110129828
    Abstract: 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: Application
    Filed: August 11, 2010
    Publication date: June 2, 2011
    Applicant: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Qingge Li, Jixuan Liang, Guoyan Luan
  • Patent number: 7799522
    Abstract: 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: Grant
    Filed: October 5, 2001
    Date of Patent: September 21, 2010
    Assignee: The Public Health Research Institute Of the City of New York, Inc.
    Inventors: Qingge Li, Jixuan Liang, Guoyan Luan
  • Publication number: 20100120048
    Abstract: 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: Application
    Filed: November 9, 2009
    Publication date: May 13, 2010
    Applicant: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Sanjay Tyagi, Fred Kramer, David Alland
  • Publication number: 20080213792
    Abstract: 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: Application
    Filed: May 7, 2008
    Publication date: September 4, 2008
    Applicant: The Public Health Research Institute of the City of New York, Inc.
    Inventor: Fred R. Kramer
  • Patent number: 7385043
    Abstract: 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: Grant
    Filed: April 30, 2003
    Date of Patent: June 10, 2008
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventor: Fred R. Kramer
  • Patent number: 7313482
    Abstract: 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: Grant
    Filed: May 15, 2002
    Date of Patent: December 25, 2007
    Assignee: The Public Health Research Institute of the city of New York, Inc.
    Inventors: Karl Drlica, Jian-Ying Wang
  • Patent number: 7129087
    Abstract: 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: Grant
    Filed: October 11, 2001
    Date of Patent: October 31, 2006
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Fred R. Kramer, Osama A. Alsmadi, Sanjay Tyagi
  • Patent number: 7097810
    Abstract: 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: Grant
    Filed: June 26, 2002
    Date of Patent: August 29, 2006
    Assignees: The Public Health Research Institute of the City of New York, Inc., New Jersey Institute of Technology
    Inventors: Timothy Chang, Peter Tolias
  • Patent number: 6815201
    Abstract: 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: Grant
    Filed: January 2, 2002
    Date of Patent: November 9, 2004
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventor: Abraham Pinter
  • Publication number: 20030162210
    Abstract: 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: Application
    Filed: December 31, 2002
    Publication date: August 28, 2003
    Applicant: PUBLIC HEALTH RESEARCH INSTITUTE OF THE CITY OF NEW YORK, INC., a New York Corporation
    Inventors: Alexander B. Chetverin, Fred Russell Kramer
  • Patent number: 6596281
    Abstract: 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: Grant
    Filed: January 26, 2000
    Date of Patent: July 22, 2003
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Maria L. Gennaro, Konstantin P. Lyashchenko, Claudia M. A. Manca
  • Publication number: 20030105282
    Abstract: 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: Application
    Filed: January 2, 2002
    Publication date: June 5, 2003
    Applicant: The Public Health Research Institute of the City of New York, Inc., a New York corporation
    Inventor: Abraham Pinter
  • Patent number: 6365729
    Abstract: 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: Grant
    Filed: July 12, 2001
    Date of Patent: April 2, 2002
    Assignee: The Public Health Research Institute of the city of New York, Inc.
    Inventors: Sanjay Tyagi, Fred R. Kramer, Robert Vartikian
  • Publication number: 20020004220
    Abstract: 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: Application
    Filed: July 9, 2001
    Publication date: January 10, 2002
    Applicant: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Yuzhi Dong, Karl Drlica, Xilin Zhao
  • Patent number: 6322971
    Abstract: 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: Grant
    Filed: September 30, 1998
    Date of Patent: November 27, 2001
    Assignee: The Public Health Research Institute of the city of New York, Inc.
    Inventors: Alexander B. C{acute over (h)}etverin, Fred Russell Kramer
  • Patent number: 6265181
    Abstract: 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: Grant
    Filed: September 24, 1999
    Date of Patent: July 24, 2001
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Yuzhi Dong, Karl Drlica, Xilin Zhao
  • Patent number: 6150097
    Abstract: 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: Grant
    Filed: December 12, 1997
    Date of Patent: November 21, 2000
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Sanjay Tyagi, Fred Russell Kramer
  • Patent number: 6103463
    Abstract: 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: Grant
    Filed: May 23, 1994
    Date of Patent: August 15, 2000
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Alexander B. Chetverin, Fred Russell Kramer
  • Patent number: 6103476
    Abstract: Unimolecular and bimolecular hybridization probes for the detection of nucleic acid target sequences comprise a target complement sequence, an affinity pair holding the probe in a closed conformation in the absence of target sequence, and either a label pair that interacts when the probe is in the closed conformation or, for certain unimolecular probes, a non-interactive label. Hybridization of the target and target complement sequences shifts the probe to an open conformation. The shift is detectable due to reduced interaction of the label pair or by detecting a signal from a non-interactive label. Certain unimolecular probes can discriminate between target and non-target sequences differing by as little as one nucleotide. Also, universal stems and kits useful for constructing said probes. Also, assays utilizing said probes and kits for performing such assays.
    Type: Grant
    Filed: March 15, 1999
    Date of Patent: August 15, 2000
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Sanjay Tyagi, Fred R. Kramer, Paul M. Lizardi
  • Patent number: 6087163
    Abstract: 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: Grant
    Filed: February 6, 1997
    Date of Patent: July 11, 2000
    Assignee: The Public Health Research Institute of the City of New York, Inc.
    Inventors: Maria L. Gennaro, Konstantin P. Lyashchenko, Claudia M.A. Manca