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Small Subunit Ribosomal RNA (small + subunit_ribosomal_rna)

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Life Sciences100%

Terms modified by Small Subunit Ribosomal RNA

  • small subunit ribosomal rna gene
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    Selected Abstracts

    Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

    ENVIRONMENTAL MICROBIOLOGY, Issue 7 2009
    -Stojanovi, Mirjana Rajili
    Summary In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota , referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose,response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition. [source]

    Identification and differentiation of Heterotardigrada and Eutardigrada species by riboprinting

    JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2007
    R. O. Schill
    Abstract In the last decades, the number of known tardigrade species has considerably increased to more than 960 species with new ones being discovered every year. However, the study of tardigrade species presents a general problem which is frequently encountered during the work with invertebrates: small size and remarkable degrees of phenotypic plasticity may sometimes not permit a definite identification of the species. In this investigation we have used riboprinting, a tool to study rDNA sequence variation, in order to distinguish tardigrade species from each other. The method combines a restriction site variation approach of ribotyping with amplified DNAs. In eight investigated species of heterotardigrades and eutardigrades we have amplified the genes for the small subunit ribosomal RNA (SSU; 18S) and subsequently sequenced the genes. Virtual riboprints were used for identification of restriction sites from ten already published 18S rDNA sequences and seven new 18S rDNA sequences. On the basis of the obtained sequences, diagnostic restriction fragment patterns can be predicted with only 11 restriction enzymes. The virtual digestion confirmed the obtained restriction fragment patterns and restriction sites of all amplified and digested tardigrade DNAs. We show that the variation in positions and number of restriction sites obtained by standard restriction fragment analysis on agarose gels can be used successfully for taxonomic identification at different taxonomic levels. The simple restriction fragment analysis provides a fast and convenient method of molecular barcoding for species identification in tardigrades. Zusammenfassung Im Laufe der letzten Jahrzehnte wurden viele neue Tardigradenarten beschrieben. Zur Zeit sind mehr als 960 Arten bekannt und jedes Jahr kommen neue Arten hinzu. Die Arbeit mit Tardigraden stellt jedoch oftmals ein Problem dar, das generell auch bei anderen Organismen von großer Bedeutung ist: die geringe Größe und die außergewöhnliche phenotypische Plastizität machen in vielen Fällen eine genaue Artidentifikation schwierig. In der vorliegenden Untersuchung verwenden wir das Riboprinting, eine Technik, rDNA Sequenzunterschiede zu erfassen, um damit verschiedene Tardigradenarten voneinander zu differenzieren. Diese Methode vereint den Ansatz der Restriktionsschnittstellenanalyse des Riboprinting mit amplifizierten DNAs. Von acht untersuchten Heterotardigraden und Eutardigraden wurden die Gene für die kleine ribosomale RNA Untereinheit (SSU; 18S) amplifiziert und sequenziert. Virtuelle Riboprints wurden zur Identifikation von zehn bereits publizierten 18S rDNA Sequenzen und sieben neuen 18S DNA Sequenzen erstellt. Auf der Basis der vorliegenden Sequenzen können die diagnostischen Restriktionsfragmentmuster mit insgesamt elf Restriktionsenzyme vorhergesagt werden. Der virtuelle Verdau bestätigt die Restriktionsfragmentmuster und Restriktionsschnittstellen aller amplifizierten und verdauten Tardigraden DNAs. Wir zeigen, dass die unterschiedlichen Variationen in den Positionen und Anzahl der Restriktionsschnittstellen erfolgreich zur taxonomischen Identifikation auf verschiedenen taxonomischen Ebenen verwendet werden können. Die einfache Restriktionsfragmentanalyse stellt eine schnelle und geeignete Methode für das molekulare Barcoding zur Artidentifikation bei Tardigraden dar. [source]

    The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol

    MOLECULAR ECOLOGY, Issue 10 2005
    P. B. HAMILTON
    Abstract Wild rabbits (Oryctolagus cuniculus) in Australia are the descendents of 24 animals from England released in 1859. We surveyed rabbits and rabbit fleas (Spilopsyllus cuniculi) in Australia for the presence of trypanosomes using parasitological and PCR-based methods. Trypanosomes were detected in blood from the European rabbits by microscopy, and PCR using trypanosome-specific small subunit ribosomal RNA (SSU rRNA) gene primers and those in rabbit fleas by PCR. This is the first record of trypanosomes from rabbits in Australia. We identified these Australian rabbit trypanosomes as Trypanosoma nabiasi, the trypanosome of the European rabbit, by comparison of morphology and SSU rRNA gene sequences of Australian and European rabbit trypanosomes. Phylogenetic analysis places T. nabiasi in a clade with rodent trypanosomes in the subgenus Herpetosoma and their common link appears to be transmission by fleas. Despite the strict host specificity of trypanosomes in this clade, phylogenies presented here suggest that they have not strictly cospeciated with their vertebrate hosts. We suggest that T. nabiasi was inadvertently introduced into Australia in the 1960s in its flea vector Spilopsyllus cuniculi, which was deliberately introduced as a potential vector of the myxoma virus. In view of the environmental and economic damage caused by rabbits in Australia and other islands, the development of a virulent or genetically modified T. nabiasi should be considered to control rabbits. [source]

    Ultrastructural Description of Breviata anathema, N. Gen., N. Sp., the Organism Previously Studied as "Mastigamoeba invertens"

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2006
    GISELLE WALKER
    ABSTRACT. An understanding of large-scale eukaryotic evolution is beginning to crystallise, as molecular and morphological data demonstrate that eukaryotes fall into six major groups. However, there are several taxa of which the affinities are yet to be resolved, and for which there are only either molecular or morphological data. One of these is the amoeboid flagellate Mastigamoeba invertens. This organism was originally misidentified and studied as a pelobiont using molecular data. We present its first light microscopical and ultrastructural characterisation. We demonstrate that it does not show affinities to the amoebozoan pelobionts, because unlike the pelobionts, it has a double basal body and two flagellar roots, a classical Golgi stack, and a large branching double membrane-bound organelle. Phylogenetic analyses of small subunit ribosomal RNA suggest an affinity with the apusomonads, when a covariotide correction for rate heterogeneity is used. We suggest that previous molecular results have been subject to artefacts from an insufficient correction for rate heterogeneity. We propose a new name for the taxon, Breviata anathema; and the unranked, apomorphy-based name "Breviates" for Breviata and its close relatives. [source]

    Comparison of Small Subunit Ribosomal RNA Gene and Internal Transcribed Spacer Sequences Among Isolates of the Intranuclear Microsporidian Nucleospora salmonis

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2000
    STEPHANE J. GRESOVIAC
    ABSTRACT. Nucleospora salmonis is an intranuclear microsporidian associated with a proliferative disorder of the lymphoid cells of captive salmonid fish in the northwestern and northeastern regions of North America, in France, and in Chile. Newer diagnostic approaches have used the polymerase chain reaction (PCR) to detect the parasite in fish tissues. The target sequences for these assays lie in the small subunit ribosomal RNA (ssu rRNA) gene or internal transcribed spacer (ITS) as determined from N. salmonis from chinook salmon (Oncorhynchus tshawytscha) from the Pacific Northwest of North America. The lack of sequence data on parasites from diverse geographic origins and hosts led us to compare several isolates of N. salmonis. There was a high degree of similarity in the ssu rDNA sequences (> 98%) among all the isolates of N. salmonis examined, regardless of host or geographic origin. The greatest sequence differences were found between isolates from the Pacific regions of America. Isolates from Chile shared sequences with one or both geographic groups from North America. A similar distribution of sequence types was observed when ITS-1 sequences of selected isolates were analyzed. Sequence data from two N. salmonis -like isolates from marine non-salmonid fish showed one closely related and the second less closely related to N. salmonis isolates from salmonid fish. These results provide evidence for a homogeneous group of aquatic members of the genus Nucleospora found among salmonid fish (N. salmonis) that can be detected using diagnostic PCR assays with ssu rDNA target sequences. The presence of parasites related to N. salmonis among marine fish suggests a potentially broad host and geographic distribution of members of the family Enterocytozoonidae. [source]