scholarly journals Confirmatory Evidence from 18S rRNA Gene Analysis for In Vivo Development of Propamidine Resistance in a Temporal Series ofAcanthamoeba Ocular Isolates from a Patient

1998 ◽  
Vol 42 (8) ◽  
pp. 2144-2145 ◽  
Author(s):  
Dolena R. Ledee ◽  
David V. Seal ◽  
Thomas J. Byers
Keyword(s):  
Mixed Infection ◽  
Dna Sequences ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gene Analysis ◽  
Rrna Gene ◽  
Temporal Series ◽  
Before And After

ABSTRACT DNA sequences of three 18S rRNA gene alleles present in trophozoites obtained before and after therapy forAcanthamoeba keratitis substantiate a previous report that the infection was due to a single Acanthamoeba strain. Thus, the possibility that propamidine resistance which developed during therapy was due to a mixed infection was ruled out.

scholarly journals Eukaryotic phylotypes in aquatic moss pillars inhabiting a freshwater lake in East Antarctica, based on 18S rRNA gene analysis

Polar Biology ◽  
2012 ◽  
Vol 35 (10) ◽  
pp. 1495-1504 ◽  
Author(s):  
Ryosuke Nakai ◽  
Takashi Abe ◽  
Tomoya Baba ◽  
Satoshi Imura ◽  
Hiroshi Kagoshima ◽  
...  
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Freshwater Lake ◽  
East Antarctica ◽  
Gene Analysis ◽  
Rrna Gene ◽  
Aquatic Moss ◽  
Moss Pillars

Morphology, morphogenesis, and molecular phylogeny of a new brackish water ciliate, Pseudourostyla cristatoides n. sp., from Songjiho lagoon on the coast of East Sea, South Korea

Zootaxa ◽  
2012 ◽  
Vol 3334 (1) ◽  
pp. 42 ◽  
Author(s):  
JAE-HO JUNG ◽  
KYUNG-MIN PARK ◽  
GI-SIK MIN
Keyword(s):  
South Korea ◽  
Body Length ◽  
Brackish Water ◽  
Body Shape ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Genetic Distances ◽  
Rrna Gene ◽  
Contractile Vacuoles

A new brackish water urostylid ciliate, Pseudourostyla cristatoides n. sp. was collected from Songjiho lagoon on the coast ofEast Sea, South Korea, and investigated based on morphology, morphogenesis, and 18S rRNA gene sequences.Pseudourostyla cristatoides is characterized by the following features: slender to elliptical body shape; colourless to dark greyin colour; size in vivo about 220–265 × 85–125μm; flexible and slightly contractile body with narrowly spaced extrusomes(trichocyst type) throughout the whole cell; 2 contractile vacuoles on left side of cell at about 25% and 75% of body length;84–115 adoral membranelles, 20–30 frontal cirri, 1 buccal cirrus, 2 frontoterminal cirri, 17–25 midventral pairs, 2pretransverse, 6–12 transverse cirri, 5–7 left and 4–5 right marginal rows, and 10–13 dorsal kineties; 30–106 macronuclearnodules and 3–5 micronuclei; brackish habitat (salinity 3–5‰). This new species is very similar to P. cristata, but distinguishedprimarily by contractile vacuoles (2 vs. 1 in number; positioned 25%, 75% of body length vs. ahead of mid-body), dorsalkineties (10–13 vs. 8), hyaline layer underneath pellicle (inconspicuous vs. conspicuous), habitat (brackish vs. freshwater), andparticipation of posterior cirri of rear corona in fronto-ventral-transverse cirral anlagen (yes vs. no). Additionally, intra-/inter-specific pairwise genetic distances of the 18S rRNA gene sequences supported that the Songjiho population is a novel species(intra-specific distances of 0.07–0.12% among three P. cristata populations vs. inter-specific distances of 0.93–1.00% between P. cristatoides and three P. cristata populations).

scholarly journals Molecular systematics of the Phyllachorales (ascomycota, fungi) based on 18S ribosomal DNA sequences

2003 ◽  
Vol 46 (3) ◽  
pp. 315-322 ◽  
Author(s):  
Denise Wanderlei-Silva ◽  
Eduardo Ramalho Neto ◽  
Richard Hanlin
Keyword(s):  
Molecular Systematics ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
The Other ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Parsimony Analysis

In order to evaluate the monophyly of the Phyllachorales from a molecular standpoint and elucidate its phylogenetic relationships with other orders, a segment of the 18S rRNA gene from several representatives of the Phyllachorales, including species of Glomerella, Phyllachora, Coccodiella (=Coccostroma), Sphaerodothis, Ophiodothella, as well as Magnaporthe was sequenced. Maximum Parsimony analysis revealed that the Phyllachorales was a polyphyletic assemblage of taxa. None of the other members of the Phyllachorales, which produced either a clypeus or stroma, clustered with Glomerella. Of the taxa examined, was Coccodiella the closest relative of Phyllachora. Magnaporthe was closely related to the Diaporthales. Our 18S rDNA data highly supported Glomerella being accommodated in a separate family.

scholarly journals An analysis on the divergence of Chironomid spp. based on the study of 18S rRNA and polytene chromosome organization in the species revealing the role of environment on speciation

2021 ◽  
Vol 82 (1) ◽  
Author(s):  
Sanjay Kumar Dey ◽  
Swapna Bhaduri ◽  
Trilochan Midya
Keyword(s):  
Polytene Chromosome ◽  
Dna Sequences ◽  
18S Rrna ◽  
Molecular Classification ◽  
18S Rrna Gene ◽  
Chromosome Band ◽  
Chromosome Organization ◽  
Rrna Gene ◽  
Molecular Architecture ◽  
Chironomid Species

Abstract Background Nine species of Chironomus evolved throughout the world were measured for their divergence with regard to their DNA sequences concerning 18S rRNA since it is conserved for a specific species. With the advancement of the field of molecular evolution, cytogenetics requires further correlation between molecular architecture and morphological features of a species to compare amongst others to decipher their role in speciation. Therefore, divergence of DNA sequences of the Chironomus were compared with differences in the polytene chromosome features of most of the species under this investigation to evaluate underlying correlation among them, if any, to finally establish a novel method of molecular classification broadly applicable in cytogenetics studies. Results When Chironomus javanus Kieffer was considered as a reference organism, an in silico pair-wise alignment of sequences for the 18S rRNA gene regions of the other eight different species of the same genus exhibited nucleotide sequence homology ranging from 67 to 98%. This divergence of the species under consideration might be due to environmental impact causing alteration of nitrogenous bases probably due to mismatch pairing in DNA replication. This may be suggested as a cause of evolution of species in nature. A concomitant study on the polytene chromosome band patterns of majority of these species belonging to this series also indicated a divergence ranging from 10% to 30%. Conclusions Sequence analysis based on 18S rRNA of nine species of Chironomus under this investigation shows a similarity in the polytene chromosome organization in most of the Chironomid species of the series. Hence, molecular divergence in the species is consistent with cytological difference among Chironomid species. Therefore, molecular data based on 18S rRNA and cytological characters based on the polytene chromosome features of the Chironomid species may be useful for their taxonomical recognition. Moreover, variations concerning two aspects of this study may be correlated to their environmental distinctions.

scholarly journals Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Claire Y. T. Wang ◽  
Emma L. Ballard ◽  
Zuleima Pava ◽  
Louise Marquart ◽  
Jane Gaydon ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Plasmodium Falciparum ◽  
18S Rrna ◽  
Drug Efficacy ◽  
18S Rrna Gene ◽  
Molecular Techniques ◽  
Qpcr Assay ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Blood Samples

Abstract Background Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials. Methods A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed. Results The reportable range was 1.50 to 6.50 log10 parasites/mL with a limit of detection of 2.045 log10 parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (Cq) units [0.137 log10 parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 Cq units [0.182 log10 parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log10 parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples. Conclusions The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals 18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tsuyoshi Watanabe ◽  
Satoshi Nagai ◽  
Yoko Kawakami ◽  
Taiga Asakura ◽  
Jun Kikuchi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
North Pacific ◽  
Western North Pacific ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gut Contents ◽  
Rrna Gene ◽  
Marine Snow ◽  
Chlorophyll Maximum

AbstractEel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

scholarly journals Molecular Characterization of Ciliate Diversity in Stream Biofilms

2008 ◽  
Vol 74 (6) ◽  
pp. 1740-1747 ◽  
Author(s):  
Andrew Dopheide ◽  
Gavin Lear ◽  
Rebecca Stott ◽  
Gillian Lewis
Keyword(s):  
18S Rrna ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Sequence Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Specific Pcr ◽  
Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

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