scholarly journals Natural hosts of the larvae of Nuttalliella sp. (N. namaqua?) (Acari: Nuttalliellidae)

2012 ◽  
Vol 79 (1) ◽  
Author(s):  
Ivan G. Horak ◽  
Heike Lutermann ◽  
Katarina Medger ◽  
Dmitry A. Apanaskevich ◽  
Conrad A. Matthee
Keyword(s):  
South Africa ◽  
Genomic Dna ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Limpopo Province ◽  
Rrna Gene ◽  
Mountain Range ◽  
Natural Hosts ◽  
Murid Rodents ◽  
Northern Cape

The first collection of unengorged and fully engorged larvae of Nuttalliella sp. (N. namaqua?) from the murid rodents Micaelamys namaquensis, Aethomys chrysophilus and Acomys spinosissimus in Limpopo Province and from M. namaquensis in the Northern Cape Province, South Africa, is documented. A total of nine larvae were collected from two M. namaquensis in the Soutpansberg mountain range in the Limpopo Province during April 2009. During the last week of September 2011, 221 larvae were collected from rodents at the same locality and 10 of 48 M. namaquensis, 6 of 12 Ae. chrysophilus and 3 of 14 Ac. spinosissimus were infested. One of the M. namaquensis harboured 53 larvae. Five larvae were collected from two M. namaquensis in the Northern Cape Province. Total genomic DNA was extracted from two larvae and a region of the 18S rRNA gene was sequenced for these. BLASTn searches revealed similarity between these specimens and the Nuttalliella sequences published on GenBank.

scholarly journals Genomic Profiling for Piroplasms in Feeding Ixodid Ticks in the Eastern Cape, South Africa

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1061
Author(s):  
Olusesan Adeyemi Adelabu ◽  
Benson Chuks Iweriebor ◽  
Anthony Ifeanyi Okoh ◽  
Larry Chikwelu Obi
Keyword(s):  
South Africa ◽  
Nested Pcr ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rhipicephalus Appendiculatus ◽  
Ixodid Ticks ◽  
Farm Animals ◽  
Homology Search ◽  
Rrna Gene ◽  
Eastern Cape

Importation of tick-infected animals and the uncontrollable migration of birds and wild animals across borders can lead to geographical expansion and redistribution of ticks and pathogen vectors, thus leading to the emergence and re-emergence of tick-borne diseases in humans and animals. Comparatively, little is known about the occurrence of piroplasms in ixodid ticks in the Eastern Cape, South Africa, thus necessitating this study, which is aimed at detecting piroplasms (Theileria and Babesia) from feeding tick samples collected from cattle, sheep, and goats in selected sites in the Eastern Cape, South Africa. A total of 1200 feeding ixodid ticks collected from farm animals at selected homesteads were first subjected to molecular identification using mitochondrial 12S ribosomal RNA (rRNA) gene by PCR and were further tested for the presence of piroplasms through amplification of the 18S rRNA gene via nested-PCR followed by sequencing of the PCR products. The results indicated that 853 (71.1%) corresponded to the genus Rhipicephalus, 335 (27.9%) corresponded to genus Amblyomma, and 12 (1%) corresponded to genus Haemaphysalis. Amblyomma hebraeum and Rhipicephalus appendiculatus were the most common identified ticks from this study. The 18S rRNA nested-PCR revealed that 44 (3.7%) samples were confirmed positive for Theileria. A homology search for the generated sequences revealed a high percentage identity of 98–98.9% similarity to T. buffeli, T. orientalis, and T. sergenti in the GenBank. Based on the results obtained herein, we conclude that there is a big diversity of Theileria species; therefore, we suggest that this research should cover more geographical areas in order to reveal the true prevalence of this pathogen in the studied area because this will be a great step in the possible prevention of an outbreak that could have devastating effects on livestock production and human health in both the studied areas and South Africa at large.

Diversity and distribution of nematodes associated with terrestrial slugs in the Western Cape Province of South Africa

2011 ◽  
Vol 86 (2) ◽  
pp. 215-221 ◽  
Author(s):  
J.L. Ross ◽  
E.S. Ivanova ◽  
W.F. Sirgel ◽  
A.P. Malan ◽  
M.J. Wilson
Keyword(s):  
South Africa ◽  
18S Rrna ◽  
Parasitic Nematode ◽  
Gene Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Western Cape ◽  
Western Cape Province ◽  
Rrna Gene Sequencing ◽  
Three New Species

AbstractA survey of nematodes associated with native and introduced species of terrestrial slugs was conducted in the Western Cape Province of South Africa, in order to gather new data regarding diversity and distribution. A total of 521 terrestrial slugs were collected from 35 localities throughout the Western Cape. All slugs were dissected and examined for the presence of internal nematodes. Extracted nematodes were identified using a combination of molecular (18S rRNA gene sequencing) and morphological techniques. Nematodes were found parasitizing slugs at 14 of the 35 sites examined, amounting to 40% of sample sites. Of all slugs, 6% were infected with nematodes. A total of seven species of nematode were identified in the province, includingAgfa flexilis,Angiostomasp.,Phasmarhabditissp. SA1,Phasmarhabditissp. SA2,Caenorhabditis elegans,Panagrolaimussp. andRhabditissp. Of these species, four were thought to be parasitic to slugs (A. flexilis, Angiostomasp.,Phasmarhabditissp. SA1 andPhasmarhabditissp. SA2), as opposed to forming necromenic or phoretic associations. Three new species of slug-parasitic nematode were identified during this study (Angiostomasp.,Phasmarhabditissp. SA1 andPhasmarhabditissp. SA2).

scholarly journals Sequence heterogeneity in the 18S rRNA gene within Theileria equi and Babesia caballi from horses in South Africa

2009 ◽  
Vol 159 (2) ◽  
pp. 112-120 ◽  
Author(s):  
Raksha Bhoora ◽  
Linda Franssen ◽  
Marinda C. Oosthuizen ◽  
Alan J. Guthrie ◽  
Erich Zweygarth ◽  
...  
Keyword(s):  
South Africa ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Theileria Equi ◽  
Babesia Caballi ◽  
Sequence Heterogeneity

scholarly journals Molecular Screen of Trichoderma Isolates

1970 ◽  
Vol 17 ◽  
pp. 117-122
Author(s):  
Amna Ali ◽  
Rukhsana Bajwa ◽  
Nasir Mehmood ◽  
Rasheda Jabeen
Keyword(s):  
Gene Targeting ◽  
Genomic Dna ◽  
18S Rrna ◽  
Rflp Analysis ◽  
Stem Bark ◽  
18S Rrna Gene ◽  
Negative Control ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Trichoderma Species

Context: In the last few decades an ample array of molecular techniques has been introduced to obtain new disposition for the classification of Trichoderma species. Today the concern of scientists is either in the direction of gene targeting or ribotyping, the newest fingerprinting tool for genomic DNA that contain all or part of the genes coding for 18S rRNA in eukaryotes.Objectives: To take advantage of advanced molecular techniques for phylogenetic analysis of indigenous isolates of Trichoderma to comprehend our knowledge of this genus by supplementing the phenotypic identification.Materials and Methods:  Genomic DNA of twenty four isolates of Trichoderma species (T. harzianum, T. hamatum, T. koningii and T. pseudokoningii) were extracted by CTAB method and indicated band of ~15Kb on 0.8% agarose gel. Quality of DNA was determined by obtaining absorbance ratio (260/280) in the range of 1.7-1.9. Restriction fragment length polymorphism (RFLP) analyses were performed by using two restriction endonulease enzymes i.e., BamHI and HindIII. The BamHI represented results in the range of 500bp-750bp. 18S rRNA gene targeting was further carried out through optimization in ribotyping analysis.Results: The DNA bands of 24 isolates of Trichoderma species were compared with marker DNA bands and indicated the presence of genomic DNA intact band of ~15Kb. The ratio of absorbance 260/280nm (1.8-1.9 for pure DNA preparations) provided an estimate of the purity of the DNA RFLP analysis, along with the negative control of twenty four different isolates of Trichoderma species subjected to restriction using BamHI enzyme. The rRNA gene amplified band was observed at 600bp in the case of T. hamatum isolate (S. cumini stem bark, FCBP accession number 769) while in remaining isolates bands were in slightly smeared form. Furthermore, rRNA gene amplification conditions were optimized by altering different Tm and MgCl2 concentrations. Conclusion: The genomic DNA can serve as long term storage of information. Therefore advance molecular techniques can be used to study the variability in the genome of organism. RFLP are the initial steps for screening the genome of any organism.Key words: Trichoderma; DNA; RFLP; restriction endonuleases; 18S rRNA.DOI: 10.3329/jbs.v17i0.7117J. bio-sci. 17: 117-122, 2009

scholarly journals Cryptosporidium genotypes in children and calves living at the wildlife or livestock interface of the Kruger National Park, South Africa

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Nada Abu Samra ◽  
Ferran Jori ◽  
Simone M. Cacciò ◽  
John Frean ◽  
Bhavani Poonsamy ◽  
...  
Keyword(s):  
South Africa ◽  
National Park ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Kruger National Park ◽  
Rrna Gene ◽  
Genotype Distribution ◽  
Cryptosporidium Hominis ◽  
Hospital System ◽  
Pcr Targeting

Cryptosporidium infection is one of the most common causes of parasitic diarrhoea worldwide in cattle and humans. In developing countries, human cryptosporidiosis is most prevalent during early childhood and links between zoonotic infection and animal related activities have been demonstrated. This study investigated the prevalence and species/genotype distribution of Cryptosporidium among children (< 5 years) and calves (< 6 months) living in a rural farming area adjacent to the Kruger National Park in South Africa, where interactions between humans and wild and domestic animals are known to occur. Cryptosporidium oocysts were detected in 8/143 stool samples of children recruited within the hospital system (5.6%; 95% CI 2.4%, 10.7%) and in 2/352 faecal samples of calves (0.6%; 95% CI 0.1%, 2.0%) using the modified Ziehl–Neelsen (MZN) staining technique. Microscopy positive samples from children were further analysed by PCR targeting the 18S rRNA gene and identified as Cryptosporidium hominis (3/4) and Cryptosporidium meleagridis (1/4). Regardless of the microscopy outcome, randomly selected samples (n = 36) from calves 0–4 months of age were amplified and sequenced at the 18S rRNA gene using nested PCR. Two calves tested positive (5.6%; 95% CI 1.7%, 18.7%), and revealed the presence of Cryptosporidium parvum and Cryptosporidium bovis. The detection of only two zoonotic species (C. parvum in one calf and C. meleagridis in one child) suggests that zoonotic cryptosporidiosis is not currently widespread in our study area; however, the potential exists for amplification of transmission in an immunocompromised population.Keywords: Cryptosporidium; children; calves; South Africa; genotyping; GP60 subtyping

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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