Characterization of a Mycobacterium sp. in rockfish, Sebastes alutus (Gilbert) and Sebastes reedi (Westrheim & Tsuyuki), using rDNA sequences

2003 ◽  
Vol 26 (4) ◽  
pp. 241-245 ◽  
Author(s):  
C M Whipps ◽  
V G Watral ◽  
M L Kent
Keyword(s):  
Rdna Sequences

scholarly journals Characterization of the Intergenic Spacer rDNAs of Two Pig Nodule Worms,Oesophagostomum dentatumandO. quadrispinulatum

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Rui-Qing Lin ◽  
Li Shu ◽  
Guang-Hui Zhao ◽  
Tian Cheng ◽  
Shang-Shu Zou ◽  
...  
Keyword(s):  
Mainland China ◽  
Intergenic Spacer ◽  
Oesophagostomum Dentatum ◽  
Rdna Sequences ◽  
Length Polymorphisms ◽  
Different Types ◽  
Different Origins ◽  
Geographical Locations ◽  
Independent Species

The characteristics of the intergenic spacer rDNAs (IGS rDNAs) ofOesophagostomum dentatumandO. quadrispinulatumisolated from pigs in different geographical locations in Mainland China were determined, and the phylogenetic relationships of the two species were reconstructed using the IGS rDNA sequences. The organization of the IGS rDNA sequences was similar to their organization in other eukaryotes. The 28S-18S IGS rDNA sequences of bothO. dentatumandO. quadrispinulatumwere found to have variable lengths, that is, 759–762 bp and 937–1128 bp, respectively. All of the sequences contained direct repeats and inverted repeats. The length polymorphisms were related to the different numbers and organization of repetitive elements. Different types and numbers of repeats were found between the two pig nodule species, and two IGS structures were found withinO. quadrispinulatum. Phylogenetic analysis showed that allO. dentatumisolates were clustered into one clade, butO. quadrispinulatumisolates from different origins were grouped into two distinct clusters. These results suggested independent species and the existence of genotypes or subspecies within pig nodule worms. Different types and numbers of repeats and IGS rDNA structures could serve as potential markers for differentiating these two species of pig nodule worms.

scholarly journals Molecular analysis of the microflora in chronic venous leg ulceration

2003 ◽  
Vol 52 (4) ◽  
pp. 365-369 ◽  
Author(s):  
K.E. Hill ◽  
C.E. Davies ◽  
M.J. Wilson ◽  
P. Stephens ◽  
K.G. Harding ◽  
...  
Keyword(s):  
Individual Species ◽  
Venous Leg Ulcer ◽  
Bacterial Populations ◽  
Cultural Methods ◽  
Rdna Sequences ◽  
Oral Microflora ◽  
16S Rdna Sequences ◽  
First Time

There is growing evidence to suggest that the resident microflora of chronic venous leg ulcers impairs cellular wound-healing responses, thereby playing an important role in maintaining the non-healing phenotype of many of these wounds. The significance of individual species of bacteria will remain unclear until it is possible to characterize fully the microflora of such lesions. The limitations and biases of culture-based microbiology are being realized and the subsequent application of molecular methods is revealing greater diversity within mixed bacterial populations than that demonstrated by culture alone. To date, this approach has been limited to a small number of systems, including the oral microflora. Here, for the first time, the comprehensive characterization of the microflora present in the tissue of a chronic venous leg ulcer is described by the comparison of 16S rDNA sequences amplified directly from the wound tissue with sequences obtained from bacteria that were isolated by culture. The molecular approach demonstrated significantly greater bacterial diversity than that revealed by culture. Furthermore, sequences were retrieved that may possibly represent novel species of bacteria. It is only by the comprehensive analysis of the wound microflora by both molecular and cultural methods that it will be possible to further our understanding of the role of bacteria in this important condition.

Eimeria species: studies using rRNA and rDNA probes

Parasitology ◽  
1990 ◽  
Vol 101 (1) ◽  
pp. 1-6 ◽  
Author(s):  
J. Ellis ◽  
J. Bumstead
Keyword(s):  
Genomic Dna ◽  
Southern Hybridization ◽  
Eimeria Species ◽  
Small Subunit ◽  
Rrna Genes ◽  
Rdna Probe ◽  
Dna Library ◽  
Rdna Sequences ◽  
Genomic Dna Library

SUMMARYrRNA and a heterologous cloned rDNA probe have been used to detect the rRNA genes of Eimeria species which infe the chicken, and has allowed the isolation and preliminary characterization of cloned rDNA sequences from a genomic DNA library of Eimeria tenella. It is demonstrated that rRNA and rDNA probes can be used to identify individual Eimeria species by the restriction fragment patterns detected after Southern hybridization. In addition, studies have shown that the large and small subunit rRNAs are expressed throughout sporulation.

scholarly journals A Real-Time PCR Assay for Simultaneous Detection and Differentiation of Four Common Entamoeba Species That Infect Humans

2020 ◽  
Vol 59 (1) ◽  
pp. e01986-20
Author(s):  
Ibne Karim M. Ali ◽  
Shantanu Roy
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Simultaneous Detection ◽  
Small Subunit ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Content Type ◽  
Rdna Sequences ◽  
Appropriate Treatment

ABSTRACTThere are over 40 species within the genus Entamoeba, eight of which infect humans. Of these, four species (Entamoeba histolytica, E. dispar, E. moshkovskii, and E. bangladeshi) are morphologically indistinguishable from each other, and yet differentiation is important for appropriate treatment decisions. Here, we developed a hydrolysis probe-based tetraplex real-time PCR assay that can simultaneously detect and differentiate these four species in clinical samples. In this assay, multicopy small-subunit (SSU) ribosomal DNA (rDNA) sequences were used as targets. We determined that the tetraplex real-time PCR can detect amebic DNA corresponding to as little as a 0.1 trophozoite equivalent of any of these species. We also determined that this assay can detect E. histolytica DNA in the presence of 10-fold more DNA from another Entamoeba species in mixed-infection scenarios. With a panel of more than 100 well-characterized clinical samples diagnosed and confirmed using a previously published duplex real-time PCR (capable of detecting E. histolytica and E. dispar), our tetraplex real-time PCR assay demonstrated levels of sensitivity and specificity comparable with those demonstrated by the duplex real-time PCR assay. The advantage of our assay over the duplex assay is that it can specifically detect two additional Entamoeba species and can be used in conventional PCR format. This newly developed assay will allow further characterization of the epidemiology and pathogenicity of the four morphologically identical Entamoeba species, especially in low-resource settings.

Characterization of SSU and LSU rRNA genes of threeTrypanosoma (Herpetosoma) grosiisolates maintained in Mongolian jirds

Parasitology ◽  
2004 ◽  
Vol 130 (2) ◽  
pp. 157-167 ◽  
Author(s):  
H. SATO ◽  
A. OSANAI ◽  
H. KAMIYA ◽  
Y. OBARA ◽  
W. JIANG ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Geographical Origin ◽  
Large Subunit ◽  
Meriones Unguiculatus ◽  
Rrna Genes ◽  
Systematic Revision ◽  
Rdna Sequences ◽  
Relationship Of ◽  
Rna Genes

Trypanosoma (Herpetosoma) grosi, which naturally parasitizesApodemusspp., can experimentally infect Mongolian jirds (Meriones unguiculatus). Three isolates fromA. agrarius,A. peninsulae, andA. speciosus(named SESUJI, HANTO, and AKHA isolates, respectively) of different geographical origin (AKHA from Japan, and the others from Vladivostok), exhibited different durations of parasitaemia in laboratory jirds (2 weeks for HANTO, and 3 weeks for the others). To assess the genetic background of theseT. grosiisolates, their small (SSU) and large subunit (LSU) ribosomal RNA genes (rDNA) were sequenced along with those of 2 otherHerpetosomaspecies from squirrels. The SSU rDNA sequences of these 3 species along with available sequences of 3 otherHerpetosomatrypanosomes (T. lewisi,T. musculiandT. microti)seemed to reflect well the phylogenetic relationship of their hosts. Three isolates ofT. grosiexhibited base changes at 2–6 positions of 2019-base 18S rDNA, at 5–29 positions of 1817/1818-base 28Sα rDNA, or 1–5 positions of 1557–1559-base 28Sβ rDNA, and none was separated from the other 2 isolates by rDNA nucleotide sequences. Since base changes ofHerpetosomatrypanosomes at the level of inter- and intra-species might occur frequently in specified rDNA regions, the molecular analysis on these regions of rodent trypanosomes could help species/strain differentiation and systematic revision ofHerpetosomatrypanosome species, which must be more abundant than presently known.

scholarly journals Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

2014 ◽  
Vol 105 (6) ◽  
pp. 1033-1048 ◽  
Author(s):  
Sebastian Gnat ◽  
Magdalena Wójcik ◽  
Sylwia Wdowiak-Wróbel ◽  
Michał Kalita ◽  
Aneta Ptaszyńska ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Astragalus Glycyphyllos Symbionts

Molecular characterization of Candidatus Phytoplasma aurantifolia isolate infecting chickpea (Cicer arietinum) in Dharwad, Karnataka

2019 ◽  
Author(s):  
Gurupada Balol ◽  
C Channakeshava ◽  
M S Patil
Keyword(s):  
16S Rdna ◽  
Molecular Characterization ◽  
Cicer Arietinum ◽  
Nested Pcr ◽  
Rdna Sequences ◽  
Pcr Product ◽  
16S Rdna Sequences ◽  
Axillary Proliferation ◽  
Pale Green

Chickpea plants showing phytoplasma symptoms were observed in the research plots at University of Agricultural Sciences, Dharwad, Karnataka, India. The symptoms included phyllody, pale green leaves, bushy appearance and excessive axillary proliferation. The causal agent of the phyllody disease was identified based on symptoms, amplification of 16S rDNA of the phytoplasma by nested PCR with primers P1/P7 and R16F2n/R16R2 and 1,800 bp and 1,200 bp size products were amplified in first round PCR and nested-PCR respectively. The PCR product was sequenced and compared with the reference phytoplasma sequences collected from the database (NCBI). 16S rDNA sequences of Dharwad chickpea phytoplasma shared the highest nucleotide identity of (>98%) with Periwinkle phyllody16SrII-E (EU096500). This study indicated the association of ‘Candidatus Phytoplasma aurantifolia’ the 16SrII-E group infecting chickpea from Northern Karnataka.

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