polymerase chain reaction

Summary

Summary: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.

Top Publications

  1. ncbi Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
    K J Livak
    Applied Biosystems, Foster City, California 94404, USA
    Methods 25:402-8. 2001
  2. doi The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
    Stephen A Bustin
    Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, UK
    Clin Chem 55:611-22. 2009
  3. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
  4. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
  5. ncbi Human papillomavirus is a necessary cause of invasive cervical cancer worldwide
    J M Walboomers
    Department of Pathology, University Hospital Vrije Universiteit, Amsterdam, The Netherlands
    J Pathol 189:12-9. 1999
  6. doi Sequencing technologies - the next generation
    Michael L Metzker
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Nat Rev Genet 11:31-46. 2010
  7. doi Accurate determination of microbial diversity from 454 pyrosequencing data
    Christopher Quince
    Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK
    Nat Methods 6:639-41. 2009
  8. ncbi Primer3 on the WWW for general users and for biologist programmers
    S Rozen
    Whitehead Institute for Biomedical Research, Cambridge, MA, USA
    Methods Mol Biol 132:365-86. 2000
  9. ncbi Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    Christian Ramakers
    Department of Anatomy and Embryology K2 283, Experimental and Molecular Cardiology Group, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Neurosci Lett 339:62-6. 2003
  10. pmc Primer3Plus, an enhanced web interface to Primer3
    Andreas Untergasser
    Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, The Netherlands
    Nucleic Acids Res 35:W71-4. 2007

Research Grants

  1. Msec Polymerase Chain Reaction with fMolar Detection Sensitivity using SPR
    DONALD ROPER; Fiscal Year: 2007
  2. Ethanol Regulation of Serum Glucocorticoid Kinase I
    BLAIR N COSTIN; Fiscal Year: 2012
  3. ARUNKUMAR GOVINDAKARNAVAR; Fiscal Year: 2016
  4. C Michael Hart; Fiscal Year: 2016
  5. Regulation of Astrocyte TIMP-1 in HIV-Associated Dementia
    JEREL ADAM FIELDS; Fiscal Year: 2011
  6. SUSAN F KEAY; Fiscal Year: 2016
  7. Mark D Peterson; Fiscal Year: 2016
  8. Mechanisms of Early Growth Response Factor 1 (Egr-1) Induction by HSV-1 Lytic Inf
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2010
  9. Mechanisms of Astrocyte Development
    Teri L Belecky Adams; Fiscal Year: 2010
  10. RRSS #08: Evaluating Prevalence HPV Infection Among Head and Neck Cancer Patients
    Dennis M Deapen; Fiscal Year: 2009

Detail Information

Publications414 found, 100 shown here

  1. ncbi Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
    K J Livak
    Applied Biosystems, Foster City, California 94404, USA
    Methods 25:402-8. 2001
    ..In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data...
  2. doi The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
    Stephen A Bustin
    Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, UK
    Clin Chem 55:611-22. 2009
    ..The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments...
  3. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria...
  4. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
    ..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...
  5. ncbi Human papillomavirus is a necessary cause of invasive cervical cancer worldwide
    J M Walboomers
    Department of Pathology, University Hospital Vrije Universiteit, Amsterdam, The Netherlands
    J Pathol 189:12-9. 1999
    ..due to sample inadequacy or integration events affecting the HPV L1 gene, which is the target of the polymerase chain reaction (PCR)-based test which was used...
  6. doi Sequencing technologies - the next generation
    Michael L Metzker
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Nat Rev Genet 11:31-46. 2010
    ..I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest...
  7. doi Accurate determination of microbial diversity from 454 pyrosequencing data
    Christopher Quince
    Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK
    Nat Methods 6:639-41. 2009
    ..We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated...
  8. ncbi Primer3 on the WWW for general users and for biologist programmers
    S Rozen
    Whitehead Institute for Biomedical Research, Cambridge, MA, USA
    Methods Mol Biol 132:365-86. 2000
  9. ncbi Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    Christian Ramakers
    Department of Anatomy and Embryology K2 283, Experimental and Molecular Cardiology Group, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Neurosci Lett 339:62-6. 2003
    Quantification of mRNAs using real-time polymerase chain reaction (PCR) by monitoring the product formation with the fluorescent dye SYBR Green I is being extensively used in neurosciences, developmental biology, and medical diagnostics...
  10. pmc Primer3Plus, an enhanced web interface to Primer3
    Andreas Untergasser
    Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, The Netherlands
    Nucleic Acids Res 35:W71-4. 2007
    ..The Primer3Plus Perl source code is available under GPL license from SourceForge. Primer3Plus is available at http://www.bioinformatics.nl/primer3plus...
  11. pmc qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
    Jan Hellemans
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan, B 9000 Ghent, Belgium
    Genome Biol 8:R19. 2007
    ..These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data...
  12. ncbi MGMT gene silencing and benefit from temozolomide in glioblastoma
    Monika E Hegi
    Laboratory of Tumor Biology and Genetics, Department of Neurosurgery, University Hospital Lausanne, Lausanne, Switzerland
    N Engl J Med 352:997-1003. 2005
    ....
  13. pmc Genome sequencing in microfabricated high-density picolitre reactors
    Marcel Margulies
    454 Life Sciences Corp, 20 Commercial Street, Branford, Connecticut 06405, USA
    Nature 437:376-80. 2005
    ..Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine...
  14. pmc Telomere measurement by quantitative PCR
    Richard M Cawthon
    Department of Human Genetics, University of Utah, 15 N 2030 E, Room 2100, Salt Lake City, UT 84112, USA
    Nucleic Acids Res 30:e47. 2002
    ..This assay will facilitate investigations of the biology of telomeres and the roles they play in the molecular pathophysiology of diseases and aging...
  15. pmc Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry
    Mathias Ehrich
    Sequenom, Inc, 3595 John Hopkins Court, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 102:15785-90. 2005
    ....
  16. pmc Statistical analysis of real-time PCR data
    Joshua S Yuan
    Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
    BMC Bioinformatics 7:85. 2006
    ..Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data...
  17. ncbi Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma
    Y Chang
    Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, NY 10032
    Science 266:1865-9. 1994
    ..These KS-associated herpesvirus-like (KSHV) sequences appear to define a new human herpesvirus...
  18. doi Creation of a bacterial cell controlled by a chemically synthesized genome
    Daniel G Gibson
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Science 329:52-6. 2010
    ..The new cells have expected phenotypic properties and are capable of continuous self-replication...
  19. pmc High-throughput droplet digital PCR system for absolute quantitation of DNA copy number
    Benjamin J Hindson
    Bio Rad Laboratories, Inc, Pleasanton, California 94566, United States
    Anal Chem 83:8604-10. 2011
    ..We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics...
  20. ncbi An economic method for the fluorescent labeling of PCR fragments
    M Schuelke
    Department of Neuropediatrics, Charite University Hospital, Augustenburger Platz 1, D 13353 Berlin, Germany
    Nat Biotechnol 18:233-4. 2000
    ..A poor man's approach to genotyping for research and high-throughput diagnostics...
  21. ncbi Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
    Mamie Z Li
    Howard Hughes Medical Institute, Department of Genetics, Harvard Partners Center for Genetics and Genomics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 4:251-6. 2007
    ..This flexibility allows much greater versatility in the generation of recombinant DNA for the purposes of synthetic biology...
  22. ncbi Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member
    A C McPherron
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 387:83-90. 1997
    ..Using degenerate polymerase chain reaction, we have identified a new murine TGF-beta family member, growth/differentiation factor-8 (GDF-8), which ..
  23. pmc The RIN: an RNA integrity number for assigning integrity values to RNA measurements
    Andreas Schroeder
    Agilent Technologies, Hewlett Packard Strasse 8, 76337 Waldbronn, Germany
    BMC Mol Biol 7:3. 2006
    ..The advent of microcapillary electrophoretic RNA separation provides the basis for an automated high-throughput approach, in order to estimate the integrity of RNA samples in an unambiguous way...
  24. ncbi A large focus of naturally acquired Plasmodium knowlesi infections in human beings
    Balbir Singh
    Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kuching, Sarawak, Malaysia
    Lancet 363:1017-24. 2004
    ..We aimed to investigate whether such infections could be attributable to a variant form of P malariae or a newly emergent Plasmodium species...
  25. pmc A large genome center's improvements to the Illumina sequencing system
    Michael A Quail
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nat Methods 5:1005-10. 2008
    ....
  26. ncbi Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumours
    L A Donehower
    Division of Molecular Virology, Baylor College of Medicine, Houston, Texas 77030
    Nature 356:215-21. 1992
    ....
  27. ncbi RNA integrity and the effect on the real-time qRT-PCR performance
    Simone Fleige
    Physiology Weihenstephan, Center of Life and Food Sciences ZIEL, Technical University of Munich, 85350 Freising, Germany
    Mol Aspects Med 27:126-39. 2006
    ..We can recommend a RIN higher than five as good total RNA quality and higher than eight as perfect total RNA for downstream application...
  28. doi mRNA-Seq whole-transcriptome analysis of a single cell
    Fuchou Tang
    Wellcome Trust Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
    Nat Methods 6:377-82. 2009
    ..Finally, for Dicer1(-/-) and Ago2(-/-) (Eif2c2(-/-)) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common...
  29. ncbi Acquired mutation of the tyrosine kinase JAK2 in human myeloproliferative disorders
    E Joanna Baxter
    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
    Lancet 365:1054-61. 2005
    ..We investigated the role of the cytoplasmic tyrosine kinase JAK2 in patients with a myeloproliferative disorder...
  30. pmc Detection of MLV-related virus gene sequences in blood of patients with chronic fatigue syndrome and healthy blood donors
    Shyh Ching Lo
    Center for Biologics Evaluation and Research, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 107:15874-9. 2010
    ....
  31. pmc Recombinant origin of the retrovirus XMRV
    Tobias Paprotka
    Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Science 333:97-101. 2011
    ....
  32. pmc Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: rapid identification system for mec, ccr, and major differences in junkyard regions
    Yoko Kondo
    Department of Infection Control Science, Juntendo University, 2 1 1 Hongo, Bunkyo ku, Tokyo 113 8421, Japan
    Antimicrob Agents Chemother 51:264-74. 2007
    ..The SCCmec type assignments were identical to those made with a PCR system that uses numerous primer pairs to identify genes or gene alleles. Our system of six M-PCRs is thus a convenient and reliable method for typing SCCmec elements...
  33. ncbi The consensus coding sequences of human breast and colorectal cancers
    Tobias Sjoblom
    Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
    Science 314:268-74. 2006
    ..These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention, and open fertile avenues for basic research in tumor biology...
  34. pmc Biological identifications through DNA barcodes
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Proc Biol Sci 270:313-21. 2003
    ..Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution...
  35. ncbi Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
    Thomas Huber
    ComBinE group, Advanced Computational Modelling Centre, The University of Queensland, Brisbane 4072, Australia
    Bioinformatics 20:2317-9. 2004
    ..Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments...
  36. doi Experimental factors affecting PCR-based estimates of microbial species richness and evenness
    Anna Engelbrektson
    Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
    ISME J 4:642-7. 2010
    ..However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities...
  37. ncbi Review and re-analysis of domain-specific 16S primers
    G C Baker
    Department of Biotechnology, University of the Western Cape, Bellville 7335, Cape Town, South Africa
    J Microbiol Methods 55:541-55. 2003
    The Polymerase Chain Reaction (PCR) has facilitated the detection of unculturable microorganisms in virtually any environmental source and has thus been used extensively in the assessment of environmental microbial diversity...
  38. pmc HPV-associated head and neck cancer: a virus-related cancer epidemic
    Shanthi Marur
    Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
    Lancet Oncol 11:781-9. 2010
    ....
  39. ncbi Guideline to reference gene selection for quantitative real-time PCR
    Aleksandar Radonic
    Charité Campus Charité Mitte, II Medizinische Klinik mit Schwerpunkt Onkologie und Hämatologie, Humboldt Universitat, Berlin, Germany
    Biochem Biophys Res Commun 313:856-62. 2004
    ..Our results show that "Classical" reference genes are indeed unsuitable, whereas the RNA polymerase II gene was the gene with the most constant expression in different tissues and following stimulation in CCRF-HSB-2 cells...
  40. pmc Defining the normal bacterial flora of the oral cavity
    Jørn A Aas
    Institute of Oral Biology, University of Oslo, Postbox 1052 Blindern, 0316 Oslo, Norway
    J Clin Microbiol 43:5721-32. 2005
    ..It is important to fully define the human microflora of the healthy oral cavity before we can understand the role of bacteria in oral disease...
  41. ncbi Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR
    Mukesh Jain
    Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India
    Biochem Biophys Res Commun 345:646-51. 2006
    ..The expression of these genes (with more uniform expression) can be used for normalization of real-time PCR results for gene expression studies in a wide variety of samples in rice...
  42. pmc Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability
    Asad Umar
    Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    J Natl Cancer Inst 96:261-8. 2004
    ....
  43. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  44. ncbi Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR
    T Rinttilä
    Section of Microbiology, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Helsinki University, Helsinki, Finland
    J Appl Microbiol 97:1166-77. 2004
    ..We report the design and optimization of an extensive set of 16S rDNA-targeted species- and group-specific primers for more accurate quantification of bacteria from faecal samples with real-time PCR...
  45. ncbi Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing
    A Grishok
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 106:23-34. 2001
    ..Our findings suggest that a common processing machinery generates guide RNAs that mediate both RNAi and endogenous gene regulation...
  46. ncbi Identification of plasmids by PCR-based replicon typing
    Alessandra Carattoli
    Department of Infectious, Parasitic and Immune Mediated Diseases, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome, Italy
    J Microbiol Methods 63:219-28. 2005
    ..These results suggest that the method is potentially applicable to a large number of strains to trace the diffusion of specific multi-drug resistance plasmids in different environments...
  47. ncbi Rapid quantitative detection of chytridiomycosis (Batrachochytrium dendrobatidis) in amphibian samples using real-time Taqman PCR assay
    D G Boyle
    Australian Animal Health Laboratory, CSIRO Livestock Industries, Private Bag 24, Geelong, Victoria 3220, Australia
    Dis Aquat Organ 60:141-8. 2004
    ....
  48. ncbi Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction
    Y Y Zhu
    CLONTECH Laboratories, Palo Alto, CA, USA
    Biotechniques 30:892-7. 2001
    ..cDNA libraries generated using this method will be useful for accelerating the collection of mRNA 5' end sequence information, which is currently very limited in GenBank...
  49. ncbi Simultaneous identification of species and molecular forms of the Anopheles gambiae complex by PCR-RFLP
    C Fanello
    London School of Hygiene and Tropical Medicine, London, UK
    Med Vet Entomol 16:461-4. 2002
    ..This procedure is more efficient, faster and cheaper than those used before, so is recommended for large-scale processing of field-collected larval and adult specimens to be identified in malaria vector studies...
  50. ncbi Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    Gordon Robertson
    British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada
    Nat Methods 4:651-7. 2007
    ..ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%...
  51. pmc Disease-associated XMRV sequences are consistent with laboratory contamination
    Stephane Hue
    MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland St, London W1T 4JF, UK
    Retrovirology 7:111. 2010
    ..Controversy has arisen from the failure of some studies to detect XMRV in PC or CFS patients and from inconsistent detection of XMRV in healthy controls...
  52. doi Target-enrichment strategies for next-generation sequencing
    Lira Mamanova
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 7:111-8. 2010
    ..We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project...
  53. ncbi Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise
    J R Johnson
    VA Medical Center, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55417, USA
    J Infect Dis 181:261-72. 2000
    ..urosepsis isolates of Escherichia coli, 29 virulence factor (VF) genes were detected by use of a novel polymerase chain reaction (PCR) assay. Compared with probe hybridization, the PCR assay's specificity was 100% and sensitivity 97...
  54. pmc PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
    Athanasia Spandidos
    Department of Genetics, Harvard Medical School, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114 2790, USA
    Nucleic Acids Res 38:D792-9. 2010
    ..In all, 26,855 primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site...
  55. pmc Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences
    Brendan Oakes
    Department of Pathology, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA
    Retrovirology 7:109. 2010
    ..Since there is a high degree of similarity between XMRV and abundant endogenous MLV proviruses, it is important to distinguish contaminating mouse sequences from true infections...
  56. pmc Improved amplification of genital human papillomaviruses
    P E Gravitt
    Department of Human Genetics, Roche Molecular Systems, Alameda, California, USA
    J Clin Microbiol 38:357-61. 2000
    ..This new primer system will be useful in assessing the natural history of HPV infections, particularly when the analysis requires HPV typing...
  57. ncbi PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
    Owen J Marshall
    Murdoch Childrens Research Institute, Royal Childrens Hospital, Flemington Road, Parkville, Vic, 3052, Australia
    Bioinformatics 20:2471-2. 2004
    ..It aims to automate and simplify the process of primer design...
  58. pmc Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates
    Rekha Pai
    Respiratory Diseases Branch, Division of Bacterial and Mycotic Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    J Clin Microbiol 44:124-31. 2006
    ....
  59. pmc Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    Osvaldo Zagordi
    Department of Biosystems Sciences and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Germany
    Nucleic Acids Res 38:7400-9. 2010
    ..We conclude that pyrosequencing can be used to investigate genetically diverse samples with high accuracy if technical errors are properly treated...
  60. pmc Removing noise from pyrosequenced amplicons
    Christopher Quince
    Department of Civil Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
    BMC Bioinformatics 12:38. 2011
    ..We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms...
  61. pmc A large proportion of asymptomatic Plasmodium infections with low and sub-microscopic parasite densities in the low transmission setting of Temotu Province, Solomon Islands: challenges for malaria diagnostics in an elimination setting
    Ivor Harris
    Australian Army Malaria Institute, Weary Dunlop Drive, Gallipoli Barracks Enoggera, QLD 4051, Australia
    Malar J 9:254. 2010
    ....
  62. pmc Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex 130 methicillin-resistant Staphylococcus aureus
    Anna C Shore
    Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
    Antimicrob Agents Chemother 55:3765-73. 2011
    ..aureus strains were predominantly from bovine sources. The highly divergent nature of SCCmec XI relative to other SCCmec elements indicates that it may have originated in another taxon...
  63. pmc Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis
    Y M Lo
    Department of Chemical Pathology, The University of Hong Kong, Prince Wales Hospital, Shatin, New Territories, Hong Kong
    Am J Hum Genet 62:768-75. 1998
    ..These data suggest that fetal DNA can be readily detected in maternal plasma and serum and may be a valuable source of material for noninvasive prenatal diagnosis...
  64. ncbi A newly discovered human pneumovirus isolated from young children with respiratory tract disease
    B G van den Hoogen
    Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
    Nat Med 7:719-24. 2001
    ..Serological studies showed that by the age of five years, virtually all children in the Netherlands have been exposed to human metapneumovirus and that the virus has been circulating in humans for at least 50 years...
  65. pmc Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
    Andrew Adey
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Genome Biol 11:R119. 2010
    ..We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing...
  66. ncbi A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma
    P van der Bruggen
    Ludwig Institute for Cancer Research, Brussels, Belgium
    Science 254:1643-7. 1991
    ..Thus, precisely targeted immunotherapy directed against antigen MZ2-E could be provided to individuals identified by HLA typing and analysis of the RNA of a small tumor sample...
  67. ncbi APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy
    Anne Rovelet-Lecrux
    Inserm U614 IFRMP, Faculty of Medicine, Rouen, France
    Nat Genet 38:24-6. 2006
    ..37 Mb. Brains from individuals with APP duplication showed abundant parenchymal and vascular deposits of amyloid-beta peptides. Duplication of the APP locus, resulting in accumulation of amyloid-beta peptides, causes ADEOAD with CAA...
  68. pmc Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing
    Bikram Datt Pant
    Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
    Plant Physiol 150:1541-55. 2009
    ..We established a quantitative real-time polymerase chain reaction platform that allows rapid and sensitive quantification of 177 Arabidopsis primary miR transcripts (pri-..
  69. ncbi The unique mutation in ace-1 giving high insecticide resistance is easily detectable in mosquito vectors
    M Weill
    Institut des Sciences de l Evolution UMR 5554, Laboratoire Genetique et Environnement, Universite Montpellier II, Montpellier, France
    Insect Mol Biol 13:1-7. 2004
    ..albimanus. The G119S has thus occurred independently at least four times in mosquitoes and this PCR test is probably of broad applicability within the Culicidae family...
  70. pmc Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques
    S M Aljanabi
    Cenargen Embrapa, SAIN Parque Rural, W5 Norte C P 02372, CEP 70849 970 Brasilia, DF, Brazil
    Nucleic Acids Res 25:4692-3. 1997
    ..The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning...
  71. ncbi Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set
    Mangala A Nadkarni
    Institute of Dental Research, Westmead Centre for Oral Health, Westmead Hospital, PO Box 533, Wentworthville, NSW 2145, Australia
    Microbiology 148:257-66. 2002
    ....
  72. pmc Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, Massachusetts 02142, USA
    Genome Res 21:494-504. 2011
    ..Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys...
  73. pmc Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification
    Leonardo B Pinheiro
    National Measurement Institute, Lindfield, New South Wales, Australia
    Anal Chem 84:1003-11. 2012
    Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample...
  74. pmc An efficient one-step site-directed and site-saturation mutagenesis protocol
    Lei Zheng
    Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH 3012 Berne, Switzerland
    Nucleic Acids Res 32:e115. 2004
    ..This method should be useful to facilitate the preparation of high-quality site saturation libraries...
  75. doi Submicroscopic infection in Plasmodium falciparum-endemic populations: a systematic review and meta-analysis
    Lucy C Okell
    Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
    J Infect Dis 200:1509-17. 2009
    ..Quantifying these submicroscopic infections is therefore key to understanding transmission dynamics and successfully reducing parasite transmission...
  76. ncbi Strategies for microsatellite isolation: a review
    L Zane
    Dipartimento di Biologia, Università di Padova Via Ugo Bassi 58 B, 35121, Padova, Italy
    Mol Ecol 11:1-16. 2002
    ..In addition, we propose a fast and easy protocol which is a combination of different published methods...
  77. pmc Failure to detect Xenotropic murine leukaemia virus-related virus in Chinese patients with chronic fatigue syndrome
    Ping Hong
    Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People s Republic of China
    Virol J 7:224. 2010
    ..The assay was standardized by constructing plasmid DNAs and armored RNAs as XMRV standards and competitive internal controls (CICs), respectively...
  78. pmc Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
    Scot E Dowd
    USDA ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA
    BMC Microbiol 8:125. 2008
    ..We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows...
  79. ncbi Human papillomavirus and oral cancer: the International Agency for Research on Cancer multicenter study
    Rolando Herrero
    International Agency for Research on Cancer, Lyon, France rherrero amnet co cr
    J Natl Cancer Inst 95:1772-83. 2003
    ..To investigate these associations, we conducted a multicenter case-control study of cancer of the oral cavity and oropharynx in nine countries...
  80. ncbi Molecular identification of bacteria associated with bacterial vaginosis
    David N Fredricks
    Program in Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    N Engl J Med 353:1899-911. 2005
    ..The cause of bacterial vaginosis remains poorly understood despite numerous studies based on cultures. Bacteria in microbial communities can be identified without cultivation by characterizing their ribosomal DNA (rDNA) sequences...
  81. pmc Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus
    M C Enright
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, Oxford University, Oxford OX1 3FY
    J Clin Microbiol 38:1008-15. 2000
    ..MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet...
  82. pmc Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer
    Stefan Ambs
    Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892 4258, USA
    Cancer Res 68:6162-70. 2008
    ..In summary, microRNA expression becomes altered with the development and progression of prostate cancer. Some of these microRNAs regulate the expression of cancer-related genes in prostate cancer cells...
  83. pmc Detection of a substantial number of sub-microscopic Plasmodium falciparum infections by polymerase chain reaction: a potential threat to malaria control and diagnosis in Ethiopia
    Lemu Golassa
    Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
    Malar J 12:352. 2013
    ..This study aimed to explore the presence of sub-microscopic Plasmodium falciparum infections using polymerase chain reaction (PCR). The PCR-based parasite prevalence was compared against microscopy and rapid diagnostic test (RDT).
  84. pmc High throughput gene expression measurement with real time PCR in a microfluidic dynamic array
    Sandra L Spurgeon
    Fluidigm Corporation, South San Francisco, California, USA
    PLoS ONE 3:e1662. 2008
    ..The data have excellent concordance with conventional real time PCR and the microfluidic dynamic arrays show better reproducibility than commercial DNA microarrays...
  85. pmc Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium
    Richard A Stabler
    London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
    Genome Biol 10:R102. 2009
    ..difficile (CD196), a recent epidemic and hypervirulent 027 (R20291) and a previously sequenced PCR-ribotype 012 strain (630)...
  86. pmc Mouse DNA contamination in human tissue tested for XMRV
    Mark J Robinson
    Section of Infectious Diseases, Jefferiss Research Trust Laboratories, Imperial College London, St Mary s Campus, London, W2 1PG, UK
    Retrovirology 7:108. 2010
    ..To control for contamination, PCR assays to detect either mouse mitochondrial DNA (mtDNA) or intracisternal A particle (IAP) long terminal repeat DNA were run on all samples, owing to their very high copy number in mouse cells...
  87. ncbi MethPrimer: designing primers for methylation PCRs
    Long Cheng Li
    Department of Urology, Veterans Affairs Medical Center, and University of California San Francisco, San Francisco, CA 94121, USA
    Bioinformatics 18:1427-31. 2002
    ..Therefore, the present study was designed to develop a program for such applications...
  88. ncbi Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936
    J J M van Dongen
    Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
    Leukemia 17:2257-317. 2003
    ..The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease...
  89. ncbi Damage formation and repair efficiency in the p53 gene of cell lines and blood lymphocytes assayed by multiplex long quantitative polymerase chain reaction
    Yu Chieh Wang
    Department of Biology, National Taiwan Normal University, Taipei, Taiwan, ROC
    Anal Biochem 319:206-15. 2003
    ..gene of various cultured cell lines and lymphocytes using a nonradioactive multiplex long quantitative polymerase chain reaction (QPCR) assay, which amplified a 7-kb fragment of the target gene and a 500-bp fragment of the template ..
  90. pmc A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region
    W John Kress
    Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
    PLoS ONE 2:e508. 2007
    ..This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level...
  91. ncbi Capturing chromosome conformation
    Job Dekker
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Science 295:1306-11. 2002
    ..Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring...
  92. doi Improved survival of patients with human papillomavirus-positive head and neck squamous cell carcinoma in a prospective clinical trial
    Carole Fakhry
    Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    J Natl Cancer Inst 100:261-9. 2008
    ....
  93. pmc Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology
    Danica Helb
    Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry, New Jersey, Newark, New Jersey 07103, USA
    J Clin Microbiol 48:229-37. 2010
    ..2%) susceptible cases. Specificity rose to 100% after correcting for a conventional susceptibility test error. In conclusion, this highly sensitive and simple-to-use system can detect M. tuberculosis directly from sputum in less than 2 h...
  94. pmc Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study
    Laura García-Álvarez
    Department of Veterinary Medicine, University of Cambridge, UK
    Lancet Infect Dis 11:595-603. 2011
    ....
  95. doi Human papillomavirus testing for the detection of high-grade cervical intraepithelial neoplasia and cancer: final results of the POBASCAM randomised controlled trial
    Dorien C Rijkaart
    Department of Pathology, VU University Medical Centre, Amsterdam, Netherlands
    Lancet Oncol 13:78-88. 2012
    ..The aim of this study was to assess whether HPV DNA testing in the first screen decreases detection of cervical intraepithelial neoplasia (CIN) grade 3 or worse, CIN grade 2 or worse, and cervical cancer in the second screening...
  96. pmc ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
    Eva Bellemain
    National Centre for Biosystematics, University of Oslo, Norway
    BMC Microbiol 10:189. 2010
    ..We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates...
  97. pmc Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands
    J G Herman
    Oncology Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    Proc Natl Acad Sci U S A 93:9821-6. 1996
    ....
  98. pmc An efficient recombination system for chromosome engineering in Escherichia coli
    D Yu
    Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 97:5978-83. 2000
    ..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
  99. ncbi Negative control of p53 by Sir2alpha promotes cell survival under stress
    J Luo
    Institute of Cancer Genetics and Department of Pathology, College of Physicians and Surgeons, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Cell 107:137-48. 2001
    ..These results have significant implications regarding an important role for Sir2alpha in modulating the sensitivity of cells in p53-dependent apoptotic response and the possible effect in cancer therapy...
  100. pmc Transposable elements: targets for early nutritional effects on epigenetic gene regulation
    Robert A Waterland
    Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell Biol 23:5293-300. 2003
    ..These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans...

Research Grants75

  1. Msec Polymerase Chain Reaction with fMolar Detection Sensitivity using SPR
    DONALD ROPER; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): Polymerase chain reaction (PCR) has a host of applications including genotyping specific mutations, genetic fingerprinting, gene cloning and mutagenesis...
  2. Ethanol Regulation of Serum Glucocorticoid Kinase I
    BLAIR N COSTIN; Fiscal Year: 2012
    ..acute ethanol exposure through western blotting followed by densitometry analysis and the quantitative polymerase chain reaction (Q-rtPCR). There are 5 total isoforms of Sgk1-4 resulting from translational events and 1 (Sgk1...
  3. ARUNKUMAR GOVINDAKARNAVAR; Fiscal Year: 2016
    ..b>Polymerase chain reaction (PCR) and serologic analyses of patient blood, CSF, Throat swab and Stool samples will be used to ..
  4. C Michael Hart; Fiscal Year: 2016
    ..endothelin-1, and thrombospondin-1) will be measured in the proposed models using quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting...
  5. Regulation of Astrocyte TIMP-1 in HIV-Associated Dementia
    JEREL ADAM FIELDS; Fiscal Year: 2011
    ..like cytokines and viral proteins will be used along with analysis tools such as western blot, real-time polymerase chain reaction, immunocytochemistry and enzyme linked immunosorbent assay...
  6. SUSAN F KEAY; Fiscal Year: 2016
    ..Western blot, chromatin immunoprecipita- tion (ChIP), microRNA microarray, and quantitative real-time polymerase chain reaction (qRT-PCR) techniques...
  7. Mark D Peterson; Fiscal Year: 2016
    ..studies for markers of inflammation and insulin resistance, and immunohistochemical quantification and polymerase chain reaction studies of skeletal muscle and adipose tissue...
  8. Mechanisms of Early Growth Response Factor 1 (Egr-1) Induction by HSV-1 Lytic Inf
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2010
    ..Reverse transcriptase polymerase chain reaction (RT-PCR) analyses indicated that Egr-1 mRNA was transcribed as early as 1 hpi and did not require de ..
  9. Mechanisms of Astrocyte Development
    Teri L Belecky Adams; Fiscal Year: 2010
    ..in vitro and in vivo using immunohistochemistry, Western blots, in situ hybridization, quantitative polymerase chain reaction and image analysis...
  10. RRSS #08: Evaluating Prevalence HPV Infection Among Head and Neck Cancer Patients
    Dennis M Deapen; Fiscal Year: 2009
    ....
  11. Metabolic Pathways and Defects in Fructose Metabolism
    DEAN TOLAN; Fiscal Year: 2009
    ..and characterization of these global predictions will be done by quantitative reverse-transcriptase polymerase chain reaction (Q-PCR), RNA in situ hybridization (RISH), and identification of metabolic intermediates during the ..
  12. Astrocyte Development and Reactive Gliosis
    Teri L Belecky-Adams; Fiscal Year: 2012
    ..in vitro and in vivo using immunohistochemistry, Western blots, in situ hybridization, quantitative polymerase chain reaction and image analysis...
  13. Modeling schizophrenia gamma deficits using cell-specific RNAi knockdown of GAD67
    RITCHIE EDWARD BROWN; Fiscal Year: 2012
    ..Effectiveness of the KD of the target gene (GAD67) will be assessed by: (i) Quantitative Polymerase chain reaction (PCR) performed on mRNA harvested from transfected PV-Pos neurons using laser capture microdissection (..
  14. ROLE OF OPIATES IN ALCOHOL-INDUCED NEUROTOXICITY
    DIPAK SARKAR; Fiscal Year: 2009
    ..state-of-the-art techniques like combined laser capture microdissection and quantitative real-time polymerase chain reaction to determine changes in gene expression in beta-endorphin cells in vivo...
  15. DIPAK KUMAR SARKAR; Fiscal Year: 2016
    ..state-of-the-art techniques like combined laser capture microdissection and quantitative real-time polymerase chain reaction to determine changes in gene expression in beta-endorphin cells in vivo...
  16. Role of Microbial Translocation in Cardiopulmonary Disease in Children with HIV
    Alison Morris; Fiscal Year: 2013
    ..We will use polymerase chain reaction to detect bacterial 16S ribosomal DNA (rDNA) and fungal18S rDNA and will also measure peripheral LPS and ..
  17. Human Papillomavirus Association with Subsets of Colorectal Cancer
    Polly A Newcomb; Fiscal Year: 2010
    ..We will test these DNA samples for HPV-specific DNA using polymerase chain reaction (PCR)-based methods and conduct HPV genotyping of all HPV positive samples...
  18. Chicago Community-Acquired Pneumonia Consortium
    Richard G Wunderink; Fiscal Year: 2010
    ..Developments in molecular diagnostic techniques, such as urinary antigen testing and polymerase chain reaction (PCR) detection of bacterial and viral genes, have not only made documentation of etiology more accurate ..
  19. Identification of an Epigenetic Risk Marker for PTSD
    Rachel Yehuda; Fiscal Year: 2010
    ..Cytosine methylation will be quantified using polymerase chain reaction (PCR) primers developed by Michael Meaney, Ph.D...
  20. CHRISTINA A FISKE; Fiscal Year: 2015
    ..Measurements of quantity and function will be performed using polymerase chain reaction (PCR) and flow cytometry...
  21. Manipulation of Host Angiogenesis as a Therapeutic Strategy against Invasive Pulm
    Dimitrios P Kontoyiannis; Fiscal Year: 2010
    ..over a period of 7 days (pulmonary model only);(2) Tissue fungal burden, measured by quantitative polymerase chain reaction (qPCR);and (3) Angiogenesis at the site of infection, assessed in vivo in the myocutaneous model using ..
  22. William L Hughes; Fiscal Year: 2015
    ..tool for lung cancer in vitro that exceeds the performance of quantitative reverse transcription polymerase chain reaction (qRT-PCR)...
  23. SERGE P NANA-SINKAM; Fiscal Year: 2014
    ..have been quantitatively measured in human sera or plasma using quantitative reverse transcription polymerase chain reaction (qRT-PCR) with pre-concentration techniques such as ultra-centrifugation or ExoQuickTM exosome ..
  24. Bharat Thyagarajan; Fiscal Year: 2015
    ..include mitochondrial DNA copy number, mitochondria DNA damage as measured by quantitative real time polymerase chain reaction and oxidative damage as measured by urinary F2-isoprostanes and plasma fluorescent oxidation products...
  25. EGFRvIII in Pancreatic Cancer
    Maneesh Jain; Fiscal Year: 2010
    ..the expression of EGFR and EGFR variants in human pancreatic tumors by reverse transcriptase- polymerase chain reaction (RT-PCR) and immunohistochemical analysis. PCR- amplification will demonstrate the expression of mRNA...
  26. JEREL ADAM FIELDS; Fiscal Year: 2014
    ..expression and their interactions with HIV proteins by co-immunoprecipitation, immunoblot, real-time polymerase chain reaction (RT2PCR), enzyme-linked immunosorbent assay (ELISA) and quantitative immunohistochemistry...
  27. Brian Wigdahl; Fiscal Year: 2014
    ..The specific aims of this application are to continue to: (1) construct a HIV-1 (subtype B) LTR and Env polymerase chain reaction (PCR) product sequence database and clone bank derived from peripheral blood mononuclear cells (PBMCs) ..
  28. Strain Specific Detection of Influenza at the Point-of-Care
    HYONGSOK TOM SOH; Fiscal Year: 2012
    ..Currently, polymerase chain reaction (PCR) offers the highest sensitivity in a much shorter turn-around time (2-4 hours) (29, 61, 67)...
  29. Receptor/Ligand Signals for Ovarian Follicular Angiogenesis
    Leon J Spicer; Fiscal Year: 2010
    ..in theca cells during follicular development in vivo using real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) as well as measure ANG and FGF9 in follicular fluid via ELISA...
  30. Extracellular Scaffold Elasticity and Binding Sites in Acinar Differentiation
    Melinda Larsen; Fiscal Year: 2013
    ..green fluorescent protein;IKVAV, Isoleucine-Lysine-Valine-Alanine-Valine;PEG, poly(ethylene glycol);PCR, polymerase chain reaction;PEG-DMA, PEG-dimethylacrylate;PEG-TMA, PEG-trimethylacrylate;OMMA, oxiran-2-ylmethyl methacrylate;POMO, ..
  31. The new biology of estrogen action in aromatase resistance breast cancer cells
    JOAN SUEDEE LEWIS-WAMBI; Fiscal Year: 2011
    ..research techniques will be used;Western blot analysis to measure protein expression, Real-Time polymerase chain reaction (PCR) to measure changes in mRNA levels, confocal microscopy to study protein translocalization, small ..
  32. STRESS-RELATED CHANGES IN GENE EXPRESSION AS BIOMARKERS OF RELAPSE VULNERABILITY
    ROBERT DAVID BEECH; Fiscal Year: 2010
    ..of selected genes of interested will be confirmed using Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR)...
  33. Barcoded Magnetic Beads for Rapid Tests of MRSA and Respiratory Viral Panels
    WINSTON Z HO; Fiscal Year: 2010
    ..MSI) has successfully combined Barcoded Magnetic Bead (BMB)(R) and Target Enriched Multiplex Polymerase Chain Reaction (Tem-PCR) technologies for simple, rapid, multiplex tests including: 14-plex Respiratory Viral Pathogen (..
  34. Thomas Tuschl; Fiscal Year: 2014
    ..We have also adapted quantitative reverse-transcription polymerase chain reaction (qRT-PCR) technology to allow non- invasive verification and validation in larger study cohorts of ..
  35. RICHARD JASON LAMONTAGNE; Fiscal Year: 2014
    ..in miRNA expression levels will be determined by miRNA microarray and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) studies...
  36. Telomere Attrition Rate and Periodontitis: a nested case control study in the ARI
    ANNE ELIZABETH SANDERS; Fiscal Year: 2013
    ..Relative LTL will be measured using a well- established method of quantitative polymerase chain reaction. Cross-sectional evidence shows that shorter LTL is associated with higher risk for many chronic and age-..
  37. Somatostain & Stress-Related Genes in HIV & Comorbid Major Depressive Disorder
    Ian Paul Everall; Fiscal Year: 2010
    ..We have validated the loss of somatostatin gene expression by quantitative real-time polymerase chain reaction (qRT-PCR), which correlates with the density of calbindin immunopositive interneurons and we noted a ..
  38. Novel Bacterial Pathogens in Pelvic Inflammatory Disease
    Catherine L Haggerty; Fiscal Year: 2012
    ..We propose a polymerase chain reaction (PCR) study of Leptotrichia sanguinegens/amnionii, A...
  39. CHARACTERIZATION OF NOVEL BUTADIENE-INDUCED PUTATIVE p53 TARGET GENES
    Perpetua M Muganda; Fiscal Year: 2010
    ..small interfering RNA, chromatin immunoprecipitation-quantitative PCR assays, reporter gene assays, polymerase chain reaction arrays, primary lymphocytes, as well as genetically-paired p53-deficient and proficient cell lines to ..
  40. JEFFREY THOMAS MASON; Fiscal Year: 2016
    ..to solubilize tissue proteins and a novel and highly sensitive immunoassay format, called immunoliposome-polymerase chain reaction (ILPCR), developed in our laboratory will achieve the level of quantification for uPA and PAI-1 stated ..
  41. Vivian Gahtan; Fiscal Year: 2015
    ..smooth muscle cell chemotaxis;2) western blot and ELISA for cell signaling;3) quantitative real time polymerase chain reaction for gene expression;4) two animal models of IH - carotid artery ligation in the TSP-1 knockout mouse and ..
  42. Calcium channels in arterial smooth muscle cells
    Jonathan H Jaggar; Fiscal Year: 2013
    ..To investigate these aims, we will use a wide variety of techniques, including quantitative polymerase chain reaction, patch-clamp electrophysiology, laser-scanning confocal microscopy, Western blotting, RNA interference, ..
  43. Progesterone-Induced Gene Expression Changes and Risk of Relapse to Cocaine Use
    Rajita Sinha; Fiscal Year: 2010
    ..of selected genes of interested will be confirmed using Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR)...
  44. Laurence Huang; Fiscal Year: 2016
    ..The OPW specimens will be analyzed using polymerase chain reaction (PCR) assays for Pneumocystis and M...
  45. Central Endocannabinoid System Dysfunction and Hypertension
    Jeanne L Seagard; Fiscal Year: 2013
    ..in the dorsal medulla, including the NTS, or 2) CB1R message using quantitative reverse transcription-polymerase chain reaction (RT-PCR) specifically in the NTS in spontaneously hypertensive animals...
  46. NORADRENERGIC SYSTEM IN DEPRESSION
    GREGORY ALLEN ORDWAY; Fiscal Year: 2012
    ..Laser capture microdissection and polymerase chain reaction methods will be employed to study LC neurons, astrocytes, and oligodendrocytes, 3 major cell types in ..
  47. Rapid and Cost-Effective Diagnostic System for Sexually Transmitted Infections
    John E Mueller; Fiscal Year: 2011
    ..It will perform rapid polymerase chain reaction (PCR) for CT/NG targets in a simplified architecture that creates a stable thermal gradient from a ..
  48. The Role of SaeR/S During Staphylococcus aureus Skin Infections
    Jovanka M Voyich; Fiscal Year: 2012
    ..In vitro oligonucleotide microarray and real-time reverse-transcriptase polymerase chain reaction assays identified numerous extracellular virulence genes down-regulated in USA300?saeR/S and direct ..
  49. Steven J Norris; Fiscal Year: 2015
    ..effects of environmental conditions on vlsE expression and variation will be analyzed by quantitative polymerase chain reaction (qPCR) and sequence specific PCR...
  50. Chicago Community-Acquired Pneumonia Consortium II
    Richard G Wunderink; Fiscal Year: 2013
    ..Conversely, developments in molecular diagnostic techniques, such as urinary antigen testing and polymerase chain reaction (PCR) detection of bacterial and viral genes, have not only made documentation of etiology more accurate ..
  51. Real-Time Reagent-Free Noninvasive Diagnosis of Tuberculosis
    Payam Nahid; Fiscal Year: 2013
    ..phase in clinical settings previously but such detection was performed labor-intensively using the polymerase chain reaction (PCR) to analyze samples collected over a matter of hours [Chen 2005]...
  52. Social, Genetic Determinants of Blood Pressure in Underserved African Americans
    SANDRA MARIE COULON; Fiscal Year: 2013
    ..rs 41423247;FKBP5, rs1360780;92, rs6198) will be extracted from buccal swab samples and assayed via polymerase chain reaction, under the guidance of Dr. Matthew Kostek, a co-sponsor of this application...
  53. Central Molecular Mechanisms of Stress-Induced Visceral Hypersensitivity
    ANTHONY CHRISTOPHER JOHNSON; Fiscal Year: 2012
    ..tools to perform the molecular techniques necessary to monitor both total (quantitative reverse polymerase chain reaction, western blotting) and localized (in situ hybridization, immunohistochemistry) gene and protein ..
  54. Micromagnetic Aptamer PCR System for Ultrasensitive Multiplexed Protein Detection
    HYONGSOK TOM SOH; Fiscal Year: 2010
    ..We propose to develop the the Micro-Magnetic Separation - Quantitative Polymerase Chain Reaction (MMS-QPCR) system wherein we integrate chip-based, high-gradient micro-magnetic separation with aptamer-..
  55. Warren Phipps; Fiscal Year: 2015
    ..serially over the course of therapy up to one year, and we will quantify HHV-8 in specimens using polymerase chain reaction (PCR), including novel PCR assays to evaluate specific HHV-8 gene mRNA in tumors...
  56. New Strategies to Decipher the Pathophysiology of Chronic Fatigue Syndrome
    Vincent C Lombardi; Fiscal Year: 2013
    ..1.2) Quantitative polymerase chain reaction Q-PCR will be used for confirmation of virus gene expression. 1...
  57. LESZEK K KUBIN; Fiscal Year: 2015
    ..time course of 5-HT receptor expression in the XII nucleus using quantitative reverse 2A transcription-polymerase chain reaction, Western blots and immunohistochemistry to identify its phase relationship within the circadian cycle ..
  58. MOUSE MODEL OF LYME BORRELIOSIS
    STEPHEN WILLIAM BARTHOLD; Fiscal Year: 2012
    ..disease remission will be examined, using laser capture microdissection, quantitative real-time polymerase chain reaction for spirochetal DNA and RNA, and immunohistochemistry...
  59. Annual Estimates of Influenza Vaccine Effectiveness: Davidson County, TN
    Marie R Griffin; Fiscal Year: 2010
    ..Cases will be defined by detection of influenza virus by reverse transcriptase- polymerase chain reaction (RT-PCR) or viral culture...
  60. Bruce P Barrett; Fiscal Year: 2016
    ..For each ARI illness episode, nasal samples will be tested with multiplex PCR (polymerase chain reaction) to identify viruses, and will be analyzed for neutrophil count, interleukin-6, and interleukin-8 ..
  61. BH4 in hyperoxic lung injury in newborn
    Ru Jeng Teng; Fiscal Year: 2013
    ..and post-translational levels by chromatin immunoprecipitation, DNA methylation, quantitative real-time polymerase chain reaction, and immunoblotting...
  62. Quantitative Trait Genes for Circadian Phenotypes
    John R Hofstetter; Fiscal Year: 2013
    ..Measuring function requires three technically challenging assays: the quantitative real-time polymerase chain reaction (qRT-PCR);the microarray system;and a specialized cell culture system called gene dosage network ..
  63. Investigation of the characteristics and persistence of memory B cells following
    Jiraprapa Wipasa; Fiscal Year: 2012
    ..Transcription factors involved in development and survival of memory B cells will be analysed by polymerase chain reaction. We will track the fate of malaria-specific human B cells in the days, months and years after infection ..
  64. Stress and Memory Formation Across the Female Lifespan
    Tracey Shors; Fiscal Year: 2009
    ..trace eyeblink conditioning in the rat, Golgi impregnation and light microscope analysis, real-time polymerase chain reaction, in situ hybridization, radioimmunoassay, and surgical manipulation of glucocorticoids and ovarian ..
  65. Oral H. pylori Prevalence in Intellectually/Developmentally Disabled Adults
    Catherine Binkley; Fiscal Year: 2009
    ..Nested Polymerase Chain Reaction (PCR) analyses will be used to detect H. pylori in the dental plaque...
  66. SIMULTANEOUS SCREENING FOR A/H3N2, A/H1N1, A/H5N1 AND B INFLUENZA VIRUSES
    Erica Dawson; Fiscal Year: 2009
    ..The advantages of the proposed approach over existing polymerase chain reaction (PCR) methods for influenza viruses stem from the use of a single gene segment for identification of ..
  67. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2009
    ..Two other types of WGA have been commercialized for research applications: 1) methods derived from the polymerase chain reaction and 2) multiple displacement amplification (MDA)...
  68. CONFERENCE--ISOLATED FETAL CELLS IN MATERNAL BLOOD
    Joe Simpson; Fiscal Year: 1993
    ..After nearly a decade of ostensible inactivity, several groups have recently used polymerase chain reaction (PCR) to show that fetal cells very likely exist in maternal blood...
  69. APOPTOSIS--LENS DIFFERENTIATION AND CATARACT DEVELOPMENT
    David Li; Fiscal Year: 2000
    ..To analyze gene expression, reverse-transcription-linked polymerase chain reaction and in situ hybridization will be used to determine the presence or absence of the mRNAs for the ..
  70. PATHOGENESIS AND PREVENTION OF IDDM
    Hugh McDevitt; Fiscal Year: 2002
    ..In a collaboration between Dr. Chien and Dr. Mark Davis, the polymerase chain reaction (PCR) will be used to characterize and sequence T cell receptor V alpha and V beta sequences from single ..
  71. Combination Antibotics as a Treatment for Chlamydia-Induced Reactive Arthritis
    John Carter; Fiscal Year: 2007
    ..Persistent Ct has been demonstrated by polymerase chain reaction (PCR) in the synovial tissue of patients with ReA years after their initial exposure...
  72. Detection of Category A Pathogens by Gold Nanoparticles
    Steven Wolinsky; Fiscal Year: 2007
    ..for rapid and accurate pathogen detection is the development of methods that do not rely on the polymerase chain reaction (PCR) or comparable target- or signal-amplification systems to minimize instrumentation and reagent ..
  73. WHIPPLE BACILLUS AND THE ETIOLOGY OF SARCOIDOSIS
    David Fredricks; Fiscal Year: 1999
    Simultaneous technological and conceptual advances in molecular microbiology, i.e., the polymerase chain reaction (PCR) and molecular phylogenetics, together form a powerful new experimental approach that will be used to investigate the ..