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1. Full Text Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater
by Seurinck, Sylvie and Defoirdt, Tom and Verstraete, Willy and Siciliano, Steven D
Environmental Microbiology, ISSN 1462-2912, 02/2005, Volume 7, Issue 2, pp. 249 - 259
The human-specific HF183 Bacteriodes 16S rRNA genetic marker can be used to detect human faecal pollution in water environments. However, there is currently no... 
QUANTITATIVE DETECTION | INDICATOR BACTERIA | PROFILES | RDNA CLONE LIBRARIES | PHYLOGENETIC ANALYSIS | DISCRIMINANT-ANALYSIS | ACTIVATED-SLUDGE | DNA | ESCHERICHIA-COLI | MICROBIOLOGY | IDENTIFICATION | Fresh Water - microbiology | Reproducibility of Results | Temperature | DNA, Ribosomal - analysis | Humans | Molecular Sequence Data | Organic Chemicals - metabolism | Colony Count, Microbial | Genetic Markers | Sequence Analysis, DNA | Bacteroides - genetics | Feces - microbiology | Time Factors | Sensitivity and Specificity | Polymerase Chain Reaction | RNA, Bacterial - genetics | RNA, Ribosomal, 16S - genetics | DNA, Bacterial - analysis | Genes, rRNA | Bacteroides - isolation & purification | Water Microbiology
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2. Full Text Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes
by Schmitz, Kerstin-Maike and Mayer, Christine and Postepska, Anna and Grummt, Ingrid
Genes and Development, ISSN 0890-9369, 10/2010, Volume 24, Issue 20, pp. 2264 - 2269
Noncoding RNAs are important components of regulatory networks controlling the epigenetic state of chromatin. We analyzed the role of pRNA (promoter-associated... 
DNMTs | DNA methylation | Noncoding RNA | RNA polymerase I | DNA:RNA triplexes | noncoding RNA | CHROMATIN | SEQUENCES | TRANSCRIPTION | REMODELING COMPLEX NORC | MECHANISMS | DEVELOPMENTAL BIOLOGY | GENOME | CELL BIOLOGY | DNA | GENETICS & HEREDITY | NIH 3T3 Cells | RNA, Untranslated - metabolism | Humans | Molecular Sequence Data | Green Fluorescent Proteins - genetics | DNA, Ribosomal - chemistry | Genes, rRNA - genetics | Promoter Regions, Genetic - genetics | RNA, Untranslated - genetics | DNA (Cytosine-5-)-Methyltransferases - metabolism | DNA-Binding Proteins - metabolism | DNA Methylation | Chromatin Immunoprecipitation | Base Sequence | RNA, Untranslated - chemistry | Nucleic Acid Conformation | DNA, Ribosomal - genetics | Cell Line | Green Fluorescent Proteins - metabolism | Gene Expression Regulation | DNA-Binding Proteins - genetics | DNA - genetics | DNA (Cytosine-5-)-Methyltransferases - genetics | Microscopy, Confocal | DNA - chemistry | Animals | CpG Islands - genetics | Mice | Transcription Factors | Mutation | Epigenetic inheritance | Gene silencing | Transcription factors | RNA | Analysis | Chemical properties | Research | Methylation | Research Communication
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3. Full Text Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes
by Kuan-Liang Liu and Andrea Porras-Alfaro and Cheryl R. Kuske and Stephanie A. Eichorst and Gary Xie
Applied and Environmental Microbiology, ISSN 0099-2240, 03/2012, Volume 78, Issue 5, pp. 1523 - 1533
Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit... 
PHYLOGENY | IMPACT | KINGDOM FUNGI | SEQUENCE-DATA | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MICROBIOLOGY | DIVERSITY | NETWORKS | COMMUNITIES | Computational Biology - methods | Time Factors | Fungi - classification | Sensitivity and Specificity | Classification - methods | RNA, Fungal - genetics | Fungi - genetics | Genes, rRNA - genetics | RNA, Ribosomal - genetics | Fungi | Microbial genetics | Research | Identification and classification | Microbial Ecology
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4. Full Text Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes
by Anna Y. Pei and William E. Oberdorf and Carlos W. Nossa and Ankush Agarwal and Pooja Chokshi and Erika A. Gerz and Zhida Jin and Peng Lee and Liying Yang and Michael Poles and Stuart M. Brown and Steven Sotero and Todd DeSantis and Eoin Brodie and Karen Nelson and Zhiheng Pei
Applied and Environmental Microbiology, ISSN 0099-2240, 06/2010, Volume 76, Issue 12, pp. 3886 - 3897
ERRATUM ( vol. 76 , p. 5333 ) Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg... 
VISUALIZATION | RECOMBINATION | ESCHERICHIA-COLI O157-H7 | OPERONS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DISTINCT TYPES | SEQUENCE HETEROGENEITY | HALOARCULA-MARISMORTUI | MICROBIOLOGY | SECONDARY STRUCTURE | BACTERIAL | PREDICTION | RNA, Ribosomal, 16S - genetics | Genome, Bacterial | Genes, rRNA - genetics | Genome, Archaeal | Polymorphism, Genetic | Physiological aspects | Genetic aspects | Structure | Prokaryotes | Ribosomal RNA | Classification | Microbial Ecology
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5. Full Text Quantitative Detection of the nosZ Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA, narG, nirK, and nosZ Genes in Soils
by S. Henry and D. Bru and B. Stres and S. Hallet and L. Philippot
Applied and Environmental Microbiology, ISSN 0099-2240, 08/2006, Volume 72, Issue 8, pp. 5181 - 5189
Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit... 
REAL-TIME PCR | DENITRIFYING BACTERIA | COMMUNITY | DENITRIFICATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | QUANTIFICATION | PSEUDOMONAS | PURIFICATION | ENVIRONMENT | ABILITIES | MICROBIOLOGY | DIVERSITY | Nitrite Reductases - genetics | Nitrate Reductase - genetics | Organic Chemicals | Oxidoreductases - genetics | Soil Microbiology | Molecular Sequence Data | Bacillus - genetics | Soil - analysis | Phylogeny | DNA Primers | Genes, rRNA - genetics | Proteobacteria - genetics | Sequence Analysis, DNA | Polymerase Chain Reaction - methods | Bacillus - enzymology | Sensitivity and Specificity | RNA, Ribosomal, 16S - genetics | Proteobacteria - enzymology | Nitrous oxide | Chemical properties | Research | Bacterial genetics | Microbial Ecology
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6. Full Text Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database
by Garcia, Sònia and Kovařík, Ales and Leitch, Andrew R and Garnatje, Teresa
The Plant Journal, ISSN 0960-7412, 03/2017, Volume 89, Issue 5, pp. 1020 - 1030
The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S‐5.8S‐26S (35S)... 
rDNA | ribosomal | DNA | chromosome | 18S‐5.8S‐26S | genome evolution | loci | rDNA loci | 18S-5.8S-26S | ribosomal DNA | 45S RDNA | ARABIDOPSIS-THALIANA | IN-SITU HYBRIDIZATION | CONCERTED EVOLUTION | PLANT SCIENCES | 35S | 5S RDNA | POLYPLOIDY | GENOME SIZE | ASTERACEAE | Plants - genetics | RNA, Ribosomal, 18S - genetics | Databases, Genetic | Embryophyta - genetics | Phylogeny | Chromosomes, Plant - genetics | Genes, rRNA - genetics | DNA, Plant - genetics | Karyotype | RNA, Ribosomal, 5S - genetics | DNA, Ribosomal - genetics | Databases | RNA | Analysis | Genes | Genomics | Plant genetics | Evolution | Plants | Phylogenetics | Genetics | Botany | Ribosomal DNA
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7. Full Text Bacterial Diversity at Abandoned Uranium Mining and Milling Sites in Bulgaria as Revealed by 16S rRNA Genetic Diversity Study
by Radeva, Galina and Kenarova, Anelia and Bachvarova, Velina and Flemming, Katrin and Popov, Ivan and Vassilev, Dimitar and Selenska-Pobell, Sonja
Water, Air, & Soil Pollution, ISSN 0049-6979, 11/2013, Volume 224, Issue 11, pp. 1 - 14
Radionuclide and heavy metal contamination influences the composition and diversity of bacterial communities, thus adversely affecting their ecological role in... 
Environment, general | Hydrogeology | Climate Change | Bacterial diversity | Environment | Waste Water Technology / Water Pollution Control / Water Management / Aquatic Pollution | Atmospheric Protection/Air Quality Control/Air Pollution | Uranium and heavy metal contamination | Soil Science & Conservation | 16S rRNA gene | SORPTION | WATER RESOURCES | CONTAMINATED SUBSURFACE SEDIMENTS | MOLECULAR ANALYSIS | ENVIRONMENTAL SCIENCES | MICROBIAL COMMUNITIES | REDUCTION | WASTE PILES | VOLCANIC DEPOSITS | SOIL | MONOXIDE-OXIDIZING BACTERIA | METEOROLOGY & ATMOSPHERIC SCIENCES | WATER | Studies | Phylogenetics | Soil contaminants | Bacteria | Mining industry | Heavy metals
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8. Full Text Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome
by Nossa, Carlos W and Oberdorf, William E and Yang, Liying and Aas, Jørn A and Paster, Bruce J and de Santis, Todd Z and Brodie, Eoin L and Malamud, Daniel and Poles, Michael A and Pei, Zhiheng
World Journal of Gastroenterology, ISSN 1007-9327, 09/2010, Volume 16, Issue 33, pp. 4135 - 4144
AIM: To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.... 
Primer | 454 sequencing | 16S | Foregut | Microbiome | DISTAL ESOPHAGUS | AMPLIFICATION | SEQUENCES | BACTERIAL BIOTA | DNA | DIVERSITY | GASTROENTEROLOGY & HEPATOLOGY | Adenocarcinoma - microbiology | Gastroesophageal Reflux - microbiology | Esophageal Neoplasms - microbiology | Gastroesophageal Reflux - physiopathology | Humans | Helicobacter pylori - genetics | Upper Gastrointestinal Tract - microbiology | Genes, rRNA - genetics | Disease Progression | RNA - genetics | Sequence Analysis, RNA - methods | Metagenome - genetics | Streptococcus pneumoniae - isolation & purification | Adenocarcinoma - physiopathology | Escherichia coli - genetics | Escherichia coli - isolation & purification | Streptococcus pneumoniae - genetics | Esophageal Neoplasms - physiopathology | RNA, Ribosomal, 16S - genetics | Helicobacter pylori - isolation & purification | Helicobacter pylori - physiology | Escherichia coli - physiology | Streptococcus pneumoniae - physiology | Original
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9. Full Text Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in arabidopsis
by Chandrasekhara, Chinmayi and Mohannath, Gireesha and Blevins, Todd and Pontvianne, Frederic and Pikaard, Craig S
Genes and Development, ISSN 0890-9369, 01/2016, Volume 30, Issue 2, pp. 177 - 190
In eukaryotes, scores of excess ribosomal RNA (rRNA) genes are silenced by repressive chromatin modifications. Given the near sequence identity of rRNA genes... 
Nucleolus organizer region | Gene silencing | Chromatin | Transcription | rRNA gene subtypes | transcription | DNA METHYLATION | gene silencing | MECHANISMS | DEVELOPMENTAL BIOLOGY | chromatin | RECOMBINANT INBRED LINES | CELL BIOLOGY | rRNA gene wsubtypes | DOMINANCE | THALIANA | GENETICS & HEREDITY | POLYMERASE-I TRANSCRIPTION | PLANTS | nucleolus organizer region | RFLP | Arabidopsis - genetics | Genome, Plant - genetics | Arabidopsis - growth & development | Breeding | Gene Silencing | Nucleolus Organizer Region - genetics | Polymorphism, Genetic - genetics | Gene Dosage | Chromosomes, Plant - genetics | Genes, rRNA - genetics | Arabidopsis | Ribosomal RNA | Analysis | Plant chromosomes | Genetic aspects | Research | Life Sciences | Molecular biology | Cellular Biology | Biochemistry, Molecular Biology | Research Paper
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10. Full Text Reconstructing 16S rRNA genes in metagenomic data
by Yuan, Cheng and Lei, Jikai and Cole, James and Sun, Yanni
Bioinformatics, ISSN 1367-4803, 06/2015, Volume 31, Issue 12, pp. i35 - i43
Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly... 
BACTERIA | EXTREME ENVIRONMENTS | BIOCHEMICAL RESEARCH METHODS | COMMUNITIES | CHALLENGES | DE-NOVO ASSEMBLER | ARCHAEA | ALIGNMENT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MICROBIAL DIVERSITY | SEQUENCE | MATHEMATICAL & COMPUTATIONAL BIOLOGY | ECOLOGY | Computational Biology - methods | Sequence Analysis, RNA | Microbiota - genetics | Metagenomics - methods | RNA, Bacterial - genetics | RNA, Ribosomal, 16S - genetics | Phylogeny | Databases, Nucleic Acid | Genes, rRNA - genetics | Ismb | Eccb 2015 Proceedings Papers Committee July 10 to July 14, 2015, Dublin, Ireland
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11. Full Text Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons
by Kamke, Janine and Taylor, Michael W and Schmitt, Susanne
The ISME Journal, ISSN 1751-7362, 04/2010, Volume 4, Issue 4, pp. 498 - 508
The phylogenetic diversity of microorganisms in marine sponges is becoming increasingly well described, yet relatively little is known about the activities of... 
Marine sponges | 16S rRNA | Activity | Bacteria | Microbial symbionts | MEDITERRANEAN SEA | activity | bacteria | CLONE LIBRARIES | CORAL-REEF SPONGES | MICROBIAL COMMUNITY | microbial symbionts | GULF-OF-MEXICO | APLYSINA-AEROPHOBA | NITROGEN-FIXATION | marine sponges | BACTERIOPLANKTON COMMUNITY | ECOLOGY | VERTICAL TRANSMISSION | ELECTRON-MICROSCOPE | Molecular Sequence Data | DNA, Bacterial - chemistry | Biodiversity | Bacteria - genetics | Genes, rRNA - genetics | Sequence Analysis, DNA | Bacteria - isolation & purification | Animals | DNA, Bacterial - genetics | Bacteria - classification | RNA, Bacterial - genetics | RNA, Ribosomal, 16S - genetics | Porifera - microbiology | Symbionts | Marine microorganisms | Microorganisms | rRNA 16S | DNA | Abundance | Phylogeny | Electron microscopy
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12. Full Text The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions
by Wenbing Xie and Te Ling and Yonggang Zhou and Weijun Feng and Qiaoyun Zhu and Henk G. Stunnenberg and Ingrid Grummt and Wei Tao
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 5/2012, Volume 109, Issue 21, pp. 8161 - 8166
rRNA genes (rDNA) exist in two distinct epigenetic states, active promoters being unmethylated and marked by euchromatic histone modifications, whereas silent... 
Chromatin | 3T3 cells | NIH 3T3 cells | DNA | Ribosomal DNA | rRNA genes | Histones | Nucleosomes | Cellular differentiation | Renovations | Epigenetic dynamics | Cell differentiation | Poised chromatin | NoRC | cell differentiation | METHYLATION | PROTEIN | METHYLTRANSFERASE | MULTIDISCIPLINARY SCIENCES | epigenetic dynamics | MI-2-BETA | POLYMERASE-I TRANSCRIPTION | poised chromatin | CHROMODOMAINS | TERMINATION | BINDING | EXPRESSION | Chromatin - metabolism | NIH 3T3 Cells | DNA Repair Enzymes - genetics | Mi-2 Nucleosome Remodeling and Deacetylase Complex - genetics | Mi-2 Nucleosome Remodeling and Deacetylase Complex - metabolism | RNA Polymerase I - metabolism | Genes, rRNA - genetics | RNA, Ribosomal - genetics | DNA-Binding Proteins - metabolism | Epigenesis, Genetic - physiology | Poly-ADP-Ribose Binding Proteins | DNA Repair Enzymes - metabolism | Cell Differentiation - physiology | DNA Helicases - genetics | RNA Polymerase I - genetics | Adenosine Triphosphatases - metabolism | Nucleosomes - metabolism | Nucleosomes - genetics | DNA-Binding Proteins - genetics | DNA Helicases - metabolism | Animals | Histones - genetics | Adenosine Triphosphatases - genetics | Mice | Transcription Factors | Transcriptional Activation - physiology | Histones - metabolism | Chromatin - genetics | RNA | Physiological aspects | Genetic aspects | Genetic transcription | Research | Health aspects | Biological Sciences
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13. Full Text SIR2 Regulates Recombination between Different rDNA Repeats, but Not Recombination within Individual rRNA Genes in Yeast
by Kobayashi, Takehiko and Horiuchi, Takashi and Tongaonkar, Prasad and Vu, Loan and Nomura, Masayasu
Cell, ISSN 0092-8674, 2004, Volume 117, Issue 4, pp. 441 - 453
It is known that mutations in gene SIR2 increase and those in FOB1 decrease recombination within rDNA repeats as assayed by marker loss or extrachromosomal... 
SISTER-CHROMATID COHESION | PROTEIN FAMILY | LIFE-SPAN | REPLICATION FORK BLOCKING | DEACETYLASE ACTIVITY | SHUTTLE VECTORS | BIOCHEMISTRY & MOLECULAR BIOLOGY | SACCHAROMYCES-CEREVISIAE | TRANSCRIPTION FACTOR UAF | POLYMERASE-I | DNA-REPLICATION | CELL BIOLOGY | Sister Chromatid Exchange - genetics | Histone Deacetylases - genetics | Saccharomyces cerevisiae - genetics | Chromosomal Proteins, Non-Histone | DNA Repair - genetics | Saccharomyces cerevisiae Proteins - genetics | DNA-Binding Proteins - genetics | Mutation - genetics | Genes, rRNA - genetics | RNA Stability - genetics | Silent Information Regulator Proteins, Saccharomyces cerevisiae - genetics | Nuclear Proteins | Saccharomyces cerevisiae - metabolism | Sirtuin 2 | Phosphoproteins | Cell Cycle Proteins - genetics | Recombination, Genetic - genetics | Gene Expression Regulation, Fungal - genetics | Sirtuins - genetics | DNA, Cruciform - genetics | DNA, Ribosomal - genetics | Genetic research | Genetic aspects | Yeast | Research | Recombinant DNA | Cells
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