DNA, Ribosomal

• 

  Subject Areas on Research

  • A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda). 
  • A five-gene phylogeny of Pezizomycotina. 
  • A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal. 
  • A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). 
  • A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments. 
  • A multi-locus molecular phylogeny of the Lepidoziaceae: laying the foundations for a stable classification. 
  • A new perspective on lower metazoan relationships from 18S rDNA sequences. 
  • A remarkable career in science-Joseph G. Gall. 
  • Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. 
  • Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. 
  • Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens. 
  • Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens. 
  • Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. 
  • Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from the Populus root microbiome. 
  • Characterization of Mycobacterium montefiorense sp. nov., a novel pathogenic Mycobacterium from moray eels that is related to Mycobacterium triplex. 
  • Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. 
  • Class-level relationships in the phylum Cnidaria: molecular and morphological evidence. 
  • Combined inhibition of RNA polymerase I and mTORC1/2 synergize to combat oral squamous cell carcinoma. 
  • Compact organization of rRNA genes in the filamentous fungus Ashbya gossypii. 
  • Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system. 
  • Comparison of 5.8S ribosomal DNA sequences among the basidiomycetous yeast genera Cystofilobasidium, Filobasidium and Filobasidiella. 
  • Comparison of ribosomal DNA ITS regions among geographic isolates of Cenococcum geophilum. 
  • Conformational studies of the nucleic acid binding sites for Xenopus transcription factor IIIA. 
  • Constitutive magnification by the Ybb- chromosome of Drosophila melanogaster. 
  • Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. 
  • Culture-negative prosthetic valve endocarditis with concomitant septicemia due to a nontoxigenic Corynebacterium diphtheriae biotype gravis isolate in a patient with multiple risk factors. 
  • Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns 
  • Cyclophilin A and Ess1 interact with and regulate silencing by the Sin3-Rpd3 histone deacetylase. 
  • Deciding among green plants for whole genome studies. 
  • Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants. 
  • Detection of culture-resistant bacterial pathogens by amplification and sequencing of ribosomal DNA. 
  • Determinations of restriction fragment length polymorphism in bacteria using ribosomal RNA genes. 
  • Developmental regulation of DNA replication: replication fork barriers and programmed gene amplification in Tetrahymena thermophila. 
  • Diploid apomicts of the Boechera holboellii complex display large-scale chromosome substitutions and aberrant chromosomes. 
  • Discrimination of Mycobacterium tuberculosis strains by PCR. 
  • Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. 
  • Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. 
  • Ecosystem rooting depth determined with caves and DNA. 
  • Ectomycorrhizal fungal diversity in orchards of cultivated pecan (Carya illinoinensis; Juglandaceae). 
  • Effects of camptothecin or TOP1 overexpression on genetic stability in Saccharomyces cerevisiae. 
  • Ehrlichia chaffeensis, a new species associated with human ehrlichiosis. 
  • Endocarditis in a dog due to infection with a novel Bartonella subspecies. 
  • Eukaryotic gene transcription with purified components. 
  • Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. 
  • Evaluation of the accuracy and reproducibility of a practical PCR panel assay for rapid detection and differentiation of Mycobacterium avium subspecies. 
  • Evolution of Pleopsidium (lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease. 
  • Expansion of the Stictidaceae by the addition of the saxicolous lichen-forming genus Ingvariella. 
  • Extensive DNA sequence conservation throughout the Mycobacterium tuberculosis complex. 
  • Fungal Community Responses to Past and Future Atmospheric CO2 Differ by Soil Type. 
  • Genetic variability of Bacillus anthracis and related species. 
  • Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications. 
  • Genomic organization of rat rDNA. 
  • Genotypic diversity of anaerobic isolates from bloodstream infections. 
  • Genotypic diversity of coagulase-negative staphylococci causing endocarditis: a global perspective. 
  • Global patterns in peatmoss biodiversity. 
  • Helicobacter canis bacteremia in a patient with fever of unknown origin. 
  • Heterothallic mating in Mucor irregularis and first isolate of the species outside of Asia. 
  • High-density microarray of small-subunit ribosomal DNA probes. 
  • Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. 
  • Human colonic biota studied by ribosomal DNA sequence analysis. 
  • Identification and sequence of the initiation site for rat 45S ribosomal RNA synthesis. 
  • Identification of fungi associated with municipal compost using DNA-based techniques. 
  • Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex. 
  • In situ hybridization analysis of osmotic stimulus-induced changes in ribosomal RNA in rat supraoptic nucleus. 
  • In situ hybridization detection of estradiol-induced changes in ribosomal RNA levels in rat brain. 
  • Incomplete Y chromosomes promote magnification in male and female Drosophila. 
  • Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters. 
  • Intergenic transcribed spacer PCR ribotyping for differentiation of Saccharomyces species and interspecific hybrids. 
  • Invasive disease caused by nontuberculous mycobacteria, Tanzania. 
  • Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. 
  • Isolation and characterization of a Ty element inserted into the ribosomal DNA of the yeast Saccharomyces cerevisiae. 
  • Leptotrichia endocarditis: report of two cases from the International Collaboration on Endocarditis (ICE) database and review of previous cases. 
  • Low levels of DNA polymerase alpha induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae. 
  • Magnification of the ribosomal genes in female Drosophila melanogaster. 
  • Magnification: gene amplification by an inducible system of sister chromatid exchange. 
  • Major clades of Agaricales: a multilocus phylogenetic overview. 
  • Major fungal lineages are derived from lichen symbiotic ancestors. 
  • Meiotic sister chromatid recombination. 
  • Messenger RNA intron in the nuclear 18s ribosomal RNA gene of deuteromycetes. 
  • Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. 
  • Mitotic recombination in the rDNA of S. cerevisiae is suppressed by the combined action of DNA topoisomerases I and II. 
  • Modeling in yeast how rDNA introns slow growth and increase desiccation tolerance in lichens. 
  • Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. 
  • Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA. 
  • Molecular phylogeny of the Mycobacterium avium complex demonstrates clinically meaningful divisions. 
  • Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae). 
  • Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). 
  • New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. 
  • New species and distribution records for Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, with a key to the lowland neotropical taxa. 
  • New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield. 
  • New species of Xerocomus (Boletales) from the Guiana Shield, with notes on their mycorrhizal status and fruiting occurrence 
  • Notes on Agaricus section Duploannulati using molecular and morphological data. 
  • Nuclear ribosomal DNA sequence variation and evolution of spotted marsh-orchids (Dactylorhiza maculata group) 
  • Nucleolar organization, ribosomal DNA array stability, and acrocentric chromosome integrity are linked to telomere function. 
  • Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus. 
  • One hundred and seventeen clades of euagarics. 
  • One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects. 
  • Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. 
  • Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola. 
  • Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota). 
  • Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA. 
  • Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). 
  • Phylogenetic evidence for the transfer of Pseudomonas cocovenenans (van Damme et al. 1960) to the genus Burkholderia as Burkholderia cocovenenans (van Damme et al. 1960) comb. nov. 
  • Phylogenetic placement of community members of human colonic biota. 
  • Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups, and monophyly. 
  • Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. 
  • Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. 
  • Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex. 
  • Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis. 
  • Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales. 
  • Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region. 
  • Phylogeny of the Whipple's-disease-associated bacterium. 
  • Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). 
  • RINT-1 interacts with MSP58 within nucleoli and plays a role in ribosomal gene transcription. 
  • Rapid 16S ribosomal DNA sequencing from a single colony without DNA extraction or purification. 
  • Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. 
  • Recombination between heterologous human acrocentric chromosomes. 
  • Recombination of plasmids into the Saccharomyces cerevisiae chromosome is reduced by small amounts of sequence heterogeneity. 
  • Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica. 
  • Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease. 
  • Ring chromosomes and rDNA magnification in Drosophila. 
  • SIV-induced instability of the chimpanzee gut microbiome. 
  • Sequence-based differentiation of strains in the Mycobacterium avium complex. 
  • Sequences within the spacer region of yeast rRNA cistrons that stimulate 35S rRNA synthesis in vivo mediate RNA polymerase I-dependent promoter and terminator activities. 
  • Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats. 
  • Steroid hormone regulation of ribosomal RNA in rat hypothalamus: early detection using in situ hybridization and precursor-product ribosomal DNA probes. 
  • Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex. 
  • Subspecific differentiation of Mycobacterium avium complex strains by automated sequencing of a region of the gene (hsp65) encoding a 65-kilodalton heat shock protein. 
  • Systematics of the genus Chaetosphaeria and its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa. 
  • The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. 
  • The Spatial Factor, Rather than Elevated CO(2), Controls the Soil Bacterial Community in a Temperate Forest Ecosystem 
  • The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. 
  • The diversity and biogeography of soil bacterial communities. 
  • The effects of Cenozoic global change on squirrel phylogeny. 
  • The evolution of homing endonuclease genes and group I introns in nuclear rDNA. 
  • The rRNA-encoding DNA array has an altered structure in topoisomerase I mutants of Saccharomyces cerevisiae. 
  • The use of a polymerase chain reaction as a diagnostic test for Rocky Mountain spotted fever. 
  • Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life. 
  • Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene. 
  • Transformation of Saccharomyces cerevisiae with nonhomologous DNA: illegitimate integration of transforming DNA into yeast chromosomes and in vivo ligation of transforming DNA to mitochondrial DNA sequences. 
  • Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura. 
  • Two new endophytic Atractiellomycetes, Atractidochium hillariae and Proceropycnis hameedii. 
  • Two tRNA gene clusters associated with rRNA operons rrnD and rrnE in Bacillus subtilis. 
  • Type I elements mediate replication fork pausing at conserved upstream sites in the Tetrahymena thermophila ribosomal DNA minichromosome. 
  • Unique oligonucleotide primers in PCR for identification of Cryptococcus neoformans. 
  • Unusual DNA sequences associated with the ends of yeast chromosomes. 
  • Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. 
  • Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications. 
  • Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. 
  • Yeast diversity sampling on the San Juan Islands reveals no evidence for the spread of the Vancouver Island Cryptococcus gattii outbreak to this locale. 
• 

  Keywords of People

  • Roth, V. Louise, Professor of Biology, Evolutionary Anthropology
  • Shinohara, Mari L., Professor of Integrative Immunobiology, Cell Biology
  • Sullivan, Beth Ann, Professor of Molecular Genetics and Microbiology, Duke Science & Society