scholarly journals Characteristic of ITS fragment of rDNA of Rhodotorula mucilaginosa isolated from gastrointestinal tract of centenarian

1970 ◽  
Vol 21 ◽  
pp. 283-287
Author(s):  
L. V. Polishchuk ◽  
K. S. Tkachenko ◽  
M. A. Fomyna
Keyword(s):  
Gastrointestinal Tract ◽  
Primary Structure ◽  
Its Region ◽  
Nucleotide Sequences ◽  
Rhodotorula Mucilaginosa ◽  
Yeast Isolate ◽  
Red Yeast ◽  
Ribosomal Operon ◽  
Nucleotide Database ◽  
Healthy Centenarian

Aim. The aim of the work was to analyse the primary structure of the ITS region of the ribosomal operon of the red yeast isolate Rhodotorula mucilaginosa S1 from the gastrointestinal tract of healthy centenarian compared to the available homological basidimycetous nucleotide sequences. Methods. In silico comparison of the ITS nucleotide sequences using NCBI server resources (BLAST programs and "Nucleotide" database) with the reference ITS-fragment of red yeast isolate was performed. Results. Almost 90 % of highly homologous to the reference ITS-fragment out of 800 selected sequences represented genera Rhodotorula and Rhodosporidium with the top hits for R. mucilaginosa strains PMM08-1716L, 3942L and 3684L. The most frequent nucleobases mismatches of ITS-fragments of GenBank’s R. mucilaginosa strains compared to the reference one were observed in the positions 541 (T/C) for 85 % of strains, and 129 (T/C) and 158 (G/A) for 26 % of strains. Conclusions. The primary structure of studied ITS region showed 100 % homology to R. mucilaginosa strains also isolated from humans and animals, as well as the most frequently mismatches for 129th, 158th and 541st nucleotides located in the spacers regions of the ribosomal operon. Keywords: ITS, rDNA, nucleotide sequence, red yeast, human GIT.

scholarly journals Complex Identifcation of Red Yeast Isolate from Gastrointestinal Tract of Hucul Long-Liver (Carpathians, Ukraine)

2016 ◽  
Vol 78 (5) ◽  
pp. 2-11 ◽  
Author(s):  
M.A. Fomina ◽  
◽  
L.V. Polishchuk ◽  
K.S. Tkachenko ◽  
J.W. Hong ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Yeast Isolate ◽  
Red Yeast

scholarly journals Absence of missense mutations in activated c-myc genes in avian leukosis virus-induced B-cell lymphomas.

1988 ◽  
Vol 8 (6) ◽  
pp. 2659-2663 ◽  
Author(s):  
M Hahn ◽  
W S Hayward
Keyword(s):  
B Cell ◽  
Gene Product ◽  
Primary Structure ◽  
Avian Leukosis Virus ◽  
Nucleotide Sequences ◽  
Missense Mutations ◽  
B Cell Lymphomas ◽  
Altered Expression

We have determined the nucleotide sequences of two independent DNA clones which contained the activated c-myc genes from avian leukosis virus-induced B-cell lymphomas. Neither of these c-myc genes contained missense mutations. This strongly supports the notion that the c-myc proto-oncogene in avian leukosis virus-induced B-cell lymphomas can be oncogenically activated by altered expression of the gene without a change in the primary structure of the gene product.

scholarly journals Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

2019 ◽  
Author(s):  
Michael Bradshaw ◽  
Felix Grewe ◽  
Anne Thomas ◽  
Cody H. Harrison ◽  
Hanna Lindgren ◽  
...  
Keyword(s):  
Species Complex ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Dna Barcode ◽  
Intergenic Spacer ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Position ◽  
Ribosomal Operon ◽  
Intragenomic Variation

Abstract Background: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. Results: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of thiscomplex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, IGS, and some intronic regions; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. Conclusions: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.

scholarly journals Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi

2019 ◽  
Author(s):  
Michael Bradshaw ◽  
Felix Grewe ◽  
Anne Thomas ◽  
Cody H. Harrison ◽  
Hanna Lindgren ◽  
...  
Keyword(s):  
Species Complex ◽  
Sequence Data ◽  
Dna Barcode ◽  
Intergenic Spacer ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Position ◽  
Phylogenetic Reconstructions ◽  
Ribosomal Operon ◽  
Intragenomic Variation

Abstract Background Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from approximate nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing.Results We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic reconstructions of the ITS, 28S, IGS, and some intronic regions; however, phylogenetic reconstructions based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed, previously unrecognized lineages in the nrDNA phylogeny.Conclusions The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited number of potentially polymorphic sites generally do not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution.

scholarly journals Taxonomic Position of Entomoparasitic Nematodes Isolated from Fleas in Gorno-Altai High-Mountain Natural Plague Focus

2018 ◽  
pp. 79-83
Author(s):  
E. G. Oglodin ◽  
E. G. Tokmakova ◽  
K. A. Nikiforov ◽  
A. V. Denisov ◽  
N. A. Sharapova ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Close Relation ◽  
Steppe Zone ◽  
Nucleotide Sequences ◽  
High Mountain ◽  
Separate Branch ◽  
Ribosomal Operon ◽  
Entomoparasitic Nematodes ◽  
First Time ◽  
Comparative Phylogenetic Analysis

Objective of the study was to investigate entomoparasitic nematodes from rodent fleas, collected in Gorno-Altai high-mountain natural plague focus in 2016–2017, with identification of their taxonomic status. Materials and methods. Given are the results of morphological and genetic analysis of entomoparasitic nematodes – parasites of fleas Amphipsylla primaris primaris living on flat-headed high-mountain voles Alticola strelzovi, fleas Rhadinopsylla li transbaicalica of Daurian pika Ochotona dauurica, fleas Rhadinopsylla dahurica, collected at the burrows of the rodents. Results and conclusions. Identified have been nucleotide sequences of ITS2 spacer region of ribosomal operon in entomoparasitic nematodes of three flea species: Amphipsylla primaris primaris, Rhadinopsylla li transbaicalica, and Rhadinopsylla dahurica. Based on comparative phylogenetic analysis and identified high percentage of homology of the stated nucleotide sequences (92–99 %), appurtenance to Rubzovinema spp. species and close relation to earlier proposed by us multi-host species Rubzovinema polyxenica from C. tesquorum, A. rossica, and C. secundus fleas from Volga-Ural steppe plague focus has been established. For the first time ever separate branch of evolution of entomoparasitic nematodes – flea parasites, represented by Rubzovinema ssp., has been identified. Determined has been wide spread of Rubzovinema ssp. nematodes in biocenoses of steppe zone of Russia across Precaspian territory and Altai Mountains. 

scholarly journals The occurrence of Anisakis larvae on hairtail, Trichiurus lepturus caught from the Pangandaran Waters, West Java, Indonesia

2021 ◽  
Vol 22 (3) ◽  
Author(s):  
NISA QUROTA AYUN ◽  
LUTFI SEPTIANA DEWI ◽  
MURWANTOKO MURWANTOKO ◽  
Eko Setyobudi
Keyword(s):  
Gastrointestinal Tract ◽  
Molecular Analysis ◽  
Abdominal Cavity ◽  
Its Region ◽  
Biological Indicator ◽  
Morphological Identification ◽  
Type I ◽  
West Java ◽  
Mean Intensity ◽  
Trichiurus Lepturus

Abstract. Ayun NQ, Dewi LS, Murwantoko, Setyobudi E. 2021. The occurrence of Anisakis larvae on hairtail, Trichiurus lepturus caught from the Pangandaran Waters, West Java, Indonesia. Biodiversitas 22: 1378-1384. This study aimed to investigate the prevalence, mean intensity, and type of Anisakis larvae infecting hairtail (Trichiurus lepturus) caught at Pangandaran Waters, West Java, Indonesia. It was conducted using 869 samples sourced from local fishermen. The parameters measured were the total length and weight of each T. lepturus. Furthermore, parasitological examination was carried out to investigate the occurrence of Anisakis larvae in the fishes. The selected samples of Anisakis were identified through morphological and molecular analysis. The results showed that the larvae were found either free in the abdominal cavity of the fishes or coiled and attached to the serosal layer of the gastrointestinal tract, gonad, liver, and muscle. The results showed that the larvae were found either free in the abdominal cavity of the fishes or coiled and attached to the serosal layer of the gastrointestinal tract, gonad, liver, and muscle. It also showed that their prevalence in the T. lepturus was at a moderate level (45.5%), with the mean intensity at 4.4 larvae/fish. Moreover, the larvae were mostly in the abdominal cavity (89%), as only a few were found in another part of the fishes. Morphological identification showed that the type of Anisakis present was type I, as they were characterized by the presence of mucron and ventriculus without caecum. Molecular analysis was carried out by sequencing the ITS region, and it confirmed that the nematode was Anisakis typica, a non-zoonotic parasite. These parasites were not present in the edible portion/muscle of the fishes, and had a relatively moderate prevalence and low intensity. Therefore, their presence posed a relatively low risk to human health. However, due to consumption patterns and the increasing popularity of seafood, being served raw or undercooked, the incidence of anisakiasis may increase in the future. In the other hand, the presence of these larvae might be used as a biological indicator for several ecological studies.

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