ribosomal dna

Summary

Summary: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.

Top Publications

  1. 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
  2. pmc Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
    Yong Wang
    KAUST Global Partnership Program, Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
    PLoS ONE 4:e7401. 2009
  3. pmc The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms
    M Kaeberlein
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 13:2570-80. 1999
  4. ncbi SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast
    Takehiko Kobayashi
    National Institute for Basic Biology, Okazaki, Japan
    Cell 117:441-53. 2004
  5. ncbi Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences
    C P Kurtzman
    National Center for Agricultural Utilization Research, Agricultural Research Service, U S Department of Agriculture, Peoria, Illinois 61604, USA
    Antonie Van Leeuwenhoek 73:331-71. 1998
  6. ncbi Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats
    Takehiko Kobayashi
    National Institute for Basic Biology, SOKENDAI, School of Life Science, 38 Nishigonaka, Myodaijicho, Okazaki, 444 8585 Japan
    Science 309:1581-4. 2005
  7. ncbi The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology
    M F Whiting
    Department of Zoology and M L Bean Life Science Museum, Brigham Young University, Provo, Utah 84602, USA
    Syst Biol 46:1-68. 1997
  8. pmc Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge
    J M Schroeder
    Department of Molecular Genetics, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA
    J Clin Microbiol 39:1903-11. 2001
  9. pmc Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA
    J R Marchesi
    School of Pure and Applied Biology, University of Wales College of Cardiff, United Kingdom
    Appl Environ Microbiol 64:795-9. 1998
  10. ncbi Uncultured archaea in deep marine subsurface sediments: have we caught them all?
    Andreas Teske
    Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    ISME J 2:3-18. 2008

Detail Information

Publications375 found, 100 shown here

  1. 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...
  2. pmc Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
    Yong Wang
    KAUST Global Partnership Program, Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
    PLoS ONE 4:e7401. 2009
    Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches...
  3. pmc The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms
    M Kaeberlein
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 13:2570-80. 1999
    ..Sir2p is a limiting component in promoting yeast longevity, and increasing the gene dosage extends the life span in wild-type cells. A possible role of the conserved SIR2 in mammalian aging is discussed...
  4. ncbi SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast
    Takehiko Kobayashi
    National Institute for Basic Biology, Okazaki, Japan
    Cell 117:441-53. 2004
    ..From these and other experiments, we conclude that SIR2 prevents unequal sister-chromatid recombination, probably by forming special cohesin structures, without significant effects on recombinational events within individual rRNA genes...
  5. ncbi Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences
    C P Kurtzman
    National Center for Agricultural Utilization Research, Agricultural Research Service, U S Department of Agriculture, Peoria, Illinois 61604, USA
    Antonie Van Leeuwenhoek 73:331-71. 1998
    ..anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction ..
  6. ncbi Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats
    Takehiko Kobayashi
    National Institute for Basic Biology, SOKENDAI, School of Life Science, 38 Nishigonaka, Myodaijicho, Okazaki, 444 8585 Japan
    Science 309:1581-4. 2005
    ..This transcription is regulated by the silencing gene, SIR2, and by copy number. Transcription-induced cohesin dissociation may be a general mechanism of recombination regulation...
  7. ncbi The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology
    M F Whiting
    Department of Zoology and M L Bean Life Science Museum, Brigham Young University, Provo, Utah 84602, USA
    Syst Biol 46:1-68. 1997
    ..among the holometabolous insect orders were inferred from cladistic analysis of nucleotide sequences of 18S ribosomal DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological characters...
  8. pmc Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge
    J M Schroeder
    Department of Molecular Genetics, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, USA
    J Clin Microbiol 39:1903-11. 2001
    ..Our results demonstrate the usefulness of 18S ribosomal DNA PCR amplimers ASA.S1 and GTSA...
  9. pmc Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA
    J R Marchesi
    School of Pure and Applied Biology, University of Wales College of Cardiff, United Kingdom
    Appl Environ Microbiol 64:795-9. 1998
    ..They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used...
  10. ncbi Uncultured archaea in deep marine subsurface sediments: have we caught them all?
    Andreas Teske
    Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    ISME J 2:3-18. 2008
    ....
  11. ncbi Microbial population structures in the deep marine biosphere
    Julie A Huber
    Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Science 318:97-100. 2007
    ....
  12. ncbi Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1
    Kevin J Bitterman
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 277:45099-107. 2002
    ..We discuss the possibility that nicotinamide is a physiologically relevant regulator of Sir2 enzymes...
  13. pmc Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited
    Thomas D Leser
    Department of Microbiology, Danish Veterinary Laboratory, Bulowsvej 27, DK 1790 Copenhagen V, Denmark
    Appl Environ Microbiol 68:673-90. 2002
    The phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16S ribosomal DNA (rDNA) sequence analysis...
  14. pmc Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing
    B Diez
    Departament de Biologia Marina, Institut de Ciencies del Mar, CSIC, E 08039 Barcelona, Catalunya, Spain
    Appl Environ Microbiol 67:2932-41. 2001
    ..Genetic libraries of eukaryotic ribosomal DNA were screened by restriction fragment length polymorphism analysis, and at least one clone of each operational ..
  15. ncbi c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I
    Carla Grandori
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Nat Cell Biol 7:311-8. 2005
    ..combined immunofluorescence and rRNA-FISH, we have detected endogenous c-Myc in nucleoli at sites of active ribosomal DNA (rDNA) transcription...
  16. ncbi Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae
    S J Lin
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 289:2126-8. 2000
    ..These findings suggest that the increased longevity induced by calorie restriction requires the activation of Sir2p by NAD...
  17. pmc UBF binding in vivo is not restricted to regulatory sequences within the vertebrate ribosomal DNA repeat
    Audrey C O'Sullivan
    Biomedical Research Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
    Mol Cell Biol 22:657-68. 2002
    ..can also bind in vitro to a variety of sequences found across the intergenic spacer in Xenopus and mammalian ribosomal DNA (rDNA) repeats...
  18. pmc Mammalian Sir2 homolog SIRT7 is an activator of RNA polymerase I transcription
    Ethan Ford
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 20:1075-80. 2006
    ..Depletion of SIRT7 stops cell proliferation and triggers apoptosis. Our findings suggest that SIRT7 is a positive regulator of Pol I transcription and is required for cell viability in mammals...
  19. ncbi Molecular phylogeny and evolutionary relationships among mosquitoes (Diptera: Culicidae) from the northeastern United States based on small subunit ribosomal DNA (18S rDNA) sequences
    John J Shepard
    Department of Soil and Water, The Connecticut Agricultural Experiment Station, 123 Huntington Street, P O Box 1106, New Haven, CT 06504, USA
    J Med Entomol 43:443-54. 2006
    ..of Culicidae native to the northeastern United States were investigated by analyzing small subunit ribosomal DNA (18S rDNA) sequences obtained from 39 species representing nine genera...
  20. pmc Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA
    Hans G H J Heilig
    Laboratory of Microbiology, Wageningen University, 6703 CT Wageningen, The Netherlands
    Appl Environ Microbiol 68:114-23. 2002
    A Lactobacillus group-specific PCR primer, S-G-Lab-0677-a-A-17, was developed to selectively amplify 16S ribosomal DNA (rDNA) from lactobacilli and related lactic acid bacteria, including members of the genera Leuconostoc, Pediococcus, ..
  21. ncbi Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models
    Allen G Collins
    NMFS, National Systematics Laboratory, National Museum of Natural History, MRC 153, Smithsonian Institution, Washington DC 20013 7012, USA
    Syst Biol 55:97-115. 2006
    ..18S; 28S; Cubozoa; Hydrozoa; medusa; molecular systematics; polyp; Scyphozoa; Staurozoa.]...
  22. ncbi A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA
    S Gottlieb
    Committee on Genetics, University of Chicago, Illinois 60637
    Cell 56:771-6. 1989
    ..Here we demonstrate that SIR2's effect is not restricted to controlling mating type expression, but rather that SIR2 functions in a more general way in the genome...
  23. pmc Dicer is associated with ribosomal DNA chromatin in mammalian cells
    Lasse Sinkkonen
    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    PLoS ONE 5:e12175. 2010
    ..Components of the RNA silencing machinery are involved in different aspects of chromatin function in numerous organisms. However, association of RNA silencing with chromatin in mammalian cells remains unclear...
  24. ncbi The natural history of group I introns
    Peik Haugen
    Department of Biological Sciences and Roy J Carver Center for Comparative Genomics, University of Iowa, 312 Biology Building, Iowa City, IA 52242 1324, USA
    Trends Genet 21:111-9. 2005
    ....
  25. pmc Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data
    Austen R D Ganley
    National Institute for Basic Biology, Okazaki, 444 8585, Japan
    Genome Res 17:184-91. 2007
    ..These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays...
  26. ncbi Activation of RNA polymerase I transcription by cockayne syndrome group B protein and histone methyltransferase G9a
    Xuejun Yuan
    Division of Molecular Biology of the Cell II, German Cancer Research Center, D 69120 Heidelberg, Germany
    Mol Cell 27:585-95. 2007
    ..The results reveal the mechanism underlying CSB-mediated activation of rDNA transcription and link G9a-dependent H3K9 methylation to Pol I transcription elongation through chromatin...
  27. ncbi The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus
    Jordi Torres-Rosell
    Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
    Nat Cell Biol 9:923-31. 2007
    ..Our study also suggests a key role of sumoylation for nucleolar dynamics, perhaps in the compartmentalization of nuclear activities...
  28. ncbi Distribution and abundance of uncultured heterotrophic flagellates in the world oceans
    Ramon Massana
    Department of Marine Biology and Oceanography, Institut de Ciencies del Mar, CSIC, Passeig Marítim de la Barceloneta 37 49, 08003 Barcelona, Catalonia, Spain
    Environ Microbiol 8:1515-22. 2006
    ..MAST-4 cells likely contribute substantially to picoplankton grazing and nutrient re-mineralization in vast areas of the oceans and represent a key eukaryotic group in marine food webs...
  29. ncbi Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer
    I L Gonzalez
    Department of Pathology, Hahnemann University, Philadelphia, Pennsylvania 19102, USA
    Genomics 27:320-8. 1995
    We have sequenced the remaining 12.4 kb of the 30-kb human ribosomal DNA intergenic spacer (IGS), which allows us to piece together both a complete IGS and a 43-kb rDNA unit...
  30. ncbi c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription
    Azadeh Arabi
    Södertörns högskola, S 141 89 Huddinge, Sweden
    Nat Cell Biol 7:303-10. 2005
    ..Here we show that the proteins c-Myc and Max interact in nucleoli and are associated with ribosomal DNA. This association is increased upon activation of quiescent cells and is followed by recruitment of the Myc ..
  31. ncbi Intergenic transcripts regulate the epigenetic state of rRNA genes
    Christine Mayer
    German Cancer Research Center, Division of Molecular Biology of the Cell II, D 69120 Heidelberg, Germany
    Mol Cell 22:351-61. 2006
    ..The results reveal an important contribution of processed IGS transcripts in chromatin structure and epigenetic control of the rDNA locus...
  32. pmc Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA gene
    C P Kurtzman
    National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, Illinois 61604, USA
    J Clin Microbiol 35:1216-23. 1997
    ..related organisms were compared for extent of nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA (rDNA) gene...
  33. pmc Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer
    Julie Huang
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 20:2887-901. 2006
    Silencing within the yeast ribosomal DNA (rDNA) repeats protects the integrity of this highly repetitive array by inhibiting hyperrecombination and repressing transcription from foreign promoters...
  34. ncbi Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting
    K Watanabe
    Marine Biotechnology Institute, Kamaishi Laboratories, 3 75 1 Heita, Iwate 026 0001, Kamaishi City, Japan
    J Microbiol Methods 44:253-62. 2001
    Denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA (rDNA) fragments has frequently been applied to the fingerprinting of natural bacterial populations (PCR/DGGE)...
  35. pmc Ribosomal DNA contributes to global chromatin regulation
    Silvana Paredes
    Department of Biology, Texas A and M University, College Station, TX 77843, USA
    Proc Natl Acad Sci U S A 106:17829-34. 2009
    ..We propose that the rDNA contributes to a balance between heterochromatin and euchromatin in the nucleus, and alterations in rDNA--induced or natural--affect this balance...
  36. pmc The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    J R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 33:D294-6. 2005
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  37. ncbi The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA
    A S Ivessa
    Department of Molecular Biology, Princeton University, New Jersey 08544 1014, USA
    Cell 100:479-89. 2000
    Replication of Saccharomyces ribosomal DNA (rDNA) proceeds bidirectionally from origins in a subset of the approximately 150 tandem repeats, but the leftward-moving fork stops when it encounters the replication fork barrier (RFB)...
  38. ncbi The multifunctional nucleolus
    Francois Michel Boisvert
    Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, UK
    Nat Rev Mol Cell Biol 8:574-85. 2007
    ..Nucleoli assemble around the tandemly repeated ribosomal DNA gene clusters and 28S, 18S and 5...
  39. ncbi Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle
    A Conconi
    Institute for Cell Biology, Swiss Federal Institute of Technology, Zurich
    Cell 57:753-61. 1989
    ..This suggests that the two states of chromatin are maintained independently of the transcriptional process and that they are stably propagated through the cell cycle...
  40. pmc 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM
    C W Kaplan
    Environmental Biotechnology Institute, California Polytechnic State University, San Luis Obispo, CA 93407, USA
    Appl Environ Microbiol 67:1935-9. 2001
    16S ribosomal DNA terminal restriction fragment patterns from rat fecal samples were analyzed to track the dynamics of Lactobacillus acidophilus NCFM and discern bacterial populations that changed during feeding with NCFM...
  41. pmc Optimization of real-time PCR assay for rapid and sensitive detection of eubacterial 16S ribosomal DNA in platelet concentrates
    Tamimount Mohammadi
    Sanquin Blood Bank North West Region, Amsterdam, The Netherlands
    J Clin Microbiol 41:4796-8. 2003
    A real-time PCR assay was developed for rapid detection of eubacterial 16S ribosomal DNA in platelet concentrates. The sensitivity of this assay can be hampered by contaminating DNA in the PCR reagents...
  42. ncbi Comparison of 16S ribosomal DNA sequences of all Xanthomonas species
    L Hauben
    National Research Centre for Biotechnology GBF, Braunschweig, Germany
    Int J Syst Bacteriol 47:328-35. 1997
    ..This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation...
  43. ncbi Cytogenetics for the model system Arabidopsis thaliana
    P Fransz
    School of Biological Sciences, University of Birmingham, Edgbaston, UK
    Plant J 13:867-76. 1998
    ..Together with the presented karyotype this makes Arabidopsis a model system for detailed cytogenetic mapping...
  44. ncbi Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences
    J M Moncalvo
    Department of Botany, Duke University, Durham, North Carolina 27708, USA
    Syst Biol 49:278-305. 2000
    ..of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences...
  45. ncbi DNA sequence analysis of the ribosomal DNA ITS2 region for the Anopheles punctulatus group of mosquitoes
    N W Beebe
    Molecular Parasitology Unit, Department of Cell and Molecular Biology, University of Technology, Sydney, Australia
    Insect Mol Biol 8:381-90. 1999
    The internal transcribed spacer 2 (ITS2) from the ribosomal DNA was sequenced and characterized for ten cryptic species in the Anopheles punctulatus group, the members of which are major vectors of malaria and filariasis in the south-..
  46. ncbi rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication
    Martin D Burkhalter
    Institute of Cell Biology, Department of Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Mol Cell 15:409-21. 2004
    To investigate the influence of the ribosomal DNA enhancer on initiation of replication and recombination at the ribosomal array, we used yeast S. cerevisiae strains with adjacent, tagged rRNA genes...
  47. pmc Molecular analysis of the bacterial microbiota in the human stomach
    Elisabeth M Bik
    Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild Science Building, 299 Campus Drive, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:732-7. 2006
    ..The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease...
  48. pmc Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean
    Ramon Massana
    Departament de Biologia Marina i Oceanografia, Institut de Ciencies del Mar, CMIMA, CSIC, 08003 Barcelona, Catalonia, Spain
    Appl Environ Microbiol 68:4554-8. 2002
    ....
  49. ncbi Directed gene copy number amplification in Pichia pastoris by vector integration into the ribosomal DNA locus
    Hans Marx
    Department of Biotechnology, BOKU, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    FEMS Yeast Res 9:1260-70. 2009
    ....
  50. pmc Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR
    K Tajima
    Laboratory of Rumen Microbiology, STAFF-Institute, Tsukuba, Ibaraki 305-0854, Japan
    Appl Environ Microbiol 67:2766-74. 2001
    ..This observation may explain why some predominant rumen bacteria have not been detected in PCR-generated 16S ribosomal DNA libraries.
  51. pmc characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal DNA terminal restriction fragment length polymorphism profiling
    G B Rogers
    Division of Life Sciences, King s College London, London SE1 9NN, UK
    J Clin Microbiol 42:5176-83. 2004
    ..In conclusion, this reveals the enormous complexity of bacteria within the CF lung. Although their significance is yet to be determined, these findings alter our perception of CF lung infections...
  52. pmc Hmo1, an HMG-box protein, belongs to the yeast ribosomal DNA transcription system
    Olivier Gadal
    Laboratoire de Physio Génomique, Service de Biochimie et Génétique Moléculaire, CEA Saclay, Batiment 142, F 91191 Gif sur Yvette, France
    EMBO J 21:5498-507. 2002
    ..Conversely, rpa34-Delta mutants lacking Rpa34, a non-essential subunit associated with Rpa49, are lethal in top1-Delta but not in top3-Delta...
  53. pmc Chromosomal addresses of the cohesin component Mcd1p
    S Laloraya
    Howard Hughes Medical Institute, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
    J Cell Biol 151:1047-56. 2000
    ..Thus, the periodicity of CARs in single-copy regions and the rDNA repeats is conserved. The presence and spacing of CARs in repetitive DNA has important implications for genomic stability and chromosome packaging/condensation...
  54. pmc The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork
    Takehiko Kobayashi
    National Institute for Basic Biology, 38 Nishigonaka, Myodaijicho, Okazaki 444 8585, Japan
    Mol Cell Biol 23:9178-88. 2003
    ..The gene FOB1 is required for this RFB activity. FOB1 is also necessary for recombination in the ribosomal DNA (rDNA), including increase and decrease of rDNA repeat copy number, production of extrachromosomal rDNA ..
  55. ncbi Molecular phylogenetics of tsetse flies (Diptera: Glossinidae) based on mitochondrial (COI, 16S, ND2) and nuclear ribosomal DNA sequences, with an emphasis on the palpalis group
    N A Dyer
    Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, Merseyside, L3 5QA, UK
    Mol Phylogenet Evol 49:227-39. 2008
    ..A diagnostic PCR to distinguish G. palpalis palpalis, G. tachinoides and G. palpalis gambiensis based on length differences of internal transcribed spacer 1 sequences is presented...
  56. pmc Phylogenetic and ecological analysis of novel marine stramenopiles
    Ramon Massana
    Department de Biologia Marina i Oceanografia, Institut de Ciencies del Mar, CMIMA, CSIC, 08003 Barcelona, Catalonia, Spain
    Appl Environ Microbiol 70:3528-34. 2004
    ..Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, ..
  57. pmc swi1- and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombe
    Gregor Krings
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
    Proc Natl Acad Sci U S A 101:14085-90. 2004
    ..The results support the notion that Swi1p and Swi3p act at several different protein-DNA complexes in the rDNA spacer regions to arrest replication but that not all fork barriers required their activity to arrest forks...
  58. pmc Strain-dependent variation in 18S ribosomal DNA Copy numbers in Aspergillus fumigatus
    M L Herrera
    Department of Microbiology and Immunology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 3900, USA
    J Clin Microbiol 47:1325-32. 2009
    ..This study was undertaken to determine if ribosomal DNA (rDNA) copy number was constant or variable among different A. fumigatus isolates...
  59. ncbi Phylogeography of western Pacific Leucetta 'chagosensis' (Porifera: Calcarea) from ribosomal DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritage Area (Australia)
    Gert Worheide
    Queensland Centre for Biodiversity, Queensland Museum, PO Box 3300, South Brisbane, QLD 4101, Australia
    Mol Ecol 11:1753-68. 2002
    ..In this study we explore relationships among 19 ribosomal DNA sequence types (the ITS1-5...
  60. ncbi Inferences about orthopteroid phylogeny and molecular evolution from small subunit nuclear ribosomal DNA sequences
    P K Flook
    Zoology Department, University of Basel, Switzerland
    Insect Mol Biol 7:163-78. 1998
    ..Similar observations have been made in holometabolous insects, suggesting that variation in substitution rate is a general feature of insect nuclear rRNA evolution...
  61. ncbi Molecular epidemiological investigation of Ascaris genotypes in China based on single-strand conformation polymorphism analysis of ribosomal DNA
    Weidong Peng
    Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
    Electrophoresis 24:2308-15. 2003
    ..we investigated nucleotide variation in part of the first internal transcribed spacer (pITS-1) of nuclear ribosomal DNA within and among a large number of Ascaris individuals from humans and pigs from six endemic regions in China, ..
  62. ncbi Vertical evolution and intragenic spread of lichen-fungal group I introns
    Debashish Bhattacharya
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, 239 Biology Building, Iowa City, IA 52242 1324, USA
    J Mol Evol 55:74-84. 2002
    ..Detailed phylogenetic analyses of the introns and host cells are required, therefore, to distinguish this scenario from the alternative hypothesis of widespread and independent intron gains in the different lichen-fungal lineages...
  63. pmc Rickettsial relative associated with male killing in the ladybird beetle (Adalia bipunctata)
    J H Werren
    Department of Biology, University of Rochester, New York 14627
    J Bacteriol 176:388-94. 1994
    ..Discovery of a close relative of rickettsias associated with sex ratio distortion in insects has implications for the evolution and population dynamics of this bacterial genus...
  64. pmc Clustering of dispersed ribosomal DNA and its role in gene regulation and chromosome-end associations in malaria parasites
    Liliana Mancio-Silva
    Département de Parasitologie et Mycologie, Unité de Biologie des Interactions Hôte Parasite, Institut Pasteur, 25 rue du Docteur Roux, F 75724 Paris Cedex 15, France
    Proc Natl Acad Sci U S A 107:15117-22. 2010
    ..Taken together, our results provide conceptual insights into functionally differentiated nuclear territories and their role in gene expression in malaria parasites...
  65. ncbi Mrc1 and Tof1 promote replication fork progression and recovery independently of Rad53
    Hélène Tourrière
    Institute of Human Genetics, Centre National de la Recherche Scientifique, UPR 1142, 34396 Montpellier Cedex 5, France
    Mol Cell 19:699-706. 2005
    ..The critical role of Mrc1p in HU is therefore to promote fork recovery in a Rad53p-independent manner, presumably through the formation of a stable fork-pausing complex...
  66. ncbi In vitro propagation of the microsporidian pathogen Brachiola algerae and studies of its chromosome and ribosomal DNA organization in the context of the complete genome sequencing project
    Abdel Belkorchia
    Laboratoire de Biologie des Protistes, UMR CNRS 6023, Universite Blaise Pascal, 24 avenue des Landais, Campus des Cézeaux, 63177 Aubiere Cedex, France
    Parasitol Int 57:62-71. 2008
    ..The data obtained indicate that B. algerae should be an excellent parasitic model to understand genome evolution in relation to infectious capacity...
  67. pmc Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria
    Nathaniel M Evans
    Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
    BMC Evol Biol 8:139. 2008
    ....
  68. pmc The human papillomavirus type 8 E2 tethering protein targets the ribosomal DNA loci of host mitotic chromosomes
    Atasi Poddar
    Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
    J Virol 83:640-50. 2009
    ..Furthermore, the E2 protein interacts with the repeated ribosomal DNA genes found in this location and colocalizes with UBF, the RNA polymerase I transcription factor...
  69. pmc Molecular phylogeny of choanoflagellates, the sister group to Metazoa
    M Carr
    Department of Biology, University of York, Heslington, York, YO10 5YW, United Kingdom
    Proc Natl Acad Sci U S A 105:16641-6. 2008
    ..Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor...
  70. ncbi Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments
    G Muyzer
    Molecular Ecology Unit, Max Planck Institute for Marine Microbiology, Fahrenheitstrasse 1, D 28359 Bremen, Germany
    Arch Microbiol 164:165-72. 1995
    ..The third 'phylotype' was identified as a Desulfovibrio, indicating that sulfate-reducing bacteria, as sources of sulfide, may complement sulfur- and sulfide-oxidizing bacteria ecologically in these sulfide-producing hydrothermal vents...
  71. ncbi Molecular characterization of ribosomal DNA polymorphisms discriminating among chromosomal forms of Anopheles gambiae s.s
    G Favia
    Istituto di Parassitologia, Fondazione Cenci Bolognetti, Universita di Roma La Sapienza, Piazzale Aldo Moro 5, 00185, Rome, Italy
    Insect Mol Biol 10:19-23. 2001
    ..The assay also allows to distinguish whether a given specimen could represent a heterozygote between Mopti and Savanna or Bamako...
  72. pmc Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms
    D Harmsen
    Institute of Hygiene and Microbiology, University of Wurzburg, Josef Schneider Str 2, Bau 17, 97080 Wurzburg, Germany
    J Clin Microbiol 39:936-42. 2001
    ..16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates...
  73. ncbi Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches
    Ramon Massana
    Departament de Biologia Marina i Oceanografia, Institut de Ciencies del Mar, CMIMA, CSIC, Passeig Marítim de la Barceloneta 37 49, Barcelona, Catalonia, Spain
    FEMS Microbiol Ecol 50:231-43. 2004
    ..These results will aid to focus future research, most likely based on new and imaginative culturing efforts and the design and application of specific molecular probes...
  74. pmc Environmental rRNA inventories miss over half of protistan diversity
    Sunok Jeon
    Department of Environmental Science, Kangwon National University, Kangwon Do, Korea
    BMC Microbiol 8:222. 2008
    ..Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers...
  75. pmc The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copies
    Andréia B Poletto
    UNESP Universidade Estadual Paulista, Instituto de Biociencias, Departamento de Morfologia, Botucatu, SP, Brazil
    BMC Genet 11:1. 2010
    ..Despite being widely distributed among different taxa, the genomic nature and genetic behavior of B chromosomes are still poorly understood...
  76. ncbi How to get more out of molecular fingerprints: practical tools for microbial ecology
    Massimo Marzorati
    Laboratory for Microbial Ecology and Technology LabMET, Gent University, B9000 Gent, Belgium
    Environ Microbiol 10:1571-81. 2008
    ..These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern...
  77. pmc Role of recombination in the long-term retention of transposable elements in rRNA gene loci
    Xian Zhang
    Department of Biology, University of Rochester, Rochester, New York 14627 0211, USA
    Genetics 180:1617-26. 2008
    ..These simulations suggest that the rDNA locus serves as an ideal niche for the long-term survival of transposable elements...
  78. ncbi Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results
    Marcin Górniak
    Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, Gdansk University, Al Legionów 9, 80 441 Gdańsk, Poland
    Mol Phylogenet Evol 56:784-95. 2010
    ..is congruent with those published previously based on plastid protein-coding genes and non-coding nuclear ribosomal DNA. The five subfamilies previously recognized are monophyletic and well supported...
  79. pmc Role for perinuclear chromosome tethering in maintenance of genome stability
    Karim Mekhail
    Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 456:667-70. 2008
    ..is the observation, in the budding yeast Saccharomyces cerevisiae, that stability of the highly repetitive ribosomal DNA (rDNA) sequences requires a Sir2-containing chromatin silencing complex that also inhibits transcription from ..
  80. pmc Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules
    Katharina Merz
    Universitaet Regensburg, Institut fur Biochemie, Genetik und Mikrobiologie, 93053 Regensburg, Germany
    Genes Dev 22:1190-204. 2008
    Synthesis of ribosomal RNAs (rRNAs) is the major transcriptional event in proliferating cells. In eukaryotes, ribosomal DNA (rDNA) is transcribed by RNA polymerase I from a multicopy locus coexisting in at least two different chromatin ..
  81. ncbi The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencing
    Mouhamad Al Masalma
    Pôle des Maladies Infectieuses, Assistance Publique Hôpitaux de Marseille and URMITE, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 6236, Institut pour la Recherche et le Développement 198, Universite de la Mediterranee, France
    Clin Infect Dis 48:1169-78. 2009
    ..Methods. We prospectively compared cultures to single and multiple sequenced 16S ribosomal DNA polymerase chain reaction amplifications (by cloning and/or pyrosequencing) of cerebral abscesses in 20 ..
  82. ncbi Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates
    Daniel J Thornhill
    Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, Alabama 36849, USA
    Mol Ecol 16:5326-40. 2007
    ..These considerations must be taken into account when interpreting sequence data generated by bacterial cloning of multicopy genes such as rDNA...
  83. pmc Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes
    Jeremy A Frank
    Department of Microbiology, University of Illinois at Urbana Champaign, B103 C and LSL, 601 South Goodwin Ave, Urbana, IL 61801, USA
    Appl Environ Microbiol 74:2461-70. 2008
    ..particularly under stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity...
  84. pmc Transcription-dependent recombination and the role of fork collision in yeast rDNA
    Yasushi Takeuchi
    National Institute for Basic Biology, Myodaijicho, Okazaki 444 8585, Japan
    Genes Dev 17:1497-506. 2003
    ..These results suggest that such a transcription-dependent fork collision induces recombination, and may function as a general recombination trigger for multiplication of highly transcribed single-copy genes...
  85. ncbi Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae)
    Marcus A Koch
    Institute of Botany, University of Agricultural Sciences Vienna, Vienna, Austria
    Mol Biol Evol 20:338-50. 2003
    DNA sequence variation of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA from Arabis holboellii, A. drummondii, and its putative hybrid A...
  86. pmc Condensin function at centromere chromatin facilitates proper kinetochore tension and ensures correct mitotic segregation of sister chromatids
    Vladimir Yong-Gonzalez
    NIH, NICHD, LGRD, Bethesda, Maryland, USA
    Genes Cells 12:1075-90. 2007
    ..These findings show that, in addition to its essential role in rDNA segregation, condensin mediates segregation of the whole genome by maintaining the centromere structure in Saccharomyces cerevisiae...
  87. pmc Specific detection and prevalence of Helicobacter heilmannii-like organisms in the human gastric mucosa by fluorescent in situ hybridization and partial 16S ribosomal DNA sequencing
    K Trebesius
    Max von Pettenkofer Institute for Hygiene and Medical Microbiology, Ludwig Maximilians University, Munich, Germany
    J Clin Microbiol 39:1510-6. 2001
    ..2% (1 of 84) of the monoinfected samples, respectively. Additionally, HHLO type 5 with a 16S ribosomal DNA sequence identical to that of Helicobacter salomonis was found with a prevalence of 2.4% (2 of 89)...
  88. ncbi Unveiling new microbial eukaryotes in the surface ocean
    Ramon Massana
    Department of Marine Biology and Oceanography, Institut de Ciencies del Mar, CSIC, Passeig Marítim de la Barceloneta 37 49, 08003 Barcelona, Catalonia, Spain
    Curr Opin Microbiol 11:213-8. 2008
    ..The implication of this large and novel eukaryotic diversity for biodiversity surveys and ecosystem functioning opens new avenues for future research...
  89. pmc 16S ribosomal DNA-based analysis of bacterial diversity in purified water used in pharmaceutical manufacturing processes by PCR and denaturing gradient gel electrophoresis
    Mako Kawai
    Quality Assurance Division, Biological Quality Assurance Section, Dainippon Pharmaceutical Co Ltd, Osaka 553 0001, Japan
    Appl Environ Microbiol 68:699-704. 2002
    ..16S ribosomal DNA fragments, including V6, -7, and -8 regions, were amplified with universal primers and analyzed by DGGE...
  90. pmc Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
    P Seksik
    INRA, CR de Jouy en Josas, 78352 Jouy en Josas, France
    Gut 52:237-42. 2003
    ..We investigated potential differences in the faecal microflora between patients with colonic CD in remission (n=9), patients with active colonic CD (n=8), and healthy volunteers (n=16) using culture independent techniques...
  91. ncbi The evolution of homing endonuclease genes and group I introns in nuclear rDNA
    Peik Haugen
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, USA
    Mol Biol Evol 21:129-40. 2004
    ..The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns...
  92. pmc Prospective study of use of PCR amplification and sequencing of 16S ribosomal DNA from cerebrospinal fluid for diagnosis of bacterial meningitis in a clinical setting
    Tim Schuurman
    Department of Research and Development, Regional Public Health Laboratory for Groningen and Drenthe, Groningen, The Netherlands
    J Clin Microbiol 42:734-40. 2004
    ..adapting the standard procedures in our laboratory for detecting bacterial meningitis; broad-range 16S ribosomal DNA PCR detection is indicated when antimicrobial therapy has already started at time of lumbar puncture or when ..
  93. ncbi In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis
    S Johansen
    Department of Molecular Cell Biology, Institute of Medical Biology, University of Tromsø, Norway
    Mol Microbiol 24:737-45. 1997
    DiSSU1 is an optional group I twintron present in the nuclear extrachromosomal ribosomal DNA of the myxomycete Didymium iridis. DiSSU1 appears to be complex both in structure and function...
  94. pmc The Treacher Collins syndrome (TCOF1) gene product is involved in ribosomal DNA gene transcription by interacting with upstream binding factor
    Benigno C Valdez
    Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 101:10709-14. 2004
    ..Here, we show that treacle is involved in ribosomal DNA gene transcription by interacting with upstream binding factor (UBF)...
  95. ncbi Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi
    D S Hibbett
    Harvard University Herbaria, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Mol Biol Evol 13:903-17. 1996
    Group I introns were discovered inserted at the same position in the nuclear small-subunit ribosomal DNA (nuc-ssu-rDNA) in several species of homobasidiomycetes (mushroom-forming fungi)...
  96. pmc Bacterial biota in the human distal esophagus
    Zhiheng Pei
    Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
    Proc Natl Acad Sci U S A 101:4250-5. 2004
    ..These findings provide evidence for a complex but conserved bacterial population in the normal distal esophagus...
  97. pmc Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expression
    Roman Matyasek
    Institute of Biophysics, Academy of Sciences of the Czech Republic, v v i Laboratory of Molecular Epigenetics, Kralovopolska 135, CZ 612 65 Brno, Czech Republic
    Genetics 176:2509-19. 2007
    We analyzed nuclear ribosomal DNA (rDNA) transcription and chromatin condensation in individuals from several populations of Tragopogon mirus and T...
  98. ncbi The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae
    Laura N Rusche
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720 3202, USA
    Annu Rev Biochem 72:481-516. 2003
    ..We also describe emerging evidence that mutations that cause global changes in the modification of histones can alter the balance between euchromatin and silenced chromatin within a cell...
  99. ncbi Genomic organization and evolution of the 5S ribosomal DNA in the ancient fish sturgeon
    Francisca Robles
    Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
    Genome 48:18-28. 2005
    b>Ribosomal DNA in sturgeon is informative when analyzed at the molecular level because it bears unique characteristics that are, to a certain extent, ancestral within vertebrates...
  100. ncbi Silencing in yeast rDNA chromatin: reciprocal relationship in gene expression between RNA polymerase I and II
    Francesco Cioci
    Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
    Mol Cell 12:135-45. 2003
    ..Together with the demonstration of a requirement for active Pol I in silencing, these results show a reciprocal relationship in gene expression between Pol I and Pol II in rDNA...
  101. ncbi The role of UBF in regulating the structure and dynamics of transcriptionally active rDNA chromatin
    Elaine Sanij
    Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
    Epigenetics 4:374-82. 2009
    ..In particular we discuss evidence to suggest that UBF dynamically regulates the active rRNA gene pool during differentiation and malignancy...

Research Grants67

  1. The role of novel, uncultivable bacteria in incident PID
    CATHERINE L contact HAGGERTY; Fiscal Year: 2011
    ..abstract_text> ..
  2. Role of Coxiella burnetii group I introns in growth modulation
    Michael F Minnick; Fiscal Year: 2010
    ..burnetii's molecular biology, interruption of these genetic elements and events will provide novel targets and strategies for therapeutic intervention of Q fever. ..
  3. 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 (1 3)-?-D-glucan (a polysaccharide in ..
  4. Regulation of Host Nitrogen Balance by the Gut Microbiome
    Gary D Wu; Fiscal Year: 2012
    ....
  5. Functional Consequence of Macrolide Resistance Mutations in T. pallidum
    Sheila A Lukehart; Fiscal Year: 2012
    ..If these mutations are found to be common and are shown to cause treatment failure, physicians will be advised not to use azithromycin for treating patients with syphilis. ..
  6. The Intestinal Microbiome in Pediatric NAFLD
    Nita H Salzman; Fiscal Year: 2010
    ..abstract_text> ..
  7. Role of chromatin structure in regulating gene silencing
    Mary Bryk; Fiscal Year: 2009
    ..and silencing proteins, in regulating the silencing of RNA polymerase II-transcribed genes located in the ribosomal DNA locus (rDNA) of the budding yeast Saccharomyces cerevisiae...
  8. Genetic Analysis of MSM Protein Function in S. Pombe
    Susan L Forsburg; Fiscal Year: 2012
    ..Complementing the genomics studies, this aim concludes with the hypothesis that the ribosomal DNA may be particularly sensitive to mcm induced fork collapse, and investigates whether can be used as a model ..
  9. Regulation of repetitive chromatin structures during the human cell cycle
    Paul D Kaufman; Fiscal Year: 2013
    ..Together, these studies will provide candidate direct targets of p150 regulation, and lead us to test dependency relationships for these observations. ..
  10. Peripheral blood dendritic cells and periodontitis
    CHRISTOPHER WILLIAM CUTLER; Fiscal Year: 2012
    ..We propose to ultimately develop immunotherapeutic strategies for the prevention of pathogen trafficking DCs in patients at high risk for developing coronary artery disease. ..
  11. Intestinal bacterial metagenome in pediatric NAFLD
    Nita H Salzman; Fiscal Year: 2013
    ....
  12. Treatment of Distal Tyrosine Pathway Disorders
    Markus Grompe; Fiscal Year: 2012
    ..In addition, we developed a novel AAV vector designed to integrate cDNA expression cassettes into the ribosomal DNA rDNA) locus by homologous recombination...
  13. RNAi and DNA Methylation Control Genomic Stability and Transcriptional Silencing
    JOHN KIMBLE FRAZER; Fiscal Year: 2010
    ..Employing this system, we will define the mechanism by which RNAi ensures genomic integrity within the ribosomal DNA (rDNA) and telomeric loci, both composed of repeats...
  14. Structural Studies of epigenetic regulation of rRNA gene by TTF-I
    Carlos R Escalante; Fiscal Year: 2013
    ..This work will be in close collaboration with Dr. Montserrat Samso that will provide expertise in single-particle reconstruction EM and Dr. Deepak Bastia that will provide technical help in the biochemical assays. ..
  15. Microbiomes and Inflammation in Chronic Fatigue Syndrome
    RUTH EMILY LEY; Fiscal Year: 2013
    ..Because characterization of the human microbiota is just beginning, our analyses will also make a valuable contribution to knowledge about the diversity of microbes associated with CFS. ..
  16. Mapping and Functional Analysis of RNA:DNA Hybrid-Forming Loci
    John Greally; Fiscal Year: 2013
    ..If this exploratory project is successful, we will have a clear idea how to expand the study to a more comprehensive project in the future. PHS 398/2590 (Rev. 11/07) Continuation Format Page ..
  17. Alterations in the human gut microbiome associated with travelers'diarrhea
    BONNIE PATRICIA YOUMANS; Fiscal Year: 2013
    ..This proposal outlines the necessary first steps in understanding how TD affects the gut microbiome. Results from my research could potentially lead to development of preventative treatments and novel therapeutics against TD. ) ..
  18. REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNA
    Geoffrey M Kapler; Fiscal Year: 2010
    ..Our model organism, Tetrahymena thermophila, harbors a 21 kb ribosomal DNA (rDNA) minichromosome that is amplified 9,000-fold during development, but is replicated once per cell cycle ..
  19. Retrotransposon expression within ribosomal gene loci
    Thomas H Eickbush; Fiscal Year: 2013
    ..This research also studies the regulated expression of the many ribosomal RNA genes, genes that play a key role in all aspects of cellular metabolism. ..
  20. Moving Beyond Diversity by Revealing Biological Functions of Uncultured Bacteria
    JEFFREY SCOTT MCLEAN; Fiscal Year: 2013
    ..This new approach will provide a deeper understanding of disease progression and allow for the subsequent development of novel therapeutic approaches to battle these diseases. ..
  21. Regulation of rRNA Genes by Silencing Mechanisms
    Danesh Moazed; Fiscal Year: 2010
    ....
  22. Control of meiotic double strand break formation
    Andreas Hochwagen; Fiscal Year: 2013
    ..to delayed DNA replication, (ii) DSBs are constitutively suppressed in the vicinity of the highly repetitive ribosomal DNA (rDNA)...
  23. The role of deregulated protein synthesis control in Myc-induced tumorigenesis
    Davide Ruggero; Fiscal Year: 2013
    ..Finally, in Aim 3 we will define the role of Myc-induced cell competition in cancer development. ..
  24. China's Integrated Programs for Research on AIDS
    Yiming Shao; Fiscal Year: 2009
    ..Project 5 will construct three classes of HIV-1 vaccine candidates based the NTV, Gdalt and rDNA vectors using HIV-1 antigens of Chinese origin will fully support the implementation of five projects. ..
  25. Genomic Tools For Studying The Ecology Of The Human Vaginal Microflora
    Jacques Ravel; Fiscal Year: 2010
    ..Similarly, these tools will be critical for the study and evaluation of women's health. ..
  26. Pathogenesis of Obstruction/Emphysema and the Microbiome (POEM) in HIV
    Alison Morris; Fiscal Year: 2013
    ..This information will help us understand and treat emphysema in these patients and in the many non-HIV-infected people who suffer from emphysema. ..
  27. Functional Sir2-RNA Interactions
    JEFFREY SCOTT SMITH; Fiscal Year: 2013
    ..These exploratory and developmental studies will define the basic mechanism and specificity of the functional Sir2-RNA interaction and set us up for more detailed functional and structure-function studies in the future. ..
  28. Hepatic Gene Transfer for Treatment of Hemophilias A &B
    Mark A Kay; Fiscal Year: 2013
    ..We plan to pursue a new strategy for obtaining AAV-mediated integration of the factor IX mini-gene into the ribosomal DNA locus, a benign but yet robust site for AAV- mediated transgene expression...
  29. Microbial Translocation and HIV-Related Endothelial Dysfunction
    MICHAEL PHILIP DUBE; Fiscal Year: 2010
    ..Using saved frozen specimens, levels of circulating LPS, soluble CD14, and bacterial 16S ribosomal DNA (16S rDNA) will be measured...
  30. Epigenetic regulation by TOR signaling
    RONALD LARIBEE; Fiscal Year: 2012
    ..delineate how TOR signaling regulates a histone chaperone complex to control RNA polymerase I transcription of ribosomal DNA. Aim II will use a chemical genomics-based approach to find TOR-regulated epigenetic pathways by screening a ..
  31. Helicobacter pylori and the gastric microbial community in rhesus macaques
    Jay V Solnick; Fiscal Year: 2010
    ..We hypothesize that this antimicrobial response alters the gastric microbial community and increases the competitive advantage of H. pylori in the gastric niche. ..
  32. A NOVEL, LOGICAL APPROACH TO HIV VACCINE DEVELOPMENT
    David I Watkins; Fiscal Year: 2011
    ..These experiments will allow us to determine whether rYF-17D has the potential to be advanced into human clinical trials as a prime for a recombinant viral boost. ..
  33. Metagenomic Study of the Periodontal Microbiome in Healthy and Diabetic Subjects
    Huiying Li; Fiscal Year: 2013
    ..The findings will address a fundamental gap in our understanding of the etiological agents of periodontitis and may lead to innovative strategies for diagnosing, preventing and managing periodontitis. ..
  34. Metagenomic study of the human skin microbiome associated with acne
    Huiying Li; Fiscal Year: 2010
    ..Success in this project may lead to the development of new effective therapeutic strategies for treatment of acne. ..
  35. Coinfection of Tick-borne Diseases in Areas of Wisconsin
    DIANE CAPORALE; Fiscal Year: 2001
    ..If this strain is prevalent in this state, vaccine developers should investigate the efficacy of their vaccine on this strain. ..
  36. iPSC Derived EC as Surrogates Using Pulmonary Hypertension as a Prototype Disease
    Joseph C Wu; Fiscal Year: 2013
    ..In Phase III, Aim 1 utilizes cutting edge gene therapy approaches, such as minicircles and ribosomal DNA vectors, to correct a gene variant in an iPSC-EC...
  37. MECHANISM OF TERMINATION OF DNA REPLICATION
    Deepak Bastia; Fiscal Year: 2010
    ..Finally, we wish to uncover the mode of action of the Swi1 and Swi3 proteins to determine if these act as "antisweepases". ..
  38. Mosquito larval immunity and its impact on gut microbiota and malaria competence
    Jiannong Xu; Fiscal Year: 2013
    ..This pilot project will generate data towards comprehensive understanding the tripartite ecological interactions among malaria, gut microbiota and host immunity and its impact on vectorial capacity. ..
  39. Control of RNA polymerase I transcription initiation and elongation
    DAVID ALAN SCHNEIDER; Fiscal Year: 2013
    ..identified for their roles in RNA polymerase II transcription and have been shown recently to bind the ribosomal DNA in vivo...
  40. Environmental Uncultivable Bacteria Model for Understanding Human Periodontitis
    CLEBER COSTA OUVERNEY; Fiscal Year: 2013
    ..an environmental source for a TM7 bacterium with >99% identity to a human-associated oral TM7, based on 16S ribosomal DNA gene (16S rDNA) sequence analysis (Dinis et al. 2011)...
  41. Mechanistic insights into the SHU complex and Sgs1 in DNA repair and replication
    Kara A Bernstein; Fiscal Year: 2010
    ..Functional analysis of proteins required for DNA repair is crucial for understanding the molecular basis of tumorigenesis. ..
  42. Mechanistic insights into the SHU complex and Sgs1 in DNA repair and replication
    Kara A Bernstein; Fiscal Year: 2013
    ..abstract_text> ..
  43. Population dynamics of P. acnes and their phages in the human skin microbiome
    Huiying Li; Fiscal Year: 2013
    ..The findings from the study will address a fundamental gap in our knowledge of the skin microbiome and may lead to further studies for the development of innovative clinical approaches to treating, preventing and managing the disease. ..
  44. Basonuclin and Ribosome Biogenesis in Mouse Oocyte and Embryo
    Richard M Schultz; Fiscal Year: 2010
    ..Such information may ultimately translate to improving the practice of Assisted Reproductive Technology (ART). ..
  45. REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNA
    Geoffrey Kapler; Fiscal Year: 2000
    ..By understanding the relationship of gene amplification to cell cycle-regulated replication in Tetrahymena, mechanisms that control these processes in higher eukaryotes may become clear. ..
  46. DNA Probes for Acanthamoeba Genomics and Epidemiology
    Paul Fuerst; Fiscal Year: 2007
    ..Preliminary results show that this region can be amplified in disparate genotypes. Further, these results may provide potential targets for future treatment, since products of these genes may be antibiotic targets. ..
  47. PROTEIN BINDING DOMAINS ON EUKARYOTIC 5S RRNA AND RDNA
    Paul Huber; Fiscal Year: 2000
    ..A similar analysis of the complex of ribosomal protein L5 with 5S rRNA will be undertaken. This affords the opportunity to examine the binding of two proteins, that exhibit no sequence identity, to congruent sites on an RNA molecule. ..
  48. Yellow Fever, rDNA (EP+IL-12) and rAd35 as Vectors for AIDS Vaccine Development
    David I Watkins; Fiscal Year: 2013
    ..Second, we will develop three entirely novel vaccine vectors. If we are successful in this endeavor, our results will have a profound effect on HIV vaccine design. ..
  49. Development of Paratransgenic ticks for Disease Control
    Ulrike Munderloh; Fiscal Year: 2001
    ..Finally, we will work towards 3. stable transformation of A. peacockii with cecropina will then test the transformants for antimicrobial activity in vitro and in ticks, and by sequence analysis. ..
  50. Murine Typhus: Vector Biology & Transmission
    Abdu Azad; Fiscal Year: 2007
    ..typhi and ELB upon challenge with[unreadable] the heterologous rickettsiae and involvement of 120 kDa in the protection.[unreadable] [unreadable]..
  51. WHIPPLE BACILLUS AND THE ETIOLOGY OF SARCOIDOSIS
    David Fredricks; Fiscal Year: 1999
    ..causative agent of Whipple's disease and its phylogenetic relationships, as revealed by small subunit or 16S ribosomal DNA (rDNA) sequence analysis...
  52. Vascular Tissue Invasion by Porphyromonas gingivalis
    Ling Li; Fiscal Year: 2005
    ..The completion of this study will contribute to the long-term goal of understanding this bacterially induced vascular inflammation and identification of new therapeutic targets. ..
  53. RADIATION INDUCED CHROMATIN CHANGES IN A DEFINED ORIGIN
    James Larner; Fiscal Year: 2001
    ..Since loss of this pathway in Ataxia Telangiectasia renders cells exquisitely sensitive to ionizing radiation, we hope to develop novel radiation sensitization strategies by manipulation of the pathway. ..
  54. DNA TOPOISOMERASES--BIOLOGICAL FUNCTIONS AND MECHANISMS
    James Wang; Fiscal Year: 1999
    ..Experiments will also be carried out to test further the dispensability of DNA topoisomerases in the initiation of replication in eukaryotes. ..
  55. HUMAN GENOME ANALYSIS WITH YAC CLONES
    David Schlessinger; Fiscal Year: 1990
    ....
  56. The Molecular Microbiology of Bacterial Vaginosis
    David Fredricks; Fiscal Year: 2003
    ..In future studies, vaginal fluid samples from a larger cohort of women will be assayed to determine if a candidate pathogen is specifically associated with BV. ..
  57. ULTRASTRUCTURAL STUDIES OF GENETIC ACTIVITY
    Oscar Miller; Fiscal Year: 1992
    ..Together, these studies should provide significant new insights into the regulation of genetic activity at the level of individual genes and the physical interactions between the processes of transcription and genome replication...
  58. Ribosome Biogenesis: A Molecular Checkpoint for Cardiac Hypertrophy
    Lawrence Rothblum; Fiscal Year: 2009
    ..The results of these experiments will increase our understanding of the signal transduction pathway(s) that lead to the process of cardiac hypertrophy. ..
  59. Urological Studies of Ideopathic Lower Tract Syndrome
    JOHN KRIEGER; Fiscal Year: 2005
    ..These studies will determine if EPS or SFA can be used to identify prostatic bacteria and may result in clinical methods for non-invasive diagnosis of prostatic infection. ..
  60. Regulation of rRNA transcription in Entamoeba histolyti*
    William Petri; Fiscal Year: 2003
    ..histolytica vectors. In addition it is envisaged that knowledge about the protein factors that regulate rDNA transcription may provide novel drug targets to interfere with this essential process. ..
  61. NORMAL AND MUTANT CHORION GENES OF DROSOPHILA
    Allan Spradling; Fiscal Year: 2003
    ..Therefore, these studies will elucidate the structure and function of eukaryotic chromosomes, a subject of widespread importance to the genetics of all organisms, including humans. ..
  62. PROTEIN BINDING DOMAINS--EUKARYOTIC FIVE-S RRNA & RDNA
    Paul Huber; Fiscal Year: 1991
    ..The unique properties of TFIIIA allow us to make certain invaluable comparisons: between the structures of two nucleic acids that are recognized by this protein, and between two proteins that recognize the same binding site on 5S rRNA...
  63. CHRONIC PROSTATITIS CLINICAL RESEARCH CENTER
    Michel Pontari; Fiscal Year: 1999
    ....
  64. SPECIFIC TARGETING AND TRANSCRIPTION OF METAZOAN RDNA
    Barbara Sollner Webb; Fiscal Year: 2000
    ..Through these studies we hope to get a better understanding about the action of transcriptional enhancers and about the interactions that serve to differentiate and organize the different domains of the eukaryotic nucleus. ..
  65. REGULATION AS A BASIS FOR ORGANISMAL DIFFERENCES
    JACK KIRSCH; Fiscal Year: 1993
    ..Two model systems are proposed that meet these requirements, namely the lysozyme and ribosomal DNA systems...
  66. MOLECULAR GENETICS OF A CELL-CELL RECOGNITION SYSTEM
    Eduardo Orias; Fiscal Year: 1990
    ....
  67. REGULATION AS A BASIS FOR ORGANISMAL DIFFERENCES
    Allan Wilson; Fiscal Year: 1991
    ..Two model systems are proposed that meet these requirements, namely the lysozyme and ribosomal DNA systems...