scholarly journals Genetic Diversity and Emerging Zoonotic Onchocerca Species in Human Populations in Taraba State, Nigeria

2021 ◽  
Author(s):  
Danlami Akafyi ◽  
Iliya Shehu Ndams ◽  
Ishaya Haruna Nock ◽  
Gloria Chechet ◽  
Renz Alfons ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pcr Amplification ◽  
Human Populations ◽  
Rrna Gene ◽  
Species Identity ◽  
Multiple Sequence ◽  
Centrifuge Tube ◽  
Polymerase Chain ◽  
Endemic Areas ◽  
Skin Snips

Abstract Background: A better understanding of parasite population genetic processes in specific biogeography is needed to support onchocerciasis elimination goals. The genetic diversity of Onchocerca microfilariae was explored by amplifying a fragment of the 16S rRNA gene in the endemic area in Taraba State, Nigeria, Methods: Eight (8) communities were selected including six onchocerciasis endemic communities with records of ivermectin treatment having been annually distributed for 10 to 16 years, and two non-onchocerciasis endemic areas. The participants were 211 from endemic and 110 from non-endemic areas as control. Skin snips were taken from consenting participants by convenience sampling methods using a sterile sclera punch, from males and females residing within the communities for ten years and above or since birth, microfilaria and residual skin snips were preserved in RNALater® in a 1.5 ml micro-centrifuge tube. DNA was extracted from microfilariae recovered and from those in residual skin snip specimens. Polymerase Chain Reaction (PCR) amplification using specific primers for 16S genes was done to detect the identity of Onchocerca species. The amplified products were sequenced and analyzed for species identity. Results: Multiple sequence alignment and phylogenetic analysis results showed distinct diversity of two sample sequences (G49_O.v. Gashaka and Y02_O.v. Yorro) from other samples from the study area and other regions, indicating emergence of a new polymorphic strain of O. volvulus. Report of a preliminary case of emerging zoonosis of O. ochengi infection in human (skin snips) sample (O. ochengi G44) in this study. Conclusions: It is clear there is genetic diversity of Onchocerca species and emerging zoonosis in the study site. We suggest further investigation on the extent and potentials of emerging zoonotic onchocerciasis by O. ochengi, in the light of cattle, Simulium vectors, environmental and humans overlap in the study area.

scholarly journals Genetic diversity of Ehrlichia canisstrains from naturally infected dogs in Rio de Janeiro, Brazil

2014 ◽  
Vol 23 (3) ◽  
pp. 301-308 ◽  
Author(s):  
Renata Fernandes Ferreira ◽  
Aloysio de Mello Figueiredo Cerqueira ◽  
Tatiana Xavier de Castro ◽  
Eliane de Oliveira Ferreira ◽  
Felipe Piedade Gonçalves Neves ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rio De Janeiro ◽  
Complete Sequence ◽  
Rrna Gene ◽  
Hybrid Strain ◽  
The Us ◽  
Polymerase Chain ◽  
Hematological Manifestations ◽  
Pcr Targeting ◽  
The 16S Rrna Gene

The aim of this study was to characterize Ehrlichia canis strains from naturally infected dogs in Rio de Janeiro, Brazil. In addition, all the clinical and hematological findings observed in these dogs were reported. PCR targeting the 16S rRNA gene was used for diagnostic purposes, and the TRP19 and TRP36 genes were sequenced to evaluate the genetic diversity. Fifteen samples were positive for E. canis. The polymerase chain reaction for the TRP19 gene resulted in 11 amplicons (11/15), which were cloned into the pGEM-T easy vector for sequencing. The complete sequence of TRP19 gene was compared to those in the GenBank, revealing high identicalness. Phylogenetic analysis on the TRP36 gene sequences demonstrated two distinct strains from two dogs, named 56C and 70C. The 56C strain was grouped with the strain Cuiaba 16, which is a hybrid strain formed by Brazilian and US genogroups; and the 70C strain was grouped with other strains of the US genogroup, thus suggesting that there are at least two genogroups of E. canis in Rio de Janeiro (US and Brazilian). Those animals, in which the 70C and 56C strains were isolated, showed distinct clinical and hematological manifestations of 1the disease. The appearance of different genotypes may express new phenotypes, thus resulting in different forms of presentation of the disease and making its diagnosis more complex.

scholarly journals Genetic Diversity in Ficus Sycomorus L. Species (Moraceae) Using Rapd and Irap Markers

2013 ◽  
Vol 59 (3) ◽  
pp. 120-130 ◽  
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Pcr Amplification ◽  
Coastal Regions ◽  
Chain Reaction ◽  
Marker Index ◽  
Irap Markers ◽  
Irap Marker ◽  
Repeatability And Reproducibility ◽  
Ficus Sycomorus ◽  
Polymerase Chain

Abstract This study was conducted in order to assess accuracy, repeatability and reproducibility of the RAPD and IRAP techniques for determining the genetic variability in 10 Ficus sycomorus L. genotypes grown in the coastal regions of Syria. Thirty-six RAPD primers applied gave 352 discernible loci, of which 252 (71.59%) were polymorphic. Polymerase chain reaction (PCR) amplification with 36 RAPD primers gave an average of 9.778 selected markers/primers, with a maximum of 21 (OPA18) and a minimum of five (OPG11, OPK12 and OPT18). The amplification with 22 IRAP primers (single or combination) generated 178 bands, of which 151 (84.83%) were polymorphic, with an average of 11.125 selected markers/ primer, with a maximum of 17 (IRAP-TDK11F) and a minimum of seven (BREP1F+BREP1R, IRAP-TDK1F+IRAP- TDK1R and IRAP-TDK2F+IRAP-TDK2R). In the present investigation, the IRAP marker was more efficient than the RAPD assay, where the latter exhibited a lower marker index (MI) average (1.629) compared with the IRAP technique (2.941). Otherwise, F. sycomor4 genotype showed the highest dissimilarity compared with other genotypes studied in this investigation. Based upon the estimated percent disagreement values (PDV), we can suggest that there are three subspecies present among the 10 samples tested.

scholarly journals Molecular and Symptom Analysis Reveal the Presence of New Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1413-1418 ◽  
Author(s):  
Kanchan Nasare ◽  
Amit Yadav ◽  
Anil K. Singh ◽  
K. B. Shivasharanappa ◽  
Y. S. Nerkar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Saccharum Officinarum ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequence Alignments ◽  
High Sequence Similarity ◽  
Multiple Sequence ◽  
Very High

A total of 240 sugarcane (Saccharum officinarum) plants showing phenotypic symptoms of sugarcane grassy shoot (SCGS) disease were collected from three states of India, Maharashtra, Karnataka, and Uttar Pradesh. Phytoplasmas were detected in all symptomatic samples by the polymerase chain reaction (PCR) amplification of phytoplasma-specific 16S rRNA gene and 16S-23S rRNA spacer region (SR) sequences. No amplification was observed when DNA from asymptomatic plant samples was used as a template. Sixteen samples were selected on the basis of phenotypic symptoms and geographic location, and cloning and sequencing of the 16S rRNA and spacer regions were performed. Multiple sequence alignments of the 16S rRNA sequences revealed that they share very high sequence similarity with phytoplasmas of rice yellow dwarf, 16SrXI. However, the 16S-23S rRNA SR sequence analysis revealed that while the majority of phytoplasmas shared very high (>99%) sequence similarity with previously reported sugarcane phytoplasmas, two of them, namely BV2 (DQ380342) and VD7 (DQ380343), shared relatively low sequence similarity (79 and 84%, respectively). Therefore, these two phytoplasmas may be previously unreported ones that cause significant yield losses in sugarcane in India.

scholarly journals Morphological and Molecular Identification of Fusarium oxysporum Sch. Isolated From Guava Wilt in Bangladesh

2012 ◽  
Vol 41 (1) ◽  
pp. 49-54 ◽  
Author(s):  
M Zakir Hussain ◽  
MA Rahman ◽  
Mohammad Nurul Islam ◽  
MA Latif ◽  
MA Bashar
Keyword(s):  
Fusarium Oxysporum ◽  
Psidium Guajava ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Species Identity ◽  
Specific Primers ◽  
Polymerase Chain ◽  
Serious Disease ◽  
Species Specific

Wilt of guava plants (Psidium guajava L.) is a serious disease in Bangladesh. Sixteen isolates of Fusarium oxysporum Sch. were collected from the root and stem fragments of guava plants growing in six districts of Bangladesh. Species identity was based on the colony character, nature of conidiogenous cell, morphology of microconidia, macroconidia and chlamydospores. Eleven isolates were confirmed as F. oxysporum through polymerase chain reaction (PCR) using species specific primers designed from the conserved regions of 18S rRNA gene. DOI: http://dx.doi.org/10.3329/bjb.v41i1.11082 Bangladesh J. Bot. 41(1): 49-54, 2012 (June)

scholarly journals Assessment of genetic structure and diversity of Erodium (Geranaiceae) species

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 507-520
Author(s):  
Lejing Lin ◽  
Li Lin ◽  
Abdul Waheed
Keyword(s):  
Genetic Diversity ◽  
Isolation By Distance ◽  
Pcr Amplification ◽  
Molecular Data ◽  
Mantel Test ◽  
Test Results ◽  
Species Characteristics ◽  
Polymerase Chain ◽  
Morphological And Molecular Data ◽  
Genetic Structure And Diversity

Erodium Aiton (Geraniaceae) with 75 species is distributed in all continents except Antarctic. Its main diversification center is Mediterranean region with 62 species. The genetic diversity was assessed through Sequence-related amplified polymorphism. To uncover genetic diversity and species characteristics in Erodium species, were studied through a combination of morphological and molecular data. 70 individuals related to seven Erodium were collected in 7 provinces. A total of 96 (Number of total loci) (NTL) DNA bands were produced through polymerase chain reaction amplifications (PCR) amplification of seven Erodium species. These bands were produced with the combinations of six selective primers. The total number of amplified fragments ranged from 10 to 25. The genetic similarities between seven species are estimated from 0.70 to 0.85. Clustering results showed two major clusters. This study also detected a significant signature of isolation by distance (Mantel test results). Present results showed that sequence-related amplified polymorphism have the potential to identify and decipher genetic affinity in Erodium species. Current results have implications in biodiversity and conservation programs. Besides this, present results could pave the way for selecting suitable ecotypes for forage and pasture purposes in Iran.

scholarly journals The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

2021 ◽  
Vol 9 (5) ◽  
pp. 898
Author(s):  
Ren Min Oh ◽  
Elena Bollati ◽  
Prasha Maithani ◽  
Danwei Huang ◽  
Benjamin J. Wainwright
Keyword(s):  
Coral Reef ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Benthic Organisms ◽  
Polymerase Chain ◽  
Microbial Change ◽  
The 16S Rrna Gene

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

scholarly journals DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

2014 ◽  
Vol 80 (16) ◽  
pp. 5116-5123 ◽  
Author(s):  
Luisa W. Hugerth ◽  
Hugo A. Wefer ◽  
Sverker Lundin ◽  
Hedvig E. Jakobsson ◽  
Mathilda Lindberg ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Pcr Primers ◽  
Primer Design ◽  
Taxonomic Composition ◽  
Degenerate Primer ◽  
Rrna Gene ◽  
Multiple Sequence ◽  
High Coverage ◽  
Shotgun Metagenomics ◽  
Taxonomic Range

ABSTRACTThe taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571–1579, 2011,http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.

scholarly journals Prevalence and Subtypes of Blastocystis in Alpacas, Vicugna pacos in Shanxi Province, China

2020 ◽  
Vol 58 (2) ◽  
pp. 181-184 ◽  
Author(s):  
Ye-Ting Ma ◽  
Qing Liu ◽  
Shi-Chen Xie ◽  
Xiao-Dong Li ◽  
Yuan-Yuan Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pcr Amplification ◽  
Northern China ◽  
Small Subunit ◽  
Human Infection ◽  
Shanxi Province ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Potential Source ◽  
And Gender

<i>Blastocystis</i>, an enteric protist, has been reported to be an important cause of protozoal gastrointestinal manifestations in humans and animals worldwide. Animals harboring certain <i>Blastocystis</i> subtypes (STs) may serve as a potential source of human infection. However, information about the prevalence and genetic diversity of <i>Blastocystis</i> in alpacas is limited. In the present study, a total of 366 fecal samples from alpacas in Shanxi Province, northern China, were examined for <i>Blastocystis</i> by PCR amplification of the small subunit rRNA gene, followed by sequencing and phylogenetic analysis. The prevalence of <i>Blastocystis</i> in alpacas was 23.8%, and gender difference in the prevalence of <i>Blastocystis</i>was observed. The most predominant <i>Blastocystis</i> ST was ST10, followed by ST14 and ST5. The detection of ST5, a potentially zoonotic genotype, indicates that alpacas harboring ST5 could be a potential source of human infection with <i>Blastocystis</i>. These data provide new insight into the prevalence and genetic diversity of <i>Blastocystis</i> in alpacas.

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