scholarly journals Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
David Squarre ◽  
Yukiko Nakamura ◽  
Kyoko Hayashida ◽  
Naoko Kawai ◽  
Herman Chambaro ◽  
...  
Keyword(s):  
18S Rrna ◽  
Variable Region ◽  
Parasite Community ◽  
Sequence Variant ◽  
Cattle Population ◽  
Bioinformatics Pipeline ◽  
High Resolution Data ◽  
Sequencing Platform ◽  
Wild Dog ◽  
Hyper Variable Region

Abstract Background Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when a common ecological niche is shared in the presence of a competent vector. Method To investigate piroplasm diversity in wildlife and the cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using the Illumina MiSeq sequencing platform and amplicon sequence variant (ASV)-based bioinformatics pipeline to generate high-resolution data that discriminate sequences down to a single nucleotide difference. Results A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella, were identified in wildlife and the cattle population from the study area. Theileria species were detected in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to the cattle population in the wildlife-livestock interface. Conclusion We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate a possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

scholarly journals Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

2020 ◽  
Author(s):  
David Squarre ◽  
Yukiko Nakamura ◽  
Kyoko Hayashida ◽  
Naoko Kawai ◽  
Herman Chambaro ◽  
...  
Keyword(s):  
18S Rrna ◽  
Variable Region ◽  
Parasite Community ◽  
Sequence Variant ◽  
Cattle Population ◽  
Bioinformatics Pipeline ◽  
High Resolution Data ◽  
Sequencing Platform ◽  
Wild Dog ◽  
Hyper Variable Region

Abstract Background: Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when common ecological niche is shared in the presence of a competent vector. Method: To investigate piroplasm diversity in wildlife and cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using illumina MiSeq sequencing platform and amplicon sequence variant (ASV) based bioinformatics pipeline to generate high resolution data which discriminate sequences down to a single nucleotide difference. Results: A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella, were identified in wildlife and cattle population from the study area. Theileria species were detected in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to cattle population in the wildlife-livestock interface.Conclusion: We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

scholarly journals Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

2020 ◽  
Author(s):  
David Squarre ◽  
Yukiko Nakamura ◽  
Kyoko Hayashida ◽  
Naoko Kawai ◽  
Herman Chambaro ◽  
...  
Keyword(s):  
18S Rrna ◽  
Variable Region ◽  
Parasite Community ◽  
Sequence Variant ◽  
Cattle Population ◽  
Bioinformatics Pipeline ◽  
Vector Method ◽  
Sequencing Platform ◽  
Wild Dog ◽  
Hyper Variable Region

Abstract Background Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when common ecological niche is shared in the presence of a competent vector. Method To investigate piroplasm diversity in parasite community in wildlife and cattle population of the greater Kafue ecosystem , we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using illumina MiSeq sequencing platform and amplicon sequence variant (ASV) based bioinformatics pipeline to generate high resolution data which discriminate sequences down to a single nucleotide difference. Results A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia , Theileria , Hepatozoon and Colpodella, were identified in wildlife and cattle population from the study area. Theileria species were observed in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to cattle population in the wildlife-livestock interface. Conclusion We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

scholarly journals Investigation of the Piroplasm Diversity Circulating in Wildlife and Cattle of the Greater Kafue Ecosystem, Zambia

2020 ◽  
Author(s):  
David Squarre ◽  
Yukiko Nakamura ◽  
Kyoko Hayashida ◽  
Naoko Kawai ◽  
Herman Chambaro ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Illumina Miseq ◽  
Parasite Community ◽  
Diagnostic Tools ◽  
Sequence Variant ◽  
Illumina Miseq Sequencing ◽  
Cattle Population ◽  
Miseq Sequencing ◽  
Bioinformatics Pipeline ◽  
Cryptic Variation

Abstract Background: Piroplasms are vector-borne intracellular haemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasms from wildlife to livestock is underlined when common ecological niche is shared in the presence of a competent vector. Method: To investigate piroplasm cryptic variation and diversity in parasite community in wildlife and cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using illumina MiSeq sequencing platform and amplicon sequence variant (ASV) based bioinformatics pipeline to generate high resolution data which discriminate sequences down to a single nucleotide difference. Results: A parasite community of 45 ASVs and 23 piroplasm species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella was identified in wildlife and cattle population from the study area. Conclusion: The findings of this study demonstrates the usefulness of illumina MiSeq sequencing to describe the area specific parasite composition, which is critical in the application and establishment of disease control strategy options of ideal diagnostic tools to employ and area specific vaccine development.

scholarly journals Old gene, new phenotype: splice-altering variants in CEACAM16 cause recessive non-syndromic hearing impairment

2018 ◽  
Vol 55 (8) ◽  
pp. 555-560 ◽  
Author(s):  
Kevin T Booth ◽  
Kimia Kahrizi ◽  
Hossein Najmabadi ◽  
Hela Azaiez ◽  
Richard JH Smith
Keyword(s):  
Hearing Loss ◽  
Hearing Impairment ◽  
Loss Of Function ◽  
Bioinformatics Pipeline ◽  
Exon 2 ◽  
Reading Frame ◽  
Sequencing Platform ◽  
Syndromic Hearing Impairment ◽  
Generation Sequencing

BackgroundHearing loss is a genetically and phenotypically heterogeneous disorder.ObjectivesThe purpose of this study was to determine the genetic cause underlying the postlingual progressive hearing loss in two Iranian families.MethodsWe used OtoSCOPE, a next-generation sequencing platform targeting >150 genes causally linked to deafness, to screen two deaf probands. Data analysis was completed using a custom bioinformatics pipeline, and variants were functionally assessed using minigene splicing assays.ResultsWe identified two homozygous splice-altering variants (c.37G>T and c.662–1G>C) in the CEACAM16 gene, segregating with the deafness in each family. The minigene splicing results revealed the c.37G>T results in complete skipping of exon 2 and loss of the AUG start site. The c.662–1G>C activates a cryptic splice site inside exon 5 resulting in a shift in the mRNA reading frame.ConclusionsThese results suggest that loss-of-function mutations in CEACAM16 result in postlingual progressive hearing impairment and further support the role of CEACAM16 in auditory function.

scholarly journals Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

2012 ◽  
Vol 78 (11) ◽  
pp. 3958-3965 ◽  
Author(s):  
Amy Koid ◽  
William C. Nelson ◽  
Amy Mraz ◽  
Karla B. Heidelberg
Keyword(s):  
Community Composition ◽  
18S Rrna ◽  
Northwest Pacific ◽  
Rrna Gene ◽  
Gene Transcript ◽  
Acid Extraction ◽  
Phylogenetic Groups ◽  
Northwest Pacific Ocean ◽  
Clone Libraries ◽  
Sequencing Platform

ABSTRACTEukaryotic marine microbes play pivotal roles in biogeochemical nutrient cycling and ecosystem function, but studies that focus on the protistan biogeography and genetic diversity lag-behind studies of other microbes. 18S rRNA PCR amplification and clone library sequencing are commonly used to assess diversity that is culture independent. However, molecular methods are not without potential biases and artifacts. In this study, we compare the community composition of clone libraries generated from the same water sample collected at the San Pedro Ocean Time Series (SPOTs) station in the northwest Pacific Ocean. Community composition was assessed using different cell lysis methods (chemical and mechanical) and the extraction of different nucleic acids (DNA and RNA reverse transcribed to cDNA) to build Sanger ABI clone libraries. We describe specific biases for ecologically important phylogenetic groups resulting from differences in nucleic acid extraction methods that will inform future designs of eukaryotic diversity studies, regardless of the target sequencing platform planned.

scholarly journals Activation of leukocyte rolling by the cysteine-rich domain and the hyper-variable region of HF3, a snake venom hemorrhagic metalloproteinase

FEBS Letters ◽  
2008 ◽  
Vol 582 (28) ◽  
pp. 3915-3921 ◽  
Author(s):  
Milene C. Menezes ◽  
Adriana F. Paes Leme ◽  
Robson L. Melo ◽  
Carlos A. Silva ◽  
Maisa Della Casa ◽  
...  
Keyword(s):  
Snake Venom ◽  
Variable Region ◽  
Leukocyte Rolling ◽  
Rich Domain ◽  
Hyper Variable Region ◽  
Cysteine Rich Domain

scholarly journals Population Genetics of New Zealand Nemadactylus macropterus (tarakihi) and Characterisation of their Mitochondrial Genome

2021 ◽  
Author(s):  
◽  
Alexander Halliwell
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Genetic Structure ◽  
East Coast ◽  
Demographic History ◽  
Variable Region ◽  
Sequencing Data ◽  
Commercial Catch ◽  
History Of ◽  
Hyper Variable Region

<p>Nemadactylus macropterus, commonly known as tarakihi in New Zealand is highly regarded by commercial and recreational fishers and considered a taonga by iwi and customary fisheries. For many years N. macropterus was New Zealand’s second most important commercial catch and is currently the third most valuable inshore commercial finfish fishery in which 90% is consumed by the domestic market. However, despite the apparent importance, relatively little is known about the population structure of the N. macropterus. In 2017 the first fully quantitative stock assessment was conducted on the east coast N. macropterus fisheries as one stock. Alarmingly, the east coast fishery was estimated to be 15.9% of the unexploited spawning biomass and predicted to have been declining for the past thirty years. In an effort to rebuild the fishery, several rebuild plans have been purposed and commercial catch limits have been reduced. In order to rebuild and successfully manage a viable future N. macropterus fishery, an understanding of demographic connectivity and genetic connectivity among N. macropterus populations is essential.  The overall goal of this thesis research was to investigate the population genetic structure, genetic diversity and demographic history of N. macropterus using fish sampled from around New Zealand. This was achieved by analysing hyper variable region one of mitochondrial DNA for 370 N. macropterus collected from 14 locations. No genetic differentiation was observed among the 14 locations, an indication that N. macropterus have a panmictic genetic structure. Furthermore, N. macropterus display a relatively high level of genetic diversity and appear to have a large stable population with a long evolutionary history. The Bayesian skyline analysis indicates the N. macropterus historic population has gone through two expansions. The mostly likely cause of this is an expansion before and after the last glacial maximum.  The genetic diversity and demographic history of N. sp was also studied using samples collected from around the Three Kings Islands of New Zealand. The complete mitochondrial genome of N. macropterus was reconstructed from bulk DNA sequencing data and a set of specific mtDNA primers were developed to amplify hyper variable region one. The DNA sequencing data provided by these primers with the addition of published control region sequences was used to reconstruct the Nemadactylus phylogeny.</p>

scholarly journals SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data

2021 ◽  
Author(s):  
Luca De Sabato ◽  
Gabriele Vaccari ◽  
Arnold Knijn ◽  
Giovanni Ianiro ◽  
Ilaria Di Bartolo ◽  
...  
Keyword(s):  
Open Source ◽  
Viral Genome ◽  
Rapid Analysis ◽  
Easy Access ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Bioinformatics Analyses ◽  
Sequencing Platform ◽  
Link Type ◽  
And Storage

AbstractBackgroundSince its first appearance in December 2019, the novel Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), spread worldwide causing an increasing number of cases and deaths (35,537,491 and 1,042,798, respectively at the time of writing, https://covid19.who.int). Similarly, the number of complete viral genome sequences produced by Next Generation Sequencing (NGS), increased exponentially. NGS enables a rapid accumulation of a large number of sequences. However, bioinformatics analyses are critical and require combined approaches for data analysis, which can be challenging for non-bioinformaticians.ResultsA user-friendly and sequencing platform-independent bioinformatics pipeline, named SARS-CoV-2 RECoVERY (REconstruction of CoronaVirus gEnomes & Rapid analYsis) has been developed to build SARS-CoV-2 complete genomes from raw sequencing reads and to investigate variants. The genomes built by SARS-CoV-2 RECoVERY were compared with those obtained using other software available and revealed comparable or better performances of SARS–CoV2 RECoVERY. Depending on the number of reads, the complete genome reconstruction and variants analysis can be achieved in less than one hour. The pipeline was implemented in the multi-usage open-source Galaxy platform allowing an easy access to the software and providing computational and storage resources to the community.ConclusionsSARS-CoV-2 RECoVERY is a piece of software destined to the scientific community working on SARS-CoV-2 phylogeny and molecular characterisation, providing a performant tool for the complete reconstruction and variants’ analysis of the viral genome. Additionally, the simple software interface and the ability to use it through a Galaxy instance without the need to implement computing and storage infrastructures, make SARS-CoV-2 RECoVERY a resource also for virologists with little or no bioinformatics skills.Availability and implementationThe pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) is implemented in the Galaxy instance ARIES (https://aries.iss.it).

Molecular Characterization of Hyper Variable Region of The Classical & Very Virulent Egyptian Isolates of Ibdv

2004 ◽  
Vol 1 (1) ◽  
pp. 40-40
Author(s):  
Seharn A. El-Zeedy . ◽  
Dalia A. Abd El-Moat . ◽  
H. A. Hussien . ◽  
M. A. Shalaby .
Keyword(s):  
Molecular Characterization ◽  
Variable Region ◽  
Hyper Variable Region
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