Genomes and Genes
Summary: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Publications375 found, 100 shown here
- Diversity of the human intestinal microbial floraPaul 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...
- Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studiesYong 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. 2009Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches...
- The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanismsM 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...
- SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeastTakehiko 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...
- Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequencesC 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 ..
- Recombination regulation by transcription-induced cohesin dissociation in rDNA repeatsTakehiko 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...
- The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphologyM 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...
- Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludgeJ 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...
- Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNAJ 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...
- 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....
- Microbial population structures in the deep marine biosphereJulie A Huber
Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
Science 318:97-100. 2007....
- Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1Kevin 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...
- Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisitedThomas D Leser
Department of Microbiology, Danish Veterinary Laboratory, Bulowsvej 27, DK 1790 Copenhagen V, Denmark
Appl Environ Microbiol 68:673-90. 2002The phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16S ribosomal DNA (rDNA) sequence analysis...
- Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencingB 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 ..
- c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase ICarla 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...
- Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiaeS 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...
- UBF binding in vivo is not restricted to regulatory sequences within the vertebrate ribosomal DNA repeatAudrey 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...
- Mammalian Sir2 homolog SIRT7 is an activator of RNA polymerase I transcriptionEthan 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...
- Molecular phylogeny and evolutionary relationships among mosquitoes (Diptera: Culicidae) from the northeastern United States based on small subunit ribosomal DNA (18S rDNA) sequencesJohn 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...
- Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNAHans G H J Heilig
Laboratory of Microbiology, Wageningen University, 6703 CT Wageningen, The Netherlands
Appl Environ Microbiol 68:114-23. 2002A 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, ..
- Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture modelsAllen 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.]...
- A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNAS 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...
- Dicer is associated with ribosomal DNA chromatin in mammalian cellsLasse 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...
- The natural history of group I intronsPeik 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....
- Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence dataAusten 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...
- Activation of RNA polymerase I transcription by cockayne syndrome group B protein and histone methyltransferase G9aXuejun 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...
- The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locusJordi 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...
- Distribution and abundance of uncultured heterotrophic flagellates in the world oceansRamon 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...
- Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacerI L Gonzalez
Department of Pathology, Hahnemann University, Philadelphia, Pennsylvania 19102, USA
Genomics 27:320-8. 1995We 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...
- c-Myc associates with ribosomal DNA and activates RNA polymerase I transcriptionAzadeh 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 ..
- Intergenic transcripts regulate the epigenetic state of rRNA genesChristine 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...
- Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA geneC 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...
- Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancerJulie Huang
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Genes Dev 20:2887-901. 2006Silencing within the yeast ribosomal DNA (rDNA) repeats protects the integrity of this highly repetitive array by inhibiting hyperrecombination and repressing transcription from foreign promoters...
- Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprintingK Watanabe
Marine Biotechnology Institute, Kamaishi Laboratories, 3 75 1 Heita, Iwate 026 0001, Kamaishi City, Japan
J Microbiol Methods 44:253-62. 2001Denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA (rDNA) fragments has frequently been applied to the fingerprinting of natural bacterial populations (PCR/DGGE)...
- Ribosomal DNA contributes to global chromatin regulationSilvana 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...
- The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysisJ 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 firstname.lastname@example.org...
- The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNAA S Ivessa
Department of Molecular Biology, Princeton University, New Jersey 08544 1014, USA
Cell 100:479-89. 2000Replication 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)...
- The multifunctional nucleolusFrancois 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...
- Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycleA 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...
- 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFMC W Kaplan
Environmental Biotechnology Institute, California Polytechnic State University, San Luis Obispo, CA 93407, USA
Appl Environ Microbiol 67:1935-9. 200116S 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...
- Optimization of real-time PCR assay for rapid and sensitive detection of eubacterial 16S ribosomal DNA in platelet concentratesTamimount Mohammadi
Sanquin Blood Bank North West Region, Amsterdam, The Netherlands
J Clin Microbiol 41:4796-8. 2003A 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...
- Comparison of 16S ribosomal DNA sequences of all Xanthomonas speciesL 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...
- Cytogenetics for the model system Arabidopsis thalianaP 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...
- Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequencesJ 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...
- DNA sequence analysis of the ribosomal DNA ITS2 region for the Anopheles punctulatus group of mosquitoesN W Beebe
Molecular Parasitology Unit, Department of Cell and Molecular Biology, University of Technology, Sydney, Australia
Insect Mol Biol 8:381-90. 1999The 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-..
- rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replicationMartin D Burkhalter
Institute of Cell Biology, Department of Biology, ETH Honggerberg, CH 8093 Zurich, Switzerland
Mol Cell 15:409-21. 2004To 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...
- Molecular analysis of the bacterial microbiota in the human stomachElisabeth 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...
- Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the oceanRamon 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....
- Directed gene copy number amplification in Pichia pastoris by vector integration into the ribosomal DNA locusHans Marx
Department of Biotechnology, BOKU, University of Natural Resources and Applied Life Sciences, Vienna, Austria
FEMS Yeast Res 9:1260-70. 2009....
- Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCRK 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.
- characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal DNA terminal restriction fragment length polymorphism profilingG 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...
- Hmo1, an HMG-box protein, belongs to the yeast ribosomal DNA transcription systemOlivier 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...
- Chromosomal addresses of the cohesin component Mcd1pS 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...
- The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication forkTakehiko 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 ..
- Molecular phylogenetics of tsetse flies (Diptera: Glossinidae) based on mitochondrial (COI, 16S, ND2) and nuclear ribosomal DNA sequences, with an emphasis on the palpalis groupN 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...
- Phylogenetic and ecological analysis of novel marine stramenopilesRamon 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, ..
- swi1- and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombeGregor 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...
- Strain-dependent variation in 18S ribosomal DNA Copy numbers in Aspergillus fumigatusM 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...
- 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...
- Inferences about orthopteroid phylogeny and molecular evolution from small subunit nuclear ribosomal DNA sequencesP 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...
- Molecular epidemiological investigation of Ascaris genotypes in China based on single-strand conformation polymorphism analysis of ribosomal DNAWeidong 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, ..
- Vertical evolution and intragenic spread of lichen-fungal group I intronsDebashish 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...
- 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...
- Clustering of dispersed ribosomal DNA and its role in gene regulation and chromosome-end associations in malaria parasitesLiliana 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...
- Mrc1 and Tof1 promote replication fork progression and recovery independently of Rad53Hélène 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...
- 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 projectAbdel 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...
- Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum CnidariaNathaniel M Evans
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
BMC Evol Biol 8:139. 2008....
- The human papillomavirus type 8 E2 tethering protein targets the ribosomal DNA loci of host mitotic chromosomesAtasi 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...
- Molecular phylogeny of choanoflagellates, the sister group to MetazoaM 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...
- Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragmentsG 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...
- Molecular characterization of ribosomal DNA polymorphisms discriminating among chromosomal forms of Anopheles gambiae s.sG 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...
- Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganismsD 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...
- Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approachesRamon 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...
- Environmental rRNA inventories miss over half of protistan diversitySunok 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...
- The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copiesAndréia 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...
- How to get more out of molecular fingerprints: practical tools for microbial ecologyMassimo 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...
- Role of recombination in the long-term retention of transposable elements in rRNA gene lociXian 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...
- Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA resultsMarcin 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...
- Role for perinuclear chromosome tethering in maintenance of genome stabilityKarim 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 ..
- 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 moleculesKatharina Merz
Universitaet Regensburg, Institut fur Biochemie, Genetik und Mikrobiologie, 93053 Regensburg, Germany
Genes Dev 22:1190-204. 2008Synthesis 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 ..
- The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencingMouhamad 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 ..
- Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimatesDaniel 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...
- Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genesJeremy 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...
- Transcription-dependent recombination and the role of fork collision in yeast rDNAYasushi 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...
- 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. 2003DNA sequence variation of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA from Arabis holboellii, A. drummondii, and its putative hybrid A...
- Condensin function at centromere chromatin facilitates proper kinetochore tension and ensures correct mitotic segregation of sister chromatidsVladimir 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...
- Specific detection and prevalence of Helicobacter heilmannii-like organisms in the human gastric mucosa by fluorescent in situ hybridization and partial 16S ribosomal DNA sequencingK 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)...
- Unveiling new microbial eukaryotes in the surface oceanRamon 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...
- 16S ribosomal DNA-based analysis of bacterial diversity in purified water used in pharmaceutical manufacturing processes by PCR and denaturing gradient gel electrophoresisMako 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...
- Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colonP 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...
- The evolution of homing endonuclease genes and group I introns in nuclear rDNAPeik 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...
- Prospective study of use of PCR amplification and sequencing of 16S ribosomal DNA from cerebrospinal fluid for diagnosis of bacterial meningitis in a clinical settingTim 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 ..
- In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridisS Johansen
Department of Molecular Cell Biology, Institute of Medical Biology, University of Tromsø, Norway
Mol Microbiol 24:737-45. 1997DiSSU1 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...
- The Treacher Collins syndrome (TCOF1) gene product is involved in ribosomal DNA gene transcription by interacting with upstream binding factorBenigno 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)...
- Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungiD S Hibbett
Harvard University Herbaria, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Mol Biol Evol 13:903-17. 1996Group 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)...
- Bacterial biota in the human distal esophagusZhiheng 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...
- Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expressionRoman 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. 2007We analyzed nuclear ribosomal DNA (rDNA) transcription and chromatin condensation in individuals from several populations of Tragopogon mirus and T...
- The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiaeLaura 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...
- Genomic organization and evolution of the 5S ribosomal DNA in the ancient fish sturgeonFrancisca Robles
Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
Genome 48:18-28. 2005b>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...
- Silencing in yeast rDNA chromatin: reciprocal relationship in gene expression between RNA polymerase I and IIFrancesco 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...
- The role of UBF in regulating the structure and dynamics of transcriptionally active rDNA chromatinElaine 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...
- The role of novel, uncultivable bacteria in incident PIDCATHERINE L contact HAGGERTY; Fiscal Year: 2011..abstract_text> ..
- Role of Coxiella burnetii group I introns in growth modulationMichael 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. ..
- Role of Microbial Translocation in Cardiopulmonary Disease in Children with HIVAlison 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 ..
- Regulation of Host Nitrogen Balance by the Gut MicrobiomeGary D Wu; Fiscal Year: 2012....
- Functional Consequence of Macrolide Resistance Mutations in T. pallidumSheila 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. ..
- The Intestinal Microbiome in Pediatric NAFLDNita H Salzman; Fiscal Year: 2010..abstract_text> ..
- Role of chromatin structure in regulating gene silencingMary 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...
- Genetic Analysis of MSM Protein Function in S. PombeSusan 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 ..
- Regulation of repetitive chromatin structures during the human cell cyclePaul 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. ..
- Peripheral blood dendritic cells and periodontitisCHRISTOPHER 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. ..
- Intestinal bacterial metagenome in pediatric NAFLDNita H Salzman; Fiscal Year: 2013....
- Treatment of Distal Tyrosine Pathway DisordersMarkus 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...
- RNAi and DNA Methylation Control Genomic Stability and Transcriptional SilencingJOHN 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...
- Structural Studies of epigenetic regulation of rRNA gene by TTF-ICarlos 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. ..
- Microbiomes and Inflammation in Chronic Fatigue SyndromeRUTH 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. ..
- Mapping and Functional Analysis of RNA:DNA Hybrid-Forming LociJohn 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 ..
- Alterations in the human gut microbiome associated with travelers'diarrheaBONNIE 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. ) ..
- REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNAGeoffrey 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 ..
- Retrotransposon expression within ribosomal gene lociThomas 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. ..
- Moving Beyond Diversity by Revealing Biological Functions of Uncultured BacteriaJEFFREY 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. ..
- Regulation of rRNA Genes by Silencing MechanismsDanesh Moazed; Fiscal Year: 2010....
- Control of meiotic double strand break formationAndreas Hochwagen; Fiscal Year: 2013..to delayed DNA replication, (ii) DSBs are constitutively suppressed in the vicinity of the highly repetitive ribosomal DNA (rDNA)...
- The role of deregulated protein synthesis control in Myc-induced tumorigenesisDavide Ruggero; Fiscal Year: 2013..Finally, in Aim 3 we will define the role of Myc-induced cell competition in cancer development. ..
- China's Integrated Programs for Research on AIDSYiming 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. ..
- Genomic Tools For Studying The Ecology Of The Human Vaginal MicrofloraJacques Ravel; Fiscal Year: 2010..Similarly, these tools will be critical for the study and evaluation of women's health. ..
- Pathogenesis of Obstruction/Emphysema and the Microbiome (POEM) in HIVAlison 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. ..
- Functional Sir2-RNA InteractionsJEFFREY 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. ..
- Hepatic Gene Transfer for Treatment of Hemophilias A &BMark 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...
- Microbial Translocation and HIV-Related Endothelial DysfunctionMICHAEL 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...
- Epigenetic regulation by TOR signalingRONALD 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 ..
- Helicobacter pylori and the gastric microbial community in rhesus macaquesJay 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. ..
- A NOVEL, LOGICAL APPROACH TO HIV VACCINE DEVELOPMENTDavid 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. ..
- Metagenomic Study of the Periodontal Microbiome in Healthy and Diabetic SubjectsHuiying 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. ..
- Metagenomic study of the human skin microbiome associated with acneHuiying Li; Fiscal Year: 2010..Success in this project may lead to the development of new effective therapeutic strategies for treatment of acne. ..
- Coinfection of Tick-borne Diseases in Areas of WisconsinDIANE CAPORALE; Fiscal Year: 2001..If this strain is prevalent in this state, vaccine developers should investigate the efficacy of their vaccine on this strain. ..
- iPSC Derived EC as Surrogates Using Pulmonary Hypertension as a Prototype DiseaseJoseph 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...
- MECHANISM OF TERMINATION OF DNA REPLICATIONDeepak 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". ..
- Mosquito larval immunity and its impact on gut microbiota and malaria competenceJiannong 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. ..
- Control of RNA polymerase I transcription initiation and elongationDAVID 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...
- Environmental Uncultivable Bacteria Model for Understanding Human PeriodontitisCLEBER 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)...
- Mechanistic insights into the SHU complex and Sgs1 in DNA repair and replicationKara A Bernstein; Fiscal Year: 2010..Functional analysis of proteins required for DNA repair is crucial for understanding the molecular basis of tumorigenesis. ..
- Mechanistic insights into the SHU complex and Sgs1 in DNA repair and replicationKara A Bernstein; Fiscal Year: 2013..abstract_text> ..
- Population dynamics of P. acnes and their phages in the human skin microbiomeHuiying 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. ..
- Basonuclin and Ribosome Biogenesis in Mouse Oocyte and EmbryoRichard M Schultz; Fiscal Year: 2010..Such information may ultimately translate to improving the practice of Assisted Reproductive Technology (ART). ..
- REPLICATION AND AMPLIFICATION OF TETRAHYMENA RDNAGeoffrey 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. ..
- DNA Probes for Acanthamoeba Genomics and EpidemiologyPaul 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. ..
- PROTEIN BINDING DOMAINS ON EUKARYOTIC 5S RRNA AND RDNAPaul 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. ..
- Yellow Fever, rDNA (EP+IL-12) and rAd35 as Vectors for AIDS Vaccine DevelopmentDavid 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. ..
- Development of Paratransgenic ticks for Disease ControlUlrike 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. ..
- Murine Typhus: Vector Biology & TransmissionAbdu Azad; Fiscal Year: 2007..typhi and ELB upon challenge with[unreadable] the heterologous rickettsiae and involvement of 120 kDa in the protection.[unreadable] [unreadable]..
- WHIPPLE BACILLUS AND THE ETIOLOGY OF SARCOIDOSISDavid 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...
- Vascular Tissue Invasion by Porphyromonas gingivalisLing 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. ..
- RADIATION INDUCED CHROMATIN CHANGES IN A DEFINED ORIGINJames 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. ..
- DNA TOPOISOMERASES--BIOLOGICAL FUNCTIONS AND MECHANISMSJames 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. ..
- HUMAN GENOME ANALYSIS WITH YAC CLONESDavid Schlessinger; Fiscal Year: 1990....
- The Molecular Microbiology of Bacterial VaginosisDavid 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. ..
- ULTRASTRUCTURAL STUDIES OF GENETIC ACTIVITYOscar 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...
- Ribosome Biogenesis: A Molecular Checkpoint for Cardiac HypertrophyLawrence 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. ..
- Urological Studies of Ideopathic Lower Tract SyndromeJOHN 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. ..
- 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. ..
- NORMAL AND MUTANT CHORION GENES OF DROSOPHILAAllan 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. ..
- PROTEIN BINDING DOMAINS--EUKARYOTIC FIVE-S RRNA & RDNAPaul 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...
- CHRONIC PROSTATITIS CLINICAL RESEARCH CENTERMichel Pontari; Fiscal Year: 1999....
- SPECIFIC TARGETING AND TRANSCRIPTION OF METAZOAN RDNABarbara 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. ..
- REGULATION AS A BASIS FOR ORGANISMAL DIFFERENCESJACK KIRSCH; Fiscal Year: 1993..Two model systems are proposed that meet these requirements, namely the lysozyme and ribosomal DNA systems...
- MOLECULAR GENETICS OF A CELL-CELL RECOGNITION SYSTEMEduardo Orias; Fiscal Year: 1990....
- REGULATION AS A BASIS FOR ORGANISMAL DIFFERENCESAllan Wilson; Fiscal Year: 1991..Two model systems are proposed that meet these requirements, namely the lysozyme and ribosomal DNA systems...