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RNA Gene (rna + gene)
Kinds of RNA Gene Terms modified by RNA Gene Selected AbstractsPneumocystis carinii Infection in Red-Bellied Tamarins and Cynomolgus Monkeys, and the Characterization of the Mitochondrial Large Subunit Ribosomal RNA Gene of Pneumocystis cariniiTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2001TAKAHISA FURUTA [source] Comparison of Small Subunit Ribosomal RNA Gene and Internal Transcribed Spacer Sequences Among Isolates of the Intranuclear Microsporidian Nucleospora salmonisTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2000STEPHANE 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] Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approachENVIRONMENTAL MICROBIOLOGY, Issue 8 2010Erica Lumini Summary The biodiversity of arbuscular mycorrhizal fungi (AMF) communities present in five Sardinian soils (Italy) subjected to different land-use (tilled vineyard, covered vineyard, pasture, managed meadow and cork-oak formation) was analysed using a pyrosequencing-based approach for the first time. Two regions of the 18S ribosomal RNA gene were considered as molecular target. The pyrosequencing produced a total of 10924 sequences: 6799 from the first and 4125 from the second target region. Among these sequences, 3189 and 1003 were selected to generate operational taxonomic units (OTUs) and to evaluate the AMF community richness and similarity: 117 (37 of which were singletons) and 28 (nine of which were singletons) unique AMF OTUs were detected respectively. Within the Glomeromycota OTUs, those belonging to the Glomerales order were dominant in all the soils. Diversisporales OTUs were always detected, even though less frequently, while Archaeosporales and Paraglomerales OTUs were exclusive of the pasture soil. Eleven OTUs were shared by all the soils, but each of the five AMF communities showed particular features, suggesting a meaningful dissimilarity among the Glomeromycota populations. The environments with low inputs (pasture and covered vineyard) showed a higher AMF biodiversity than those subjected to human input (managed meadow and tilled vineyard). A reduction in AMF was found in the cork-oak formation because other mycorrhizal fungal species, more likely associated to trees and shrubs, were detected. These findings reinforce the view that AMF biodiversity is influenced by both human input and ecological traits, illustrating a gradient of AMF communities which mirror the land-use gradient. The high number of sequences obtained by the pyrosequencing strategy has provided detailed information on the soil AMF assemblages, thus offering a source of light to shine on this crucial soil microbial group. [source] Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesENVIRONMENTAL MICROBIOLOGY, Issue 1 2010Victor Kunin Summary Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the ,rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on diversity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial diversity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere. [source] Novel putative nonprotein-coding RNA gene from 11q14 displays decreased expression in brains of patients with schizophreniaJOURNAL OF NEUROSCIENCE RESEARCH, Issue 1 2003Oxana O. Polesskaya Abstract A modified method of differential display was employed to identify a novel gene (named PSZA11q14), the expression of which was reduced in brains from patients with schizophrenia. Decreased expression of PSZA11q14 was identified initially in Brodmann's area (BA) 21 from a small group of patients with schizophrenia (n = 4) and normal controls (n = 6) and was confirmed subsequently using independent RT-PCR assay in BA 21, 22, and 9, and in hippocampus from a larger group of patients with schizophrenia (n = 36) and controls (n = 35). PSZA11q14 is located on chromosome 11q14, an area shown previously to co-segregate with schizophrenia and related disorders in several families. Decreased expression of PSZA11q14 in patients with schizophrenia and its location on 11q14 provide converging lines of evidence indicating that PSZA11q14 may be involved in at least some cases of schizophrenia. PSZA11q14 shows no significant homology with any known gene. It has no introns and produces two RNA transcripts of ,4.5 and ,7.0 kb. The largest open reading frame (ORF) in the PSZA11q14 transcripts may potentially encode for a short polypeptide of 71 amino acids. High frequency of rare codons, the short size of this ORF, and low homology with mouse sequences, however, indicate that PSZA11q14 may instead represent a novel member of a family of nonprotein-coding RNA genes that are not translated and that function at the RNA level. PSZA11q14 is located within the first intron of the DLG-2 gene and transcribed in the opposite direction to DLG-2. These results suggest that PSZA11q14 may be considered a candidate gene for schizophrenia acting as an antisense regulator of DLG-2, which controls assembling functional N -methyl- D -aspartate (NMDA) receptors. © 2003 Wiley-Liss, Inc. [source] Evolutionary Relationships of the Dutch Elm Disease Fungus Ophiostoma novo-ulmi to Other Ophiostoma Species Investigated by Restriction Fragment Length Polymorphism Analysis of the rDNA RegionJOURNAL OF PHYTOPATHOLOGY, Issue 9-10 2000N. D. Pipe Restriction fragment length polymorphisms (RFLPs) in the ribosomal RNA gene (rDNA) region were used to assess relationships between the Dutch elm disease fungi Ophiostoma novo-ulmi and Ophiostoma ulmi, the recently described Himalayan Dutch elm disease pathogen, Ophiostoma himal-ulmi, the morphologically similar sapstain fungi, Ophiostoma piceae and Ophiostoma quercus, and several Ophiostoma species from hardwood trees, including Ophiostoma stenoceras and Ophiostoma proliferum. A distance matrix and cluster analysis indicated that the rDNA region of O. himal-ulmi is more closely related to those of O. novo-ulmi and O. ulmi than to those of O. piceae and O. quercus and is more distantly related to O. stenoceras and the other Ophiostoma species, which formed a separate clade. The rDNA region of O. quercus was found to be at least as closely related to that of O. novo-ulmi and O. ulmi as it is to that of O. piceae. The implications of these results for the evolution of the Dutch elm disease fungi are discussed. [source] Host specificity and incidence of Trypanosoma in some African rainforest birds: a molecular approachMOLECULAR ECOLOGY, Issue 9 2001Ravinder N. M. Sehgal Abstract Studies of host,parasite interactions in birds have contributed greatly to our understanding of the evolution and ecology of disease. Here we employ molecular techniques to determine the incidence and study the host-specificity of parasitic trypanosomes in the African avifauna. We developed a polymerase chain reaction (PCR)-based diagnostic test that amplified the small subunit ribosomal RNA gene (SSU rRNA) of Trypanosoma from avian blood samples. This nested PCR assay complements and corroborates information obtained by the traditional method of blood smear analysis. The test was used to describe the incidence of trypanosomes in 479 host individuals representing 71 rainforest bird species from Cameroon, the Ivory Coast and Equatorial Guinea. Forty-two (59%) of these potential host species harboured trypanosomes and 189 individuals (35%) were infected. To examine host and geographical specificity, we examined the morphology and sequenced a portion of the SSU rRNA gene from representative trypanosomes drawn from different hosts and collecting locations. In traditional blood smear analyses we identified two trypanosome morphospecies, T. avium and T. everetti. Our molecular and morphological results were congruent in that these two morphospecies had highly divergent SSU rRNA sequences, but the molecular assay also identified cryptic variation in T. avium, in which we found seven closely allied haplotypes. The pattern of sequence diversity within T. avium provides evidence for widespread trypanosome mixing across avian host taxa and across geographical locations. For example, T. avium lineages with identical haplotypes infected birds from different families, whereas single host species were infected by T. avium lineages with different haplotypes. Furthermore, some conspecific hosts from geographically distant sampling locations were infected with the same trypanosome lineage, but other individuals from those locations harboured different trypanosome lineages. This apparent lack of host or geographical specificity may have important consequences for the evolutionary and ecological interactions between parasitic trypanosomes and their avian hosts. [source] New species of freshwater Ulva, Ulva limnetica (Ulvales, Ulvophyceae) from the Ryukyu Islands, JapanPHYCOLOGICAL RESEARCH, Issue 2 2009Kensuke Ichihara SUMMARY Ulva limnetica Ichihara et Shimada, sp. nov. (Ulvales, Ulvophyceae) is described from the Ryukyu Islands, Japan, and is characterized by thalli that are: (i) branched, tubular, fragile and wrinkled; (ii) up to 80 cm in height and up to 2 cm in diameter; (iii) light to yellowish green in color; and (iv) having an asexual reproduction by means of quadriflagellate swarmers. Rhizoidal cells bear tubular extensions on the outside of the cell layer in the stipe. Ulva limnetica is distinguished from species with similar thalli by chloroplast disposition, branching pattern, number of pyrenoids per cell and gross morphology. It is also distinguished by sequences of the nuclear-encoded 18S ribosomal RNA gene, internal transcribed spacer 2 region and the plastid-encoded large subunit of ribulose-1,5-bisphosphate carboxylase/oxgenase gene (rbcL). Ulva limnetica was clustered with other Ulva species in an early diverging lineage within the genus. [source] Nucleotide sequence diversity of the 5S rDNA spacer in the simple blade kelp genera Laminaria, Cymathaere and Kjellmaniella (Laminariales, Phaeophyceae) from northern JapanPHYCOLOGICAL RESEARCH, Issue 4 2006Norishige Yotsukura SUMMARY Tandem repeats of the 5S ribosomal RNA gene (rDNA) were confirmed for almost all laminarian, cymathaerean and kjellmaniellan species distributed in northern Japan. The nucleotide sequence of the spacer region between tandemly repeated 5S rDNA was investigated for 79 samples from 31 sites. Phylogenetic analysis of the 29 different sequences detected revealed two lineages: (1) Laminaria coriacea group, including Laminaria coriacea Miyabe, Laminaria cichorioides Miyabe, Laminaria sachalinensis (Miyabe) Miyabe, Laminaria yendoana Miyabe, Cymathaere japonica Miyabe et Nagai, Kjellmaniella gyrata (Kjellman) Miyabe and Kjellmaniella crassifolia Miyabe; (2) Laminaria japonica group including Laminaria japonica Areschoug, Laminaria religiosa Miyabe, Laminaria ochotensis Miyabe, Laminaria diabolica Miyabe, Laminaria longipedalis Okamura, Laminaria angustata Kjellman and Laminaria longissima Miyabe. In addition, the latter group was divided into two: subgroup (2a) including L. angustata and L. longissima and subgroup (2b) including L. japonica, L. religiosa, L. ochotensis, L. diabolica and L. longipedalis. Members of the three groups differ from each other in the appearance of ornaments (bullation, gyration and folds) on the surface of the blade. These are absent in group (2a), only present in the early stages of the lifespan of group (2b), and present for the duration of the lifespan in group (1). Genetic distances among samples were extremely small within group (2a). Together with previous crossing studies and data on ocean currents and distribution, these findings suggest that gene flow occurs within group (2b). [source] Recovery of Growth of Hyphochytrium catenoides after Exposure to Environmental StressTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2008FRANK H. GLEASON ABSTRACT. The survival of an isolate of Hyphochytrium catenoides collected from soil in the Blue Mountains in eastern New South Wales, Australia, was tested under extreme conditions in the laboratory. This isolate recovered growth after being subjected to drying on filter paper, to heat while desiccated, to hypersalinity, to strict anaerobic conditions, to freezing temperatures, and to a short period in solutions at pH 2.8,11.2. The capacity to survive under these conditions in the laboratory suggests adaptation to fluctuating conditions in the soil. The partial DNA sequence of the 28S ribosomal RNA gene in the isolate from New South Wales was 98% similar to that in an isolate from Arizona with a similar morphology. [source] Establishment of Liebermannia dichroplusae n. comb. on the Basis of Molecular Characterization of Perezia dichroplusae Lange, 1987 (Microsporidia)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2007YULIYA Y. SOKOLOVA ABSTRACT. Perezia dichroplusae Lange, 1987 is a parasite of the Malpighian tubules of an Argentine grasshopper, Dichroplus elongatus (Orthoptera, Acrididae, Melanoplinae). In order to determine relationships of this microsporidium with Perezia nelsoni and with other microsporidia, we sequenced its small subunit ribosomal RNA gene (SSU rDNA) (GenBank Accession No. EF016249) and performed phylogenetic analysis of the novel sequence against 17 microsporidian SSU rDNA sequences from GenBank, using neighbor-joining (NJ), maximum-parsimony (MP), and maximum-likelihood (ML) methods. This analysis revealed the highest similarity (96%) of the new sequence to Liebermannia patagonica, a parasite of gut epithelium cells of another grasshopper from Argentina, versus only 65% similarity to P. nelsoni, a parasite of muscles of paenaeid shrimps. In phylogenetic trees inferred from SSU rDNA sequences, the microsporidium from D. elongatus is sister taxon to L. patagonica and both cluster with Orthosomella operophterae. At the higher hierarchical level, the Liebermania,Orthosomella branch forms a clade with the Endoreticulatus,Cystosporogenus,Vittaforma group and with Enterocytozoon bieneusi. Perezia nelsoni falls into another large clade together with Nosema and Ameson species. We propose transferring P. dichroplusae to the genus Liebermannia and creating a new combination Liebermannia dichroplusae n. comb., based both on SSU rDNA sequence analysis and on common characters between P. dichroplusae and L. patagonica, which include the presence of elongated multinuclear sporonts, sporoblastogenesis by a similar process of sequentially splitting off sporoblasts, ovocylindrical spores of variable size, tissue tropism limited to epithelial cells, Orthoptera as hosts, and geographical distribution of hosts in the southern temperate region of Argentina. We argue that the condition of the nuclei in spores (i.e. diplokaryotic in L. patagonica or monokaryotic in L. dichroplusae) cannot be used to distinguish genera. Therefore, we remove the statement about the presence of diplokaryotic spores from the revised diagnosis of the genus Liebermannia. [source] Molecular Phytogeny and Evolution of Mosquito Parasitic Microsporidia (Microsporidia: Amblyosporidae),THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2004CHARLES R. VOSSBRINCK ABSTRACT. Amblyospora species and other aquatic Microsporidia were isolated from mosquitoes, black flies, and copepods and the small subunit ribosomal RNA gene was sequenced. Comparative phylogenetic analysis showed a correspondence between the mosquito host genera and their Amblyospora parasite species. There is a clade of Amblyospora species that infect the Culex host group and a clade of Amblyospora that infect the Aedes/Ochlerotatus group of mosquitoes. Parathelohania species, which infect Anopheles mosquitoes, may be the sister group to the Amblyospora in the same way that the Anopheles mosquitoes are thought to be the sister group to the Amblyosporo and Aedes mosquitoes. In addition, by sequence analysis of small subunit rDNA from spores, we identified the alternate copepod host for four species of Amblyospora. Amblyospora species are specific for their primary (mosquito) host and each of these mosquito species serves as host for only one Amblyospora species. On the other hand, a single species of copepod can serve as an intermediate host to several Amblyospora species and some Amblyospora species may be found in more than one copepod host. Intrapredatorus barn, a species within a monotypic genus with Amblyospora-like characteristics, falls well within the Amblyospora clade. The genera Edhazardia and Culicospora, which do not have functional meiospores and do not require an intermediate host, but which do have a lanceolate spore type which is ultrastructurally very similar to the Amblyospora spore type found in the copepod, cluster among the Amblyospora species. In the future, the genus Amblyospora may be redefined to include species without obligate intermediate hosts. Hazardia, Berwaldia, Larssonia, Trichotuzetia, and Gurleya are members of a sister group to the Amblyospora clades infecting mosquitoes, and may be representatives of a large group of aquatic parasites. [source] Deafness Due to A1555G Mitochondrial Mutation Without Use of Aminoglycoside,THE LARYNGOSCOPE, Issue 6 2004Tatsuo Matsunaga MD Abstract Objectives/Hypothesis: The objective was to clarify the characteristics of deafness associated with the A1555G mutation within mitochondrial 12S ribosomal RNA gene in the absence of aminoglycoside exposure. Study Design: Clinical and genetic studies in family members with the A1555G mitochondrial mutation were performed. Methods: The subjects were 123 maternally related members of a large Japanese family with the A1555G mutation. All subjects had no previous history of exposure to aminoglycosides. Hearing disability and handicap, tinnitus, and medical histories were analyzed by interviews in all of the subjects, genetic testing was performed in 41 subjects, and pure-tone audiometry was conducted in 26 subjects with hearing disability and handicap. Results: The A1555G mutation was detected in a homoplasmic form (meaning that all the mitochondrial DNA carries the mutation) in all 41 subjects who were screened. The risk for developing postlingual hearing loss was likely to be much higher in the present subjects than in the general population. Both the severity and age at onset of the phenotype were similar in affected subjects within the same sibling group. Pure-tone averages were significantly worse in subjects who developed hearing loss before age 10 years than in those who developed hearing loss later. Conclusion: The present study demonstrated that the prevalence of deafness in individuals with the A1555G mitochondrial mutation was likely to be high even in the absence of aminoglycoside exposure and clearly showed the association of severe to profound hearing loss with the onset of hearing loss before age 10 years. [source] Fatal encephalitozoonosis in two koalasAUSTRALIAN VETERINARY JOURNAL, Issue 10 2007JS NIMMO Two young koalas from a fauna park, recently out of the pouch and approximately 6 months old, were found dead with no previous clinical signs or gross lesions. On histopathological examination, large numbers of spores consistent with a microsporidian organism were present intracellularly within the small intestinal mucosa. Electron microscopy and polymerase chain reaction studies (sequencing the 5, end of the SSU RNA gene) identified the organism as Encephalitozoon intestinalis with 100% homology with those of previously reported human isolates. This is believed to be the first report of this organism in a marsupial. [source] Deep, hierarchical divergence of mitochondrial DNA in Amplirhagada land snails (Gastropoda: Camaenidae) from the Bonaparte Archipelago, Western AustraliaBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010MICHAEL S. JOHNSON Continental islands have experienced cycles of isolation and connection. Although complex genetic patterns have been described for mainland species affected by glacial cycles of isolation, island biotas have received little attention. We examined mitochondrial DNA in Amplirhagada land snails from 16 islands and two adjacent mainland areas of the Bonaparte Archipelago, in the Kimberley region of northern Western Australia. Four major clades, with sequence divergence of 16,27% in the 16S ribosomal RNA gene, correspond to the major geographic groupings, separated by 10,160 km. Distinct lineages also characterize islands that are only a few kilometres apart. The large differences indicate that the lineages are much older than the islands themselves, and show no evidence of geologically recent connection. Three of the major clades match the morphological description of Amplirhagada alta. Either this named species comprises several morphologically cryptic species, or it is a single, genetically very diverse species, distributed over much of the Bonaparte Archipelago. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 141,153. [source] Molecular detection of dermatophytes and nondermatophytes in onychomycosis by nested polymerase chain reaction based on 28S ribosomal RNA gene sequencesBRITISH JOURNAL OF DERMATOLOGY, Issue 5 2009M. Ebihara Summary Background, Onychomycosis is often caused by dermatophytes, but the role of nondermatophytes is underestimated due to the difficulty of identifying them by conventional direct microscopy and culture. Objectives, This study aims to detect nondermatophytes, as well as dermatophytes, in the nail samples of patients with onychomycosis using a polymerase chain reaction (PCR)-based culture-independent method. Materials and methods, The nested PCR assay targeting the sequence of the 28S ribosomal RNA gene was used to amplify fungal DNAs from 50 microscopy-positive nail specimens. Newly designed primer sets for dermatophyte universal, Trichophyton rubrum, T. mentagrophytes, Aspergillus spp., Scopulariopsis brevicaulis, Fusarium solani, F. oxysporum, F. verticillioides, Candida albicans and C. tropicalis were used after confirmation of their specificity. Results, Forty-seven cases (94%) were positive for fungal DNA, among which dermatophytes were detected in 39 cases (83·0%): T. rubrum in 35 cases (74·5%) and T. mentagrophytes in eight cases (17·0%). Surprisingly, nondermatophytes were detected in 18 cases (38·3%), both dermatophytes and nondermatophytes in 10 cases (21·3%) and nondermatophytes alone in eight cases (17·0%). Aspergillus spp. alone was observed in five cases (10·6%). Conclusions, This study indicates that most of the affected nail plates of patients with onychomycosis were positive for specific fungal DNAs, and suggests that nondermatophytes detected at high rates may be involved in the pathogenesis of onychomycosis. [source] Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota)CLADISTICS, Issue 5 2007Anders Tehler The phylogenetic relationships within the family Roccellaceae (lichen fungi) were investigated. Seventy-two nucleotide sequences of the nuclear large subunit ribosomal RNA gene (LSU) and the second largest RNA polymerase subunit (RPB2) were newly obtained from 48 taxa. The family Roccellaceae was highly supported as monophyletic. The fruticose growth habit has evolved or been lost multiple times in the family and several times even within genera. In Roccellina with 31 species it has evolved three times and in Pentagenella with three species it has been lost once. The genera Roccella and Roccellina were found paraphyletic as two Roccella species nested with Roccellina. The non-fruticose genus Roccellina was emended to include these two fruticose species as well as the monotypic, fruticose genus Roccellaria. As a result of the phylogenetic analyses six new nomenclatural combinations were made: Pentagenella corallina (Follm. and Peine) Tehler, Pentagenella ligulata (Peine and Follm.) Tehler, Roccellina cumingiana (Gay) Tehler, Roccellina hypomecha (Ach.) Tehler, Roccellina mollis (Hampe) Tehler, Roccellina portentosa (Mont. ex Gay) Tehler. Roccella is mainly distributed on the northern hemisphere while Roccellina is mainly distributed on the southern hemisphere. The Roccella species present on the Galapagos Islands are related to those in California and the northern hemisphere not, as was generally believed, to those in Chile and the southern hemisphere. The present data set may indicate that Bayesian analysis can give misleading topologies and overestimated posterior support values when insufficiently sampled taxa are included in an otherwise well sampled data set. © The Willi Hennig Society 2007. [source] Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samplesENVIRONMENTAL MICROBIOLOGY, Issue 12 2009William Marande Summary The recent introduction of molecular techniques in eukaryotic microbial diversity studies, in particular those based in the amplification and sequencing of small-subunit ribosomal DNA (SSU rDNA), has revealed the existence of an unexpected variety of new phylotypes. The taxonomic ascription of the organisms bearing those sequences is generally deduced from phylogenetic analysis. Unfortunately, the SSU rDNA sequence alone has often not enough phylogenetic information to resolve the phylogeny of fast-evolving or very divergent sequences, leading to their misclassification. To address this problem, we tried to increase the phylogenetic signal by amplifying the complete eukaryotic rDNA cluster [i.e. the SSU rDNA, the internal transcribed spacers, the 5.8S rDNA and the large-subunit (LSU) rDNA] from environmental samples, and sequencing the SSU and LSU rDNA part of the clones. Using marine planktonic samples, we showed that surveys based on either SSU or SSU + LSU rDNA retrieved comparable diversity patterns. In addition, phylogenetic trees based on the concatenated SSU + LSU rDNA sequences showed better resolution, yielding good support for major eukaryotic groups such as the Opisthokonta, Rhizaria and Excavata. Finally, highly divergent SSU rDNA sequences, whose phylogenetic position was impossible to determine with the SSU rDNA data alone, could be placed correctly with the SSU + LSU rDNA approach. These results suggest that this method can be useful, in particular for the analysis of eukaryotic microbial communities rich in phylotypes of difficult phylogenetic ascription. [source] Molecular link of different stages of the trematode host of Neorickettsia risticii to Acanthatrium oregonenseENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Kathryn E. Gibson Summary Neorickettsia risticii, the obligatory intracellular bacterium that causes Potomac horse fever, has been detected in various developmental stages of digenetic trematodes in the environment. Neorickettsia risticii -infected gravid trematodes were identified as Acanthatrium oregonense, based on morphologic keys. However, whether immature trematodes harbouring N. risticii are also A. oregonense was unknown. The objective of this study was to infer the life cycle of N. risticii -positive trematode hosts and transstadial transmission of the bacterium by molecularly characterizing the relationship among adult and immature stages of trematodes confirmed infected with N. risticii. Sequences of 18S ribosomal RNA genes up to 1922 bp in size were obtained from infected adult gravid trematodes, sporocysts and cercariae, and metacercariae. The sequences from the different immature stages of trematode are closely related to those of adult trematodes, some with 100% sequence identity; thus, they likely are life stages of A. oregonense. Comparisons with known 18S ribosomal RNA gene sequences of other digenetic trematodes indicated that all tested stages of the N. risticii -positive trematodes belong to the family Lecithodendriidae, supporting the morphological identification. [source] Sources for sedimentary bacteriohopanepolyols as revealed by 16S rDNA stratigraphyENVIRONMENTAL MICROBIOLOGY, Issue 7 2008Marco J. L. Coolen Summary Bacteriohopanoids are widespread lipid biomarkers in the sedimentary record. Many aerobic and anaerobic bacteria are potential sources of these lipids which sometimes complicates the use of these biomarkers as proxies for ecological and environmental changes. Therefore, we applied preserved 16S ribosomal RNA genes to identify likely Holocene biological sources of bacteriohopanepolyols (BHPs) in the sulfidic sediments of the permanently stratified postglacial Ace Lake, Antarctica. A suite of intact BHPs were identified, which revealed a variety of structural forms whose composition differed through the sediment core reflecting changes in bacterial populations induced by large changes in lake salinity. Stable isotopic compositions of the hopanols formed from periodic acid-cleaved BHPs, showed that some were substantially depleted in 13C, indicative of their methanotrophic origin. Using sensitive molecular tools, we found that Type I and II methanotrophic bacteria (respectively Methylomonas and Methylocystis) were unique to the oldest lacustrine sediments (> 9400 years BP), but quantification of fossil DNA revealed that the Type I methanotrophs, including methanotrophs related to methanotrophic gill symbionts of deep-sea cold-seep mussels, were the main precursors of the 35-amino BHPs (i.e. aminopentol, -tetrol and -triols). After isolation of the lake ,3000 years ago, one Type I methanotroph of the ,methanotrophic gill symbionts cluster' remained the most obvious source of aminotetrol and -triol. We, furthermore, identified a Synechococcus phylotype related to pelagic freshwater strains in the oldest lacustrine sediments as a putative source of 2-methylbacteriohopanetetrol (2-Me BHT). This combined application of advanced geochemical and paleogenomical tools further refined our knowledge about Holocene biogeochemical processes in Ace Lake. [source] Development of species-specific PCR primers on rDNA for the identification of European Armillaria speciesFOREST PATHOLOGY, Issue 5 2003G. Sicoli Summary Attempts to design species-specific PCR primers from six European Armillaria species in the ribosomal RNA genes are reported. Primers were developed on the basis of the nucleotide sequence variability of the internal transcribed spacers (ITS) and the intergenic spacer (IGS1) of the ribosomal DNA. Four sets of primers gave specific PCR products for Armillaria tabescens, Armillaria mellea and Armillaria ostoyae. However, due to the high sequence similarities between Armillaria borealis and Armillaria ostoyae and between Armillaria cepistipes and Armillaria gallica no species specific amplification was obtained for these taxa. Résumé Des essais ont été réalisés pour obtenir des amorces PCR spécifiques de 6 espèces européennes d'Armillaria dans les gènes de l'ARNr. Les amorces ont été développées sur la base de la variabilité de séquence nucléotidique dans les ITS et IGS (IGS1) de l'ADN ribosomal. Quatre couples d'amorces ont permis d'obtenir des produits PCR spécifiques pour A. tabescens, A. mellea et A. ostoyae. Cependant, compte tenu des très fortes similarités de séquence entre A. borealis et A. ostoyae, et entre A. cepistipes et A. gallica, il n'a pas été obtenu d'amplification spécifique pour ces taxons. Zusammenfassung Es wird über Versuche berichtet, artspezifische Primer für sechs europäische Armillariaarten in der Region der ribosomalen RNA-Gene zu entwickeln. Als Grundlage dafür diente die Variabilität der Nukleotidsequenzen der ITS- und der IGS 1-Region der ribosomalen DNA. Vier Primerpaare ergaben spezifische PCR-Produkte für A. tabescens, A. mellea und A. ostoyae. Dagegen wurden aufgrund der grossen Ähnlichkeit der Sequenzen von A. borealis und A. ostoyae sowie von A. cepistipes und A. gallica für diese Taxa keine artspezifischen Amplifikationsprodukte erhalten. [source] Amplification of ribosomal RNA genes in acute myeloid leukemiaGENES, CHROMOSOMES AND CANCER, Issue 1 2001Christa Fonatsch Gene amplification is a relatively rare event in acute myeloid leukemia (AML). Double minutes (dmin) and homogeneously staining regions are well established phenomena as cytogenetic correlates of gene amplification. Recently, however, two additional mechanisms leading to gene amplification, i.e., segmental jumping translocations and formation of ring chromosomes, have been described. We report four patients with AML, in whom bone marrow cells exhibited amplifications of ribosomal RNA (rRNA) genes in the form of ring chromosomes or a hsr. In two patients, the MLL gene, and in one patient the CBFA2 gene were shown to be co-amplified with rRNA genes. In two of the four patients, multiple copies of alpha-satellite sequences of the centromeres 13 and 21, respectively, were also demonstrated. In three of the four patients, the clinical course was very aggressive, leading to death within 2,8 months. In these three patients, complex karyotype abnormalities were found, whereas the karyotype of Patient 4 was characterized only by supernumerary ring 21 chromosomes of different sizes and a trisomy 8 in half of the metaphases. Modes of origin and clinical significance of the amplification of rRNA genes are discussed. © 2001 Wiley-Liss, Inc. [source] Integrated polymerase chain reaction-based procedures for the detection and identification of species and subspecies of the Gram-positive bacterial genus LactococcusJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2002Z.Y. Pu Aims:,Five species of the Gram-positive bacterial genus Lactococcus (Lactococcus lactis, L. garvieae, L. plantarum, L. piscium and L. raffinolactis) are currently recognized. The aim of this work was to develop a simple approach for the identification of these species, as well as to differentiate the industrially important dairy subspecies L. lactis subsp. lactis and L. lactis subsp. cremoris. Methods and Results:,Methods were devised based on specific polymerase chain reaction (PCR) amplifications that exploit differences in the sequences of the 16S ribosomal RNA genes of each species, followed by restriction enzyme cleavage of the PCR products. The techniques developed were used to characterize industrial cheese starter strains of L. lactis and the results were compared with biochemical phenotype and DNA sequence data. Conclusions:,The PCR primers designed can be used simultaneously, providing a simple scheme for screening unknown isolates. Strains of L. lactis show heterogeneity in the 16S ribosomal RNA gene sequence. Significance and Impact of the Study:,This work provides an integrated set of methods for differentiation and identification of lactococcal species associated with agricultural, veterinary, medical and processed food industries. [source] Polymorphisms in the sequences of Marteilia internal transcribed spacer region of the ribosomal RNA genes (ITS-1) in Spain: genetic types are not related with bivalve hostsJOURNAL OF FISH DISEASES, Issue 6 2005B Novoa Abstract Marteilia refringens is a protozoan parasite causing a disease notifiable to the Office International des Epizooties (OIE) and its distribution has implications for the transfer of live animals. The internal transcribed spacer-1 (ITS-1) from Marteilia clones contains polymorphism. Digestion with HhaI reveals two different restriction profiles, previously referred as ,O' (Marteilia from oyster or Marteilia refringens) and ,M' (Marteilia from mussels or Marteilia maurini). The aim of the present work was to determine whether the two previously described Marteilia molecular types (O and M) exist in the Iberian Peninsula and the strictness of the association with their bivalve host species. The sequence variability in the ITS-1 of Marteilia species was studied in mussels, Mytilus galloprovincialis, and flat oysters, Ostrea edulis, from different geographical locations in Spain, to establish the existence and the distribution of different species or molecular types. Although there were two distinct evolutionary lineages that corresponded more or less strictly with the ,M' and ,O' types, it was evident from the estimated phylogeny that some ,O' types have switched to ,M' type, and vice versa. Moreover, ,O' types were found in mussels and ,M' types were found in oysters, which suggests that there have been several cross-species transmissions of Marteilia between mussels and oysters. [source] Variations of 18S rDNA Loci Among Six Populations of Paeonia obovata Maxim. (Paeoniaceae) Revealed by Fluorescence In Situ HybridizationJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 5 2006Rui Luo Abstract The localization of 18S ribosomal RNA genes (rDNA) by fluorescence in situ hybridization (FISH) had been performed for some species of Paeonia. However, the pattern of 18S rDNA loci among populations is indistinct. In the present study, we localized 18S rDNA loci on meiotic or mitotic chromosomes of six populations of Paeonia obovata Maxim. (Paeoniaceae). Different numbers of rDNA loci were found with different diploid (2n=10) populations, namely eight (Lushi and Mt. Jiuhua populations), 10 (Mt. Taibai population), and seven (Mt. Guandi population), whereas tetraploid (2n=20) populations were all found with 16 loci. All rDNA loci were mapped near telomeres of mitotic chromosomes and there was no chromosome with two loci. The present results show that molecular cytological polymorphism exists among P. obovata diploid populations, indicating that structural variations occurred frequently during the evolutionary history of this species, accompanied with differentiation among populations. (Managing editor: Wei Wang) [source] New variations of Epstein,Barr virus-encoded small RNA genes in nasopharyngeal carcinomas, gastric carcinomas, and healthy donors in northern ChinaJOURNAL OF MEDICAL VIROLOGY, Issue 5 2010Yun Wang Abstract It has been generally believed that the Epstein,Barr virus (EBV)-encoded small RNA 1 and 2 (EBER1 and EBER2) genes are conserved as two families that correlated with type 1 (B95-8) and type 2 (AG876 or P3HR-1) EBV strains. EBER polymorphism and its association with EBV-associated disease have not received much attention. To explore the variations of EBER genes in different malignancies and healthy donors, the sequences of EBER genes were analyzed in 154 EBV-positive samples, including 47 nasopharyngeal carcinoma (NPC), 50 EBV-associated gastric carcinoma (EBVaGC) biopsies and 57 throat washing (TW) samples from healthy donors in northern China, where NPC is non-endemic. Three main distinct variants of EBER genes, designated as EB-6m, EB-8m, and EB-10m, were identified. EB-6m had a previously identified EBER sequence identical to P3HR-1 and was found in 33/47 (70.2%) NPC, 48/50 (96.0%) EBVaGC, and 54/57 (94.7%) TW isolates. EB-8m and EB-10m were new EBER variants with more mutations in EBER2 genes. They were found in 13/47 (27.7%) NPC cases, whereas in only 1/50 (2.0%) EBVaGC cases and not found in TW cases. The distributions were significantly different (P,<,0.05). Other five isolates (one NPC, one EBVaGC and three TW cases) showed different sequences and could not be assigned to any of the three groups. Type 1 EBV strains showed heterogeneous in terms of EBER variants. These results suggest that EBER locus can be useful to identify different EBV isolates, and it would be interesting to evaluate the association of EBER polymorphisms with EBV-associated tumors. J. Med. Virol. 82: 829,836, 2010. © 2010 Wiley-Liss, Inc. [source] Novel putative nonprotein-coding RNA gene from 11q14 displays decreased expression in brains of patients with schizophreniaJOURNAL OF NEUROSCIENCE RESEARCH, Issue 1 2003Oxana O. Polesskaya Abstract A modified method of differential display was employed to identify a novel gene (named PSZA11q14), the expression of which was reduced in brains from patients with schizophrenia. Decreased expression of PSZA11q14 was identified initially in Brodmann's area (BA) 21 from a small group of patients with schizophrenia (n = 4) and normal controls (n = 6) and was confirmed subsequently using independent RT-PCR assay in BA 21, 22, and 9, and in hippocampus from a larger group of patients with schizophrenia (n = 36) and controls (n = 35). PSZA11q14 is located on chromosome 11q14, an area shown previously to co-segregate with schizophrenia and related disorders in several families. Decreased expression of PSZA11q14 in patients with schizophrenia and its location on 11q14 provide converging lines of evidence indicating that PSZA11q14 may be involved in at least some cases of schizophrenia. PSZA11q14 shows no significant homology with any known gene. It has no introns and produces two RNA transcripts of ,4.5 and ,7.0 kb. The largest open reading frame (ORF) in the PSZA11q14 transcripts may potentially encode for a short polypeptide of 71 amino acids. High frequency of rare codons, the short size of this ORF, and low homology with mouse sequences, however, indicate that PSZA11q14 may instead represent a novel member of a family of nonprotein-coding RNA genes that are not translated and that function at the RNA level. PSZA11q14 is located within the first intron of the DLG-2 gene and transcribed in the opposite direction to DLG-2. These results suggest that PSZA11q14 may be considered a candidate gene for schizophrenia acting as an antisense regulator of DLG-2, which controls assembling functional N -methyl- D -aspartate (NMDA) receptors. © 2003 Wiley-Liss, Inc. [source] BIOCHEMICAL PHENOTYPES CORRESPONDING TO MOLECULAR PHYLOGENY OF THE RED ALGAE PLOCAMIUM (PLOCAMIALES, RHODOPHYTA): IMPLICATIONS OF INCONGRUENCE WITH THE CONVENTIONAL TAXONOMY,JOURNAL OF PHYCOLOGY, Issue 1 2006Tomomi Yano Among five species of the genus Plocamium Lamouroux distributed around Japan, P. cartilagineum (Linnaeus) Dixon, P. recurvatum Okamura and P. telfairiae (Hooker and Harvey) Harvey are often difficult to distinguish morphologically from each other. Our previous study demonstrated that P. recurvatum and P. telfairiae were divided into two groups, A and C, based on RUBISCO spacer sequence and that the specimens belonging to group C had acidic cell saps. In this study, we inferred evolutionary relationships of these Plocamium species from internal transcribed spacer sequence of the ribosomal RNA genes and obtained a similar topology to the RUBISCO spacer tree. Color of the dried specimens in the acidic group C was darker red than that in the non-acidic group A, although there was no difference in color in living thalli. The Br, concentration in the cell sap of the acidic group C was 20 times higher than that of the non-acidic group. We could not find any morphological differences to distinguish clearly between groups A and C despite exhaustive investigation of field-collected and cultured thalli in both P. recurvatum and P. telfairiae. These results suggest that the color of dried specimens and the composition of intracellular inorganic ions are significant criteria for interpreting phylogenetic relationships in Japanese Plocamium spp. [source] EVIDENCE FOR LATERAL TRANSFER OF AN IE INTRON BETWEEN FUNGAL AND RED ALGAL SMALL SUBUNIT RRNA GENES,JOURNAL OF PHYCOLOGY, Issue 2 2005Kirsten M. Müller A previous study of the North American biogeography of the red algal genus Hildenbrandia noted the presence of group I introns in the nuclear small subunit (SSU) rRNA gene of the marine species H. rubra (Sommerf.) Menegh. Group IC1 introns have been previously reported at positions 516 and 1506 in the nuclear SSU RNA genes in the Bangiales and Hildenbrandiales. However, the presence of an unclassified intron at position 989 in a collection of H. rubra from British Columbia was noted. This intron is a member of the IE subclass and is the first report of this intron type in the red algae. Phylogenetic analyses of the intron sequences revealed a close relationship between this IE intron inserted at position 989 and similar fungal IE introns in positions 989 and 1199. The 989 IE introns formed a moderately to well-supported clade, whereas the 1199 IE introns are weakly supported. Unique structural helices in the P13 domain of the 989 and 1199 IE introns also point to a close relationship between these two clades and provide further evidence for the value of secondary structural characteristics in identifying homologous introns in evolutionarily divergent organisms. The absence of the 989 IE intron in all other red algal nuclear SSU rRNA genes suggests that it is unlikely that this intron was vertically inherited from the common ancestor of the red algal and fungal lineages but rather is the result of lateral transfer between fungal and red algal nuclear SSU rRNA genes. [source] Bipolar gene flow in deep-sea benthic foraminiferaMOLECULAR ECOLOGY, Issue 19 2007J. PAWLOWSKI Abstract Despite its often featureless appearance, the deep-ocean floor includes some of the most diverse habitats on Earth. However, the accurate assessment of global deep-sea diversity is impeded by a paucity of data on the geographical ranges of bottom-dwelling species, particularly at the genetic level. Here, we present molecular evidence for exceptionally wide distribution of benthic foraminifera, which constitute the major part of deep-sea meiofauna. Our analyses of nuclear ribosomal RNA genes revealed high genetic similarity between Arctic and Antarctic populations of three common deep-sea foraminiferal species (Epistominella exigua, Cibicides wuellerstorfi and Oridorsalis umbonatus), separated by distances of up to 17 000 km. Our results contrast with the substantial level of cryptic diversity usually revealed by molecular studies, of shallow-water benthic and planktonic marine organisms. The very broad ranges of the deep-sea foraminifera that we examined support the hypothesis of global distribution of small eukaryotes and suggest that deep-sea biodiversity may be more modest at global scales than present estimates suggest. [source] | ||||||||||||||||||||||||||||