rrna genes

Summary

Summary: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.

Top Publications

  1. 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
  2. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
  3. pmc NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
    T Z DeSantis
    Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, Berkeley, CA, USA
    Nucleic Acids Res 34:W394-9. 2006
  4. pmc Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
    Peter H Janssen
    Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
    Appl Environ Microbiol 72:1719-28. 2006
  5. 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
  6. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
  7. pmc Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes
    Kerstin Maike Schmitz
    Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ ZMBH Alliance, D 69120 Heidelberg, Germany
    Genes Dev 24:2264-9. 2010
  8. pmc Finely orchestrated movements: evolution of the ribosomal RNA genes
    Thomas H Eickbush
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Genetics 175:477-85. 2007
  9. pmc Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities
    J Dunbar
    Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Appl Environ Microbiol 67:190-7. 2001
  10. 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

Research Grants

Detail Information

Publications313 found, 100 shown here

  1. 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
    ..and reevaluation of commonly used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered according to the Escherichia coli rRNA)...
  2. ncbi Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  3. pmc NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
    T Z DeSantis
    Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, Berkeley, CA, USA
    Nucleic Acids Res 34:W394-9. 2006
    ..conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample...
  4. pmc Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
    Peter H Janssen
    Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
    Appl Environ Microbiol 72:1719-28. 2006
  5. 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
    ..Formal genetic experiments measuring mitotic recombination rates within individual rRNA genes also showed no significant difference between these two strains...
  6. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria...
  7. pmc Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes
    Kerstin Maike Schmitz
    Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ ZMBH Alliance, D 69120 Heidelberg, Germany
    Genes Dev 24:2264-9. 2010
    ..RNA), a noncoding RNA that is complementary to the rDNA promoter, in mediating de novo CpG methylation of rRNA genes (rDNA)...
  8. pmc Finely orchestrated movements: evolution of the ribosomal RNA genes
    Thomas H Eickbush
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Genetics 175:477-85. 2007
    ..These studies suggest that unequal crossover is the major driving force in the evolution of the rRNA genes with sister chromatid exchange occurring more often than exchange between homologs...
  9. pmc Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities
    J Dunbar
    Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Appl Environ Microbiol 67:190-7. 2001
    Terminal restriction fragment (TRF) analysis of 16S rRNA genes is an increasingly popular method for rapid comparison of microbial communities, but analysis of the data is still in a developmental stage...
  10. 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...
  11. ncbi Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing
    Pierre E Galand
    Limnology Unit, Department of Continental Ecology, Centre d Estudis Avançats de Blanes CSIC, Blanes, Spain
    ISME J 3:860-9. 2009
    ..Our results unveiled for the first time an archaeal community dominated by group III Euryarchaeota and show biogeographical traits for marine Arctic Archaea...
  12. ncbi The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes
    David L Kirchman
    School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA
    Environ Microbiol 12:1132-43. 2010
    ....
  13. 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
    ..We demonstrate that actively transcribed rRNA genes are largely devoid of histone molecules, but instead associate with the high-mobility group protein Hmo1.
  14. 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...
  15. ncbi Isolation and characterization of arsenate-reducing bacteria from arsenic-contaminated sites in New Zealand
    Craig R Anderson
    Department of Microbiology, Otago School of Medical Sciences, University of Otago, P O Box 56, Dunedin, New Zealand
    Curr Microbiol 48:341-7. 2004
    ..As a subsidiary process to arsenate reduction, the external pH of the growth medium increased (i.e., became more alkaline), allowing these bacteria to grow for extended periods of time...
  16. pmc Nucleolar assembly of the rRNA processing machinery in living cells
    T M Savino
    Institut Jacques Monod, UMR 7592, 2 place Jussieu, 75251 Paris Cedex 05, France
    J Cell Biol 153:1097-110. 2001
    ..This demonstrates the formation of one functional domain by cooperative interactions between different chromosome territories...
  17. pmc Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes
    G Braker
    Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824 1325, USA
    Appl Environ Microbiol 67:1893-901. 2001
    ..redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis...
  18. ncbi Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
    Scot E Dowd
    USDA ARS Livestock Issues Research Unit, Lubbock, Texas 79403, USA
    Foodborne Pathog Dis 5:459-72. 2008
    ..Using bTEFAP, we can expect to gain a better understanding of how the microbiome of an animal contributes to its health and well-being...
  19. pmc Diversity of 16S rRNA genes within individual prokaryotic genomes
    Anna Y Pei
    New York University College of Arts and Science, New York, New York 10012, USA
    Appl Environ Microbiol 76:3886-97. 2010
    Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a ..
  20. ncbi Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages
    Falk Warnecke
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 6:242-53. 2004
    We analysed the phylogenetic relatedness of 16S rRNA genes from freshwater bacteria affiliated with the class Actinobacteria...
  21. pmc Variation in the strength of selected codon usage bias among bacteria
    Paul M Sharp
    Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
    Nucleic Acids Res 33:1141-53. 2005
    ..For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min...
  22. pmc The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats
    Claudio Guetg
    Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
    EMBO J 29:2135-46. 2010
    ..Our data indicated that the TIP5-mediated heterochromatin is indispensable for stability of silent rRNA genes and of major and minor satellite repeats...
  23. ncbi A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes
    Jörg Peplies
    Ribocon GmbH, D 28359 Bremen, Germany
    Syst Appl Microbiol 31:251-7. 2008
    ..Feedback and suggestions from the scientific community are welcome in order to improve these guidelines further. Any updates will be made available on the SILVA webpage at http://www.arb-silva.de/projects/soppi...
  24. ncbi The phylogeny of colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to apicomplexans
    Olga N Kuvardina
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
    J Eukaryot Microbiol 49:498-504. 2002
    ..This ancestor also very likely contained a plastid, but it is presently not certain whether it was photosynthetic, and it is not clear whether extant perkinsids or colpodellids have retained the organelle...
  25. ncbi The epigenetics of rRNA genes: from molecular to chromosome biology
    Brian McStay
    Biomedical Research Center, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, United Kingdom
    Annu Rev Cell Dev Biol 24:131-57. 2008
    ..summarizes our knowledge of the molecular mechanisms that establish and propagate the epigenetic state of rRNA genes, unraveling a complex interplay of DNA methyltransferases and histone-modifying enzymes that act in concert with ..
  26. pmc Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean
    Nasreen Bano
    Department of Marine Sciences, University of Georgia, Athens, GA 30602 3636, USA
    Appl Environ Microbiol 68:505-18. 2002
    ..over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and ..
  27. pmc Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria
    Stephanie A Eichorst
    Michigan State University, Department of Microbiology and Molecular Genetics, 6180 Biomedical and Physical Sciences Building, East Lansing, MI 48824 4320, USA
    Appl Environ Microbiol 73:2708-17. 2007
    ..The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil...
  28. pmc Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis
    J Kirk Harris
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 104:20529-33. 2007
    ..These results show that molecular techniques provide a broader perspective on airway bacteria than do routine clinical cultures and thus can identify targets for further clinical evaluation...
  29. ncbi DNA-based classification and sequence heterogeneities in the 16S rRNA genes of Lactobacillus casei/paracasei and related species
    Alejandra Vásquez
    Division of Food Technology Lab of Food Hygiene, Lund University, Lund, Sweden
    Syst Appl Microbiol 28:430-41. 2005
    The sequence differences within the 16S rRNA genes of Lactobacillus casei/paracasei and related species, Lactobacillus zeae and Lactobacillus rhamnosus, were investigated...
  30. ncbi Human Arf tumor suppressor specifically interacts with chromatin containing the promoter of rRNA genes
    Olivier Ayrault
    Laboratoire d Oncologie Moléculaire EA3805, Pôle Biologie Santé 40, avenue du Recteur Pineau, 86022 Poitiers Cedex, France
    Oncogene 23:8097-104. 2004
    ..These data, in view of the function for Topo I in rRNA transcription, are consistent with a role for the p14ARF-Topo I complex in rRNA transcription and/or maturation...
  31. pmc The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA
    R E Broughton
    Oklahoma Biological Survey and Department of Zoology, University of Oklahoma, Norman, OK 73019, USA
    Genome Res 11:1958-67. 2001
    ..It appears that even with such a large number of nucleotide characters (11,592), limited taxon sampling can lead to problems associated with extensive evolution on long phyletic branches...
  32. pmc Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies
    Rebecca J Case
    School of Biotechnology and Biomolecular Sciences and Centre for Marine Biofouling and Bio Innovation, University of New South Wales, Randwick, Sydney NSW 2052, Australia
    Appl Environ Microbiol 73:278-88. 2007
    ..This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene...
  33. pmc Bacteria and bacterial rRNA genes associated with the development of colitis in IL-10(-/-) mice
    Jingxiao Ye
    Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521, USA
    Inflamm Bowel Dis 14:1041-50. 2008
    ..This study utilized a novel population-based approach to identify bacteria and bacterial rRNA genes associated with the development of colitis in IL-10(-/-) mice.
  34. pmc Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes
    Yan Boucher
    Dalhousie University, Department of Biochemistry, Sir Charles Tupper Building, 5859 University Avenue, Room 8C, Halifax, Nova Scotia, B3H 4H7 Canada
    J Bacteriol 186:3980-90. 2004
    ..This is the first example of interspecies recombination between rRNA genes in archaea, and the recombination occurred over one of the largest phylogenetic distances ever reported for such ..
  35. ncbi The economics of ribosome biosynthesis in yeast
    J R Warner
    Dept of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, Bronx, NY 10461, USA
    Trends Biochem Sci 24:437-40. 1999
    ..Coordinate regulation of the approximately 150 rRNA genes and 137 RP genes that make such prodigious use of resources is essential for the economy of the cell...
  36. ncbi Comparative sequence analysis of 5.8S rRNA genes and internal transcribed spacer (ITS) regions of trichomonadid protozoa
    R S Felleisen
    Institute of Parasitology, University of Bern, Switzerland
    Parasitology 115:111-9. 1997
    ..mobilensis. In contrast, the genus Trichomonas shared more diversity. The results obtained in this study support a possible future revision of the taxonomic classification of tritrichomonads...
  37. ncbi Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids
    Martina Dadejova
    Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno CZ 61265, Czech Republic
    New Phytol 174:658-68. 2007
    ..We propose that nucleolus-associated transcription leaves rDNA units vulnerable to homogenization, while epigenetically inactivated units, well-separated from the nucleolus, remain unconverted...
  38. pmc Histones are required for transcription of yeast rRNA genes by RNA polymerase I
    Prasad Tongaonkar
    Department of Biological Chemistry, University of California, Irvine, CA 92697 1700, USA
    Proc Natl Acad Sci U S A 102:10129-34. 2005
    ..Other studies have shown that histones H3 and H4 are associated with actively transcribed rRNA genes. To examine their functional role in Pol I transcription, we constructed yeast strains in which synthesis of H3 ..
  39. ncbi The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes
    Kozo Tomita
    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo, Bunkyo ku, 113 8656, Japan
    J Mol Evol 54:486-500. 2002
    ..Maximum likelihood analysis of mt protein genes supports the clade Mollusca + Annelida + Brachiopoda but fails to infer the relationships among Katharina, Loligo, and three gastropod species...
  40. ncbi Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic fungi of the genus Cordyceps
    N Nikoh
    National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology, Tsukuba, Japan
    Mol Biol Evol 18:1631-42. 2001
    ..Losses of group I introns in SSU rDNA have occurred at least 27 times in the evolutionary course of the 28 Cordyceps members...
  41. pmc Diversity of 23S rRNA genes within individual prokaryotic genomes
    Anna Pei
    Washington University, College of Arts and Sciences, St Louis, MO, USA
    PLoS ONE 4:e5437. 2009
    The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept ..
  42. ncbi Gardnerella vaginalis isolated from patients with bacterial vaginosis and from patients with healthy vaginal ecosystems
    A A Aroutcheva
    Rush Presbyterian St Luke s Medical Center, Chicago, IL, USA
    Clin Infect Dis 33:1022-7. 2001
    ..Biotype 5 was predominantly associated with a healthy vaginal ecosystem (P=.0004). Biotypes 5 and 7 were the most resistant to metronidazole. No specific phenotype or genotype of G. vaginalis causes BV...
  43. ncbi Phylogenetic classification and the universal tree
    W F Doolittle
    Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Science 284:2124-9. 1999
    ..However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished...
  44. pmc Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes
    K Takai
    Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
    Appl Environ Microbiol 66:5066-72. 2000
    ..set and a domain-specific fluorogenic probe having strong and weak selectivity, respectively, for archaeal rRNA genes (rDNAs) were designed...
  45. pmc Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis
    Rita Verhelst
    Department Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
    BMC Microbiol 4:16. 2004
    ..Here, we report on the results obtained by combining culture and PCR-based methods to characterize the normal and disturbed vaginal microflora...
  46. pmc Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster
    Junqiang Ye
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Cell Biol 26:8781-90. 2006
    ..The accumulating data suggest that all units within small regions of the rDNA loci are activated for transcription, with most control over R1 and R2 activity involving steps downstream of transcription initiation...
  47. ncbi TAF12 recruits Gadd45a and the nucleotide excision repair complex to the promoter of rRNA genes leading to active DNA demethylation
    Kerstin Maike Schmitz
    Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ ZMBH Alliance, INF 581, D 69120 Heidelberg, Germany
    Mol Cell 33:344-53. 2009
    ..The results reveal a mechanism that recruits the DNA repair machinery to the promoter of active genes, keeping them in a hypomethylated state...
  48. ncbi The 160-kilobase genome of the bacterial endosymbiont Carsonella
    Atsushi Nakabachi
    Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351 0198, Japan
    Science 314:267. 2006
    ..Genes for translation and amino acid biosynthesis are relatively well represented, but numerous genes considered essential for life are missing, suggesting that Carsonella may have achieved organelle-like status...
  49. pmc Microbial community biofabrics in a geothermal mine adit
    John R Spear
    Division of Environmental Science and Engineering, Colorado School of Mines, Golden, Colorado 80401, USA
    Appl Environ Microbiol 73:6172-80. 2007
    ..These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments...
  50. pmc Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of okhotsk
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Japan
    Appl Environ Microbiol 69:7224-35. 2003
    ....
  51. pmc The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo
    Attila Nemeth
    Adolf Butenandt Institut, Molekularbiologie, Ludwig Maximilians Universitat Munchen, Schillerstrasse 44, D 80336 MUnchen, Germany
    Nucleic Acids Res 32:4091-9. 2004
    ..The association of TIP5 with the NRD facilitates DNA binding of TTF-I and leads to the recruitment of NoRC to the rDNA promoter. Thus, TTF-I and NoRC act in concert to silence rDNA transcription...
  52. pmc Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria
    Takahiro Matsuki
    Yakult Central Institute for Microbiological Research, Kunitachi, Tokyo 186 8650, Japan
    Appl Environ Microbiol 70:167-73. 2004
    ..The results showed that the composition of bifidobacterial flora was basically stable throughout the test period...
  53. pmc Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements
    J J Gillespie
    Department of Entomology, Texas A and M University, College Station, TX, USA
    Insect Mol Biol 15:657-86. 2006
    ..functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and ..
  54. ncbi Three-dimensional organization of active rRNA genes within the nucleolus
    Thierry Cheutin
    Unite MeDIAN, CNRS UMR 6142, UFR de Pharmacie, 51 rue Cognacq Jay, 51096 Reims Cedex, France
    J Cell Sci 115:3297-307. 2002
    In this work, we have localized transcribing rRNA genes at the ultrastructural level and described their three-dimensional organization within the nucleolus by electron tomography...
  55. ncbi Karyological Features of Achyrocline (Asteraceae, Gnaphalieae): stable karyotypes, low DNA content variation and linkage of rRNA genes
    C Mazzella
    Department of Plant Biology, Facultad de Agronomia, Universidad de la Republica, Montevideo 12900, Uruguay
    Cytogenet Genome Res 128:169-76. 2010
    ..Cytological data indicate that Achyrocline species are karyologically poorly differentiated, whereas the uncommon distribution of 5S and 45S rDNA suggests a close relationship with other genera of the Anthemidae tribe...
  56. pmc Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes
    Fumio Inagaki
    Subground Animalcule Retrieval SUGAR Project, Frontier Research System for Extremophiles, Yokosuka, Japan
    Appl Environ Microbiol 70:7445-55. 2004
    ....
  57. ncbi Molecular organization of 5S rDNAs in Rajidae (Chondrichthyes): Structural features and evolution of piscine 5S rRNA genes and nontranscribed intergenic spacers
    Paola Pasolini
    Molecular Genetics for Environmental and Fishery Resources Laboratory, Interdept Centre of Research in Environmental Sciences, University of Bologna, Ravenna, Italy
    J Mol Evol 62:564-74. 2006
    ..The phylogenetic analysis indicated that NTS-II is a valuable systematic tool limited to distantly related taxa of Rajiformes...
  58. pmc RNA polymerase I transcription factors in active yeast rRNA gene promoters enhance UV damage formation and inhibit repair
    Andreas Meier
    Institut fur Zellbiologie, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Mol Cell Biol 25:1586-95. 2005
    ..structure, protein-DNA interactions, and DNA repair in the spacer and promoter of Saccharomyces cerevisiae rRNA genes. Saccharomyces cerevisiae contains about 150 copies of rRNA genes separated by nontranscribed spacers...
  59. ncbi Complete rRNA gene sequences reveal that the microsporidium Nosema bombi infects diverse bumblebee (Bombus spp.) hosts and contains multiple polymorphic sites
    Wee Tek Tay
    School of Biology and Biochemistry, Queen s University Belfast, 97 Lisburn Road, BT9 7BL, United Kingdom
    J Eukaryot Microbiol 52:505-13. 2005
    ..Our data on within-genome rRNA variability call into question the usefulness of rRNA sequences to characterise intraspecific genetic variants in the Microsporidia and other groups of unicellular organisms...
  60. ncbi The characterization of microsporidian isolates (Nosematidae: Nosema) from five important lepidopteran pests in Taiwan
    Shu Jen Tsai
    Department of Entomology, National Taiwan University, Taipei 106, Taiwan
    J Invertebr Pathol 83:51-9. 2003
    ..xylostella isolate and N. bombycis yielded amplicons. Therefore, we suggest that four isolates, excluding the P. xylostella isolate, are N. spodopterae, and the taxonomic position of P. xylostella isolate needs to be elucidated...
  61. 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
    ..We show that SIRT7 is a widely expressed nucleolar protein that is associated with active rRNA genes (rDNA), where it interacts with RNA polymerase I (Pol I) as well as with histones...
  62. pmc Ecotypes of planktonic actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats
    Martin W Hahn
    Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A 5310 Mondsee, Austria
    Appl Environ Microbiol 71:766-73. 2005
    Seven strains with identical 16S rRNA genes affiliated with the Luna2 cluster (Actinobacteria) were isolated from six freshwater habitats located in temperate (Austria and Australia), subtropical (People's Republic of China), and tropical ..
  63. ncbi Host adaptation and host-parasite co-evolution in Cryptosporidium: implications for taxonomy and public health
    Lihua Xiao
    Division of Parasitic Diseases, Mail Stop F 12, Centers for Disease Control and Prevention, U S PHS DHHS, 4770 Buford Highway, Atlanta, GA 30341, USA
    Int J Parasitol 32:1773-85. 2002
    ..Understanding the evolution of Cryptosporidium species is important not only for clarification of the taxonomy of the parasites but also for assessment of the public health significance of Cryptosporidium parasites from animals...
  64. ncbi Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata)
    L Guillou
    Station Biologique de Roscoff, UMR7144, CNRS et Université Pierre et Marie Curie, BP74, 29682 Roscoff Cedex, France
    Environ Microbiol 10:3349-65. 2008
    ..Given the broad distribution of Syndiniales, our work indicates that parasitism may be a major force in ocean food webs, a force that is neglected in current conceptualizations of the marine carbon cycle...
  65. ncbi Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards
    K D Everett
    Avian and Swine Respiratory Diseases Research Unit, National Animal Disease Center, US Department of Agriculture, Ames, IA 50010, USA or
    Int J Syst Bacteriol 49:415-40. 1999
    ..In this study, phylogenetic analyses of the 16S and 23S rRNA genes are presented with corroborating genetic and phenotypic information to show that the order Chlamydiales contains ..
  66. pmc Multiple interactions between RNA polymerase I, TIF-IA and TAF(I) subunits regulate preinitiation complex assembly at the ribosomal gene promoter
    Xuejun Yuan
    Division of Molecular Biology of the Cell II, German Cancer Research Center, D 69120 Heidelberg, Germany
    EMBO Rep 3:1082-7. 2002
    ..The results uncover an interphase for essential protein-protein interactions that facilitate Pol I preinitiation complex formation...
  67. pmc Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes
    Attila Nemeth
    Department of Biochemistry III, University of Regensburg, Regensburg, Germany
    EMBO J 27:1255-65. 2008
    ..activity, but little is known about the chromatin domain organization and epigenetics of actively transcribed rRNA genes. Here, we show epigenetic and spatial organization of mouse rRNA genes at the molecular level...
  68. pmc Selective phylogenetic analysis targeted at 16S rRNA genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments
    Hiroyuki Kimura
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Central 6, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8566, Japan
    Appl Environ Microbiol 72:21-7. 2006
    ..To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation ..
  69. ncbi Analyses of the ribosomal DNA region in Nosema bombycis NIS 001
    Kazuhiro Iiyama
    Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
    J Eukaryot Microbiol 51:598-604. 2004
    ..Reverse transcription (RT)-PCR assay indicated that not only the intact SSU rDNA but also the fragmened SSU rDNA were transcribed in N. bombycis...
  70. pmc Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool
    Claudio T Sacchi
    Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    J Clin Microbiol 40:4520-7. 2002
    We investigated the diversity of the primary sequences of 16S rRNA genes among Neisseria meningitidis strains (Men) and evaluated the use of this approach as a molecular subtyping tool...
  71. ncbi Reevaluation of the phylogenetic relationship between mobilid and sessilid peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences
    Ying Chun Gong
    Laboratory of Taxonomy and Ecology of Protozoa, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
    J Eukaryot Microbiol 53:397-403. 2006
    ..This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae...
  72. pmc Rearranged subtelomeric rRNA genes in Giardia duodenalis
    Jacqueline A Upcroft
    Queensland Institute of Medical Research, The Bancroft Center, Australian Centre for International and Tropical Health and Nutrition, University of Queensland, Brisbane, Queensland, Australia
    Eukaryot Cell 4:484-6. 2005
    Giardia duodenalis has linear chromosomes capped with typical eukaryotic repeats [(TAGGG)n], subtelomeric rRNA genes, and telomere gene units...
  73. pmc Dicistronic tRNA-5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes
    Joel Acker
    Saclay Biology and Technologies Institute iBiTec S, CEA, 91191 Gif sur Yvette Cedex, France
    Nucleic Acids Res 36:5832-44. 2008
    ..Indeed, a very few cases of dicistronic Pol III genes are yet known. In contrast to other hemiascomycetes, 5S rRNA genes of Yarrowia lipolytica are not embedded into the tandemly repeated rDNA units, but appear scattered throughout ..
  74. ncbi Lactobacillus satsumensis sp. nov., isolated from mashes of shochu, a traditional Japanese distilled spirit made from fermented rice and other starchy materials
    Akihito Endo
    Department of Brewing, Tokyo University of Agriculture, Tokyo 156 8502, Japan
    Int J Syst Evol Microbiol 55:83-5. 2005
    ..The isolates are therefore considered to represent a novel species, for which the name Lactobacillus satsumensis is proposed. The type strain is NRIC 0604T (=JCM 12392T=DSM 16230T)...
  75. ncbi Characterization of the rRNA genes of Ehrlichia chaffeensis and Anaplasma phagocytophila
    Robert F Massung
    Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    DNA Cell Biol 21:587-96. 2002
    The rRNA genes of Ehrlichia chaffeensis and Anaplasma phagocytophila have been analyzed. The 16S rRNA genes were previously characterized for both of these agents...
  76. pmc The leukemogenic t(8;21) fusion protein AML1-ETO controls rRNA genes and associates with nucleolar-organizing regions at mitotic chromosomes
    Rachit Bakshi
    Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, MA 01655, USA
    J Cell Sci 121:3981-90. 2008
    ....
  77. ncbi High proportions of proinflammatory bacteria on the colonic mucosa in a young patient with ulcerative colitis as revealed by cloning and sequencing of 16S rRNA genes
    Mei Wang
    Department of Food Technology, Engineering and Nutrition, Lund University, 221 00 Lund, Sweden
    Dig Dis Sci 52:620-7. 2007
    ..The microbiota on the colonic samples was studied by cloning and sequencing of amplified 16S rRNA genes. Compared with healthy subjects, alteration of the dominant bacterial group was observed in the UC patient...
  78. ncbi Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene
    Karsten Neumann
    Institute of Zoology, Martin Luther University Halle Wittenberg, Domplatz 4, D 06108 Halle Saale, Germany
    Mol Phylogenet Evol 39:135-48. 2006
    ..DNA based divergence time estimates as well as taxonomic relationships demand a reevaluation of morphological characters previously used to identify fossils and extant hamsters...
  79. pmc Bacterial rRNA genes associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii
    Bei Yin
    Department of Plant Pathology, University of California, Riverside, CA 92521, USA
    Appl Environ Microbiol 69:1573-80. 2003
    ..Our experimental approach was to identify bacterial rRNA genes (rDNA) associated with H. schachtii cysts obtained from soil mixtures with various levels of suppressiveness...
  80. pmc Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition
    Lea Valinsky
    Department of Plant Pathology, University of California, Riverside 92521, USA
    Appl Environ Microbiol 68:5999-6004. 2002
    ..Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG)...
  81. ncbi Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II
    Jonathan P Zehr
    Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Science 322:1110-2. 2008
    ....
  82. ncbi Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast
    Ilana C Gilg
    Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy AHF 301, Los Angeles, CA 90089 0371, USA
    Protist 161:197-211. 2010
    ..Our CARD-FISH experiments targeting phylotypes from an unidentified clade offer preliminary glimpses into the morphology of these protists, while a morphology for the aphotic acantharian lineages remains unknown at this time...
  83. ncbi Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot
    Elizabeth Bent
    Department of Plant Pathology, University of California, Riverside, CA 92521, USA
    J Microbiol Methods 67:171-80. 2006
    Oligonucleotide fingerprinting of rRNA genes (OFRG) is an array-based method that generates microbial community profiles through analysis of rRNA gene clone libraries...
  84. pmc Environmental whole-genome amplification to access microbial populations in contaminated sediments
    Carl B Abulencia
    Diversa, 4955 Directors Place, San Diego, CA 92121, USA
    Appl Environ Microbiol 72:3291-301. 2006
    ..The reported SSU rRNA sequences and library clone end sequences are listed with their respective GenBank accession numbers, DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX 389173...
  85. pmc 5S Ribosomal RNA Database
    Maciej Szymanski
    Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
    Nucleic Acids Res 30:176-8. 2002
    ..The database contains 2280 primary structures of 5S rRNA and 5S rRNA genes. These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences...
  86. ncbi Evidence for adaptive selection acting on the tRNA and rRNA genes of human mitochondrial DNA
    Eduardo Ruiz-Pesini
    Center for Molecular and Mitochondrial Medicine and Genetics, Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697 3940, USA
    Hum Mutat 27:1072-81. 2006
    ..Therefore, a significant portion of ancient tRNA and rRNA polymorphisms appear to have been adaptive, and these are affecting human health today...
  87. pmc Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae
    Michael P McLeod
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030 7783, USA
    J Bacteriol 186:5842-55. 2004
    ..conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae...
  88. pmc rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch
    Sasha Preuss
    Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA
    Biochim Biophys Acta 1769:383-92. 2007
    ..In eukaryotes, there are hundreds (to thousands) of rRNA genes tandemly repeated head-to-tail within nucleolus organizer regions (NORs) that span millions of basepairs...
  89. pmc Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and phylogenetic comparison with rRNA genes
    Martin Pilhofer
    Lehrstuhl fur Mikrobiologie, Technical University Munich, Am Hochanger 4, D 85354 Freising, Germany
    J Bacteriol 190:3192-202. 2008
    ..Phylogenetic analyses of 23S rRNA genes in this study also support a monophyletic grouping and their branching order--this grouping is significant for ..
  90. pmc The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription
    Yonggang Zhou
    Division of Molecular Biology of the Cell II, Deutsches Krebsforschungszentrum, D 69120 Heidelberg, Germany
    EMBO J 21:4632-40. 2002
    ..The results suggest that NoRC silences the rDNA locus by targeting the SIN3 corepressor complex to the rDNA promoter, thereby establishing a repressed chromatin structure...
  91. ncbi A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis
    T Moss
    Cancer Research Centre and Department of Medical Biology, Laval University, CHUQ HDQ, Pavillon St Patrick, 9 rue McMahon, Québec G1R 3S3, Canada
    Cell Mol Life Sci 64:29-49. 2007
    ..It is argued that transcription elongation is a key mechanism regulating rRNA gene transcription. This unorthodox view provides a logical framework to explain the co-transcriptional phase of ribosome biogenesis...
  92. pmc Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice
    Robin Brinkmeyer
    Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
    Appl Environ Microbiol 69:6610-9. 2003
    ..We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively...
  93. ncbi Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2
    Daniel W Young
    Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
    Nature 445:442-6. 2007
    ..mitotic chromosomes we find that Runx2 is retained in large discrete foci at nucleolar organizing regions where rRNA genes reside...
  94. ncbi The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae)
    I Kim
    Department of Agricultural Biology, The National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon, Republic of Korea
    Insect Mol Biol 15:217-25. 2006
    ....
  95. ncbi Lineages of acidophilic archaea revealed by community genomic analysis
    Brett J Baker
    Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
    Science 314:1933-5. 2006
    ..45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer...
  96. ncbi Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation
    Pierre E Galand
    Département de Biologie et Québec Océan, Universite Laval, Quebec G1K 7P4, Canada
    Environ Microbiol 11:971-80. 2009
    ..This relocation could have the potential to establish a substantially different geography of microbial-driven biogeochemical processes and associated oceanic production...
  97. pmc An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP)
    Dongying Wu
    UC Davis Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 3:e2566. 2008
    ..As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate...
  98. ncbi Different epigenetic layers engage in complex crosstalk to define the epigenetic state of mammalian rRNA genes
    Ingrid Grummt
    Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
    Hum Mol Genet 16:R21-7. 2007
    ..The presence of two epigenetically distinct states of rRNA genes provides a unique opportunity to decipher the molecular mechanisms that establish the euchromatic, i.e...
  99. ncbi Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): conflict and agreement with the current system of classification
    Marshal Hedin
    San Diego State University, Department of Biology, San Diego, CA 92182, USA
    Mol Phylogenet Evol 41:454-71. 2006
    ....
  100. ncbi New insights into the phylogeny of Entamoeba species provided by analysis of four new small-subunit rRNA genes
    C Graham Clark
    Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
    Int J Syst Evol Microbiol 56:2235-9. 2006
    Sequences of small-subunit rRNA genes have been obtained for four new isolates of Entamoeba. Phylogenetic analyses give new insights into the evolution of these organisms...
  101. pmc Direct regulation of rRNA transcription by fibroblast growth factor 2
    Zhi Sheng
    Molecular and Cellular Biology Program, State University of New York, Downstate Medical Center, 450 Clarkson Ave, Brooklyn, NY 11203, USA
    Mol Cell Biol 25:9419-26. 2005
    ..The 18-kDa FGF-2 localizes to rRNA genes and is necessary for the full activation of pre-rRNA synthesis in vivo...

Research Grants62

  1. NIH Director's Pioneer Award
    ERICH JARVIS; Fiscal Year: 2009
    ..Repairing the pathway in vocal learners, when damaged, would have profound impact for correcting neurological disorders of speech. ..
  2. DNA REPAIR IN A HORMONE RESPONSIVE GENE
    Michael J Smerdon; Fiscal Year: 2013
    ..Thus, results from our laboratory have implications for the broad spectrum of cancer etiology, prevention and treatment. ..
  3. The human gut microbiome, malnutrition and vaccine responses
    ANDREW LEON KAU; Fiscal Year: 2013
    ..I will perform time series metagenomic studies on their fecal microbiomes (sequencing bacterial 16S rRNA genes, total community DNA, and expressed mRNAs). Aim 2...
  4. The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish
    Alan R Shuldiner; Fiscal Year: 2010
    ..architecture of the gut microbiota from the subjects enrolled in this study by high-throughput sequencing of 16S rRNA genes;(2) characterize the gene content (metagenome) to assess the metabolic potential of the gut microbiota in 75 ..
  5. Functional Consequence of Macrolide Resistance Mutations in T. pallidum
    Sheila A Lukehart; Fiscal Year: 2012
    ..However, recent publications document high frequencies of mutation A2058G in the 23S rRNA genes of circulating T. pallidum strains. In other bacteria, this mutation is associated with macrolide resistance...
  6. MOLECULAR GENETICS OF NUCLEOLAR DOMINANCE
    CRAIG STUART PIKAARD; Fiscal Year: 2012
    ..RNA (rRNA) genes inherited from only one parent due to the selective silencing of the other progenitor's rRNA genes. The silencing that occurs in nucleolar dominance happens on a scale of millions of basepairs, second in scope ..
  7. Visualizing Genetic Activity in Normal &Mutant Yeast
    Ann L Beyer; Fiscal Year: 2013
    ..a unique in vivo approach to this research effort by using electron microscopy to directly visualize active rRNA genes released from growing cells...
  8. Utility of Plasmids in Studying Nuclear Organizing Effects
    Barbara Sollner Webb; Fiscal Year: 2009
    ..rRNA gene (pol-I) promoter plasmids localize in nucleoli abutting the cell's rRNA genes, and 5S RNA gene (pol-III) promoter plasmids localize at peri-nucleolar sites abutting the cell's 5S RNA ..
  9. Structural Studies of epigenetic regulation of rRNA gene by TTF-I
    Carlos R Escalante; Fiscal Year: 2013
    ..In active rRNA genes, TTF-I binds to the terminator T0 site and recruits Cockayne Sindrome Protein B (CSB) that in an ATP dependent ..
  10. Type 1 diabetes: the role of commensal microbiota
    Alexander V Chervonsky; Fiscal Year: 2013
    ..To support that idea, we have performed the metagenomic analysis of the gut microbiota (16S rRNA genes sequencing) from normal NOD and MyD88 KO animals, and discovered significant and meaningful differences between ..
  11. Retrotransposon expression within ribosomal gene loci
    Thomas H Eickbush; Fiscal Year: 2013
    ..an element that inserts in a sequence specific manner into a fraction of the hundreds of tandemly repeated 28S rRNA genes found in all higher organisms...
  12. Mechanism &Function of Subnuclear Targeting of Transcription Factors in Bone
    Gary S Stein; Fiscal Year: 2011
    ..Relevance: Mechanisms that mediate the intranuclear organization of skeletal gene regulatory machinery provide necessary and novel options for targeted therapy. ..
  13. Regulation of rRNA Genes by Silencing Mechanisms
    Danesh Moazed; Fiscal Year: 2010
    ..These membrane proteins may tether rRNA genes to the nuclear periphery...
  14. New mechanism of resistance to oxazolidinone antibiotics in Staphylococcus aureus
    Alexander S Mankin; Fiscal Year: 2010
    ..This type of resistance appears rather rarely and develops slowly because of the presence of multiple copies of rRNA genes in the S. aureus genome...
  15. Microbial community profiling of sewage contamination in the Great Lakes
    Sandra L McLellan; Fiscal Year: 2010
    ....
  16. Identification of Intestinal Bacteria Protective against C. Difficile Colitis
    Michael Jay Sadowsky; Fiscal Year: 2012
    ..In this proposal we will use massively parallel pyrosequencing of hypervariable regions from SSU rRNA genes to characterize the composition of fecal material from patients with recurrent CDAD and their donors...
  17. GENETICS AND BIOCHEMISTRY OF RIBOSOME SYNTHESIS
    Masayasu Nomura; Fiscal Year: 2009
    ..Finally, we plan to study the mechanism that controls switching between active and inactive states of rRNA genes. We will compare RNA and protein components associated with active genes with those associated with inactive ..
  18. Tobacco smoking and perturbations in the subgingival microbial ecosystem
    Purnima Kumar; Fiscal Year: 2013
    ..We will initially combine a cross-sectional study design with deep sequencing of 16S rRNA genes to identify bacteria associated with smoking-related periodontitis...
  19. Interrelationships between host physiology and the gut microbial community: disc
    KHRYSTYNE DUDDLESTON; Fiscal Year: 2012
    ..of diversity of the gut microbiome will be assessed using data generated by pyrosequencing of microbial 16S rRNA genes and TRFLPs analysis;flow cytometry will be used to enumerate the community and short-chain fatty acid analysis ..
  20. The Microbiome of Impaired Wound Healing
    ELIZABETH ANNE GRICE; Fiscal Year: 2013
    ..16s rRNA genes are present in every bacterial cell and can be used to identify bacteria...
  21. 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). ..
  22. 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. ..
  23. CHROMATIN HISTONE MODIFICATIONS AND HMG PROTEINS
    EDWIN BRADBURY; Fiscal Year: 1992
    ..In closed circles containing tandemly repeated 5S rRNA genes we now have initial evidence to indicate that the linking number of acetylated nucleosomes is smaller than that ..
  24. The Oral Microbiome in HIV-associated Oral Warts and Candidiasis
    Eugene J Leys; Fiscal Year: 2013
    ..We will use PCR-amplification of 16S rRNA genes and massive parallel sequencing to test the hypothesis that both HIV infection and ART alter the composition and ..
  25. PROTEIN BINDING DOMAINS ON EUKARYOTIC 5S RRNA AND RDNA
    Paul Huber; Fiscal Year: 2000
    ..We have detected an interaction between ribosomes and the oocyte 5S rRNA genes. We will characterize this interaction to ascertain whether it is specific...
  26. Antibiotics and Human Microbial Community Dynamics
    David A Relman; Fiscal Year: 2013
    ..in healthy human adults over 36 weeks in the absence of deliberate disturbance, based on deep sequencing of 16S rRNA genes in weekly fecal samples in 10 subjects, and multivariate and time series analyses. Specific Aim 2...
  27. DRUG RESISTANCE AND GENE TRANSFER IN H PYLORI
    Douglas Berg; Fiscal Year: 2003
    ..in truncated (inactive) 23S rRNA gene in a plasmid vector, along with the duplicate expressed chromosomal 23S rRNA genes. Genetic exchange between different HP strains, and the importance of a mutS-like possible mismatch correction ..
  28. 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'
    John Atkins; Fiscal Year: 2004
    ..To keep monitoring newly reported sequences for potential new cases and to respond to suggestions of others who have encountered new cases. ..
  29. Molecular examination of the identity and activity of Po
    EUGENE MADSEN; Fiscal Year: 2004
    ..extracts microbial community DNA, separates 13C- from 12C-DNA via CsCI ultracentrifugation, and then the 16S rRNA genes present in the 13C-DNA fraction are amplified by PCR, cloned, and sequenced; (ii) verifying the PAHs are ..
  30. GENETIC ANALYSIS OF RIBOSOMAL RNA FUNCTION
    Philip Cunningham; Fiscal Year: 2000
    ..The presence of multiple rRNA genes in most organisms has complicated genetic analysis of ribosome function...
  31. ULTRASTRUCTURAL STUDIES OF GENETIC ACTIVITY
    Oscar Miller; Fiscal Year: 1992
    ..be placed on improvement of techniques using model systems for in situ hybridization of nucleic acids (amphibian rRNA genes, terminal repeats of Oxytricha) and immuno-detection of proteins (RNA polymerase II, Oxytricha telomin) at the ..
  32. Regulation of rRNA transcription in Entamoeba histolyti*
    William Petri; Fiscal Year: 2003
    ..by applicant) The aim of this proposal is to locate the regulatory elements required for transcription of rRNA genes in Entamoeba histolytica. Transcription of rDNA in E...
  33. 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. ..
  34. TRANSCIPTION OF PROTEIN CODING GENES IN T BRUCE
    Gwo Shu Lee; Fiscal Year: 2001
    ..body of indirect evidence, now available, supports the notion that RNA pol I, which normally only transcribes rRNA genes, transcribes the VSG and PARP genes...
  35. STRUCTURE/FUNCTION OF THE 790 LOOP IN RIBOSOMAL RNA
    Philip Cunningham; Fiscal Year: 2001
    ..The presence of multiple rRNA genes in most organisms has complicated genetic analysis of ribosome function...
  36. PROTEIN BINDING DOMAINS--EUKARYOTIC FIVE-S RRNA & RDNA
    Paul Huber; Fiscal Year: 1991
    The developmental control of the expression of Xenopus 5S rRNA genes is mediated by the activitiy of an exceptional protein called transcription factor IIIA (TFIIIA)...
  37. GENETIC DIVERSITY AND VIRULENCE OF CRYPTOSPORIDIUM
    Douglas Clark; Fiscal Year: 2001
    ..parvum will be cloned, sequenced and used to identify genetic polymorphism within rRNA genes from the C. parvum isolates. (3) correlate the genotype of C...
  38. REGULATION AS A BASIS FOR ORGANISMAL DIFFERENCES
    Allan Wilson; Fiscal Year: 1991
    ..is geared to the rate of morphological change in animals will be examined by directly sequencing 28S rRNA genes and measuring the sizes of rDNA repeats for selected pairs of taxa exemplifying fast and slow phenotypic ..
  39. REGULATION AS A BASIS FOR ORGANISMAL DIFFERENCES
    JACK KIRSCH; Fiscal Year: 1993
    ..is geared to the rate of morphological change in animals will be examined by directly sequencing 28S rRNA genes and measuring the sizes of rDNA repeats for selected pairs of taxa exemplifying fast and slow phenotypic ..
  40. REGULATION OF RDNA REPLICATION IN TETRAHYMENA
    DRENA LARSON; Fiscal Year: 1993
    ..the molecular details of DNA replication control in eukaryotes, by focusing on the replication of the amplified rRNA genes (rDNA) in the single-celled protozoan, Tetrahymena thermophila...
  41. MOLECULAR GENETIC ANALYSIS OF PNEUMOCYSTIS
    James Stringer; Fiscal Year: 1991
    ..Clones of rRNA genes, chromosome markers and repetitive elements will be used as hybridization probes to examine genomic variation ..
  42. Molecular Analysis of Microbes in Chronic Bowel Disease
    Norman Pace; Fiscal Year: 2004
    ..abstract_text> ..
  43. Quantitative analysis of subgingival bacteria in smokers
    Purnima Kumar; Fiscal Year: 2009
    ..We propose to use bead-probes directed to the 16S rRNA genes to simultaneously measure the levels of multiple species with a flow cytometer...
  44. TRANSCRIPTION FACTOR IIIA STRUCTURE, FUNCTION, EVOLUTION
    JAY HANAS; Fiscal Year: 1992
    ..The genes for these TFIIIA-like proteins will be isolated and sequenced to determine the degree of conservation in their amino acid sequences and intron-exon structures...
  45. ORGANELLE GENOMES OF MALARIAL PARASITES
    Akhil Vaidya; Fiscal Year: 1991
    ..The 6 kb sequence has similarities with cytochrome oxidase I and cytochrome b genes as well as with portions of rRNA genes. Sequence analyses and several other pieces of evidence strongly suggest that the 6 kb tandem arrays are ..
  46. GENE EXPRESSION IN TRYPANOSOMA CRUZI
    Gregory Buck; Fiscal Year: 2000
    ..We have begun to characterize apparent promoters for the T. cruzi SL RNA gene and rRNA genes. Both drive expression of exogenous genes in transfected plasmids, although the rRNA promoter is significantly ..
  47. FUSION OF THE RIBOSOMAL RNA PROMOTERS TO OTHER OPERONS
    Catherine Squires; Fiscal Year: 2007
    ..In fast growing bacteria how transcription of rRNA genes occurs at increased elongation rates and bypasses terminators is very poorly understood...
  48. METHYLATION OF MACRONUCLEAR DNA IN TETRAHYMENA
    KATHLEEN KARRER; Fiscal Year: 1990
    ..We will ask whether methylation patterns introduced in vitro are maintained when the DNA is microinjected into host cells and whether there are hemimethylated sites in newly replicated DNA of dividing cells...
  49. MOLECULAR SURVEY OF MICROBES IN HUMAN TUBERCULOSIS
    Norman Pace; Fiscal Year: 1999
    ..g., bacterial, archaeal, mycobacterial, fungal) rRNA genes. Mixed-species amplification products will be separated by a cloning step, sorted by restriction analysis and ..
  50. Regulation of rRNA synthesis in corneal epithelium
    Hung Tseng; Fiscal Year: 2005
    ..and ovary, is likely to be a cell type-specific, and proliferation-related transcriptional regulator for the rRNA genes, the first of its kind. Basonuclin was detected in the neonatal and adult corneal epithelium...
  51. TRANSCRIPTION FACTOR IIIA
    DAVID SETZER; Fiscal Year: 2004
    ..TFIIIA is responsible for nucleating the formation of a large macromolecular complex on 5S rRNA genes that is responsible for synthesis of 5S rRNA...
  52. GENETIC ANALYSIS OF SPIROCHETES IN THE GENUS LEPTOSPIRA
    David Ralph; Fiscal Year: 1999
    ....
  53. NEW APPROACHES TO RRNA GENES OF E COLI
    Edward Morgan; Fiscal Year: 1990
    ..Methods to select cis-acting mutations defective in feedback regulation will also be developed and employed to identify the regions involved in this regulatory response...
  54. DNA OXIDATION BY ENDOGENOUS METALS
    Peter Dedon; Fiscal Year: 2003
    ..To compare in vitro and in vivo results, we will perform these studies in a common DNA sequence, the rRNA genes. AIM 4: Nucleosome structure and metal-induced DNA damage...
  55. Mechanism of nucleolar dominance in Arabidopsis
    Sasha Preuss; Fiscal Year: 2005
    Nucleolar dominance is a stable epigenetic phenomenon by which the rRNA genes of one parent are transcriptionally repressed in an F1 hybrid...
  56. Anti-infectives that target bacterial ribosomes
    Philip Cunningham; Fiscal Year: 2007
    ..Instant evolution was initially developed using Escherichia coli, but was recently applied to the rRNA genes of several other major human pathogens including Yersinia species...
  57. TRANSCRIPTIONAL ANALYSES OF THE P. FALCIPARUM RRNA GENES
    ANNE VEZZA; Fiscal Year: 1991
    ..The plasmodial genome also contains three 5S rRNA genes which are linked. This is the lowest number reported for any organism...
  58. TRANSCRIPTIONAL ANALYSES OF THE P. FALCIPARUM RRNA GENES
    ANNE VEZZA; Fiscal Year: 1992
    ..The plasmodial genome also contains three 5S rRNA genes which are linked. This is the lowest number reported for any organism...
  59. Optimizations of rRNA-based Microbial Analyses
    Gary Olsen; Fiscal Year: 2009
    ..This requires the use of primers that are specific to the rRNA genes, yet capable of accommodating all of the natural variation of the genes...
  60. CANCER RESEARCH PROGRAM
    Harris Busch; Fiscal Year: 1991
    ..Studies are being made on activity on promoters of rRNA genes (-170 to +15), particularly the holopromoter which has a core promoter element (CPE) and an upstream promoter ..
  61. MINORITY PREDOCTORAL FELLOWSHIP PROGRAM
    TIFFANY MILES; Fiscal Year: 2005
    ..abstract_text> ..
  62. BIOLOGICAL FUNCTION OF BASONUCLIN
    Hung Tseng; Fiscal Year: 2006
    ..We will examine if this mutant can inhibit Poll transcription in the basal keratinocytes in vivo and what are the effects of this inhibition on the normal development and maintenance of the epidermis. ..