scholarly journals Occurrence and molecular characterization of Cryptosporidium sp. in sheep

2017 ◽  
Vol 38 (4) ◽  
pp. 1917 ◽  
Author(s):  
Alessandra Snak ◽  
Flavia Roberta Smiderle ◽  
Nelson Luis Mello Fernandes ◽  
Arielle Aparecida Lara ◽  
Felipe Gustavo Garcia ◽  
...  
Keyword(s):  
Farm Animals ◽  
Management Systems ◽  
Management Styles ◽  
Sequencing Data ◽  
Worldwide Distribution ◽  
Stool Samples ◽  
Sheep Feces ◽  
Fecal Smear ◽  
Cattle And Sheep

Considered a zoonosis of utmost importance, cryptosporidiosis has a worldwide distribution and can infect mammals, birds, reptiles, and amphibians. It is caused by a highly resistant protozoan present in the environment and can cause death in immunosuppressed individuals and pups, as well as in farm animals such as cattle and sheep, generating losses. The aim of this study was to investigate the presence of Cryptosporidium spp. in sheep feces from the farms of Western Paraná, which have different management styles, and compare the results with their respective management methods. One hundred and forty-four stool samples were collected (69 from Property 1 and 75 from Property 2) and analyzed using a fecal smear on slides after staining by the modified Ziehl-Neelsen method. Samples tested positive by this method were subjected to nested PCR and the products obtained were sent for sequencing to determine the species. While 82.60% of the samples from Property 1 were tested positive, only 36% of the samples from Property 2 were tested positive. On analyzing the sequencing data, it was observed that the Cryptosporidium species of samples from Property 1 showed high similarity to Cryptosporidium xiaoi and those from Property 2, to Cryptosporidium ubiquitum. The reason for divergence in results can be attributed to differences in management systems adopted by each property, thus showing the importance of detecting carrier animals, as they can contaminate the environment, especially the water sources, and spread the disease to humans and other animals.

Genetic characterization of Echinococcus granulosus in camels, cattle and sheep from the south-east of Iran indicates the presence of the G3 genotype

2011 ◽  
Vol 86 (3) ◽  
pp. 263-270 ◽  
Author(s):  
E. Hajialilo ◽  
M.F. Harandi ◽  
M. Sharbatkhori ◽  
H. Mirhendi ◽  
S. Rostami
Keyword(s):  
Echinococcus Granulosus ◽  
Human Isolate ◽  
Sequencing Data ◽  
Intermediate Hosts ◽  
Eastern Iran ◽  
East Of Iran ◽  
Animal Hosts ◽  
Polymerase Chain ◽  
Cattle And Sheep

AbstractEchinococcus granulosus, the aetiologic agent of cystic echinococcosis (CE), is one of the most important zoonotic helminthes worldwide. Isolates of the parasite show considerable genetic variation in different intermediate hosts. Several genotypes and species are described in different eco-epidemiological settings. This study investigated E. granulosus genotypes existing in livestock and humans from the province of Kerman, located in south-eastern Iran, using sequencing data of cox1 and nad1 mitochondrial genes. Fifty-eight E. granulosus isolates, including 35 from sheep, 11 from cattle, 9 from camels and 3 from goats, were collected from slaughterhouses throughout Kerman. One human isolate was obtained from a surgical case of CE. Mitochondrial cox1 and nad1 regions were amplified using polymerase chain reaction (PCR) and 38 isolates were sequenced. Genotypes G1 (73.7%), G3 (13.2%) and G6 (13.1%) were identified from the isolates. G1 was the most common genotype from sheep (86.7%), cattle (80%), camels (44.4%) and goats (100%). Sheep, cattle and camels were also found to be infected with the G3 genotype (buffalo strain). The human isolate was identified as the G6 genotype. Results showed that the G3 genotype occurred in different animal hosts in addition to G1 and G6 genotypes.

scholarly journals Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1338
Author(s):  
Morgan E. Meissner ◽  
Emily J. Julik ◽  
Jonathan P. Badalamenti ◽  
William G. Arndt ◽  
Lauren J. Mills ◽  
...  
Keyword(s):  
Error Rates ◽  
Maximum Depth ◽  
Sequencing Data ◽  
Background Error ◽  
High Background ◽  
Immunodeficiency Virus ◽  
User Friendly ◽  
Viral Mutagenesis ◽  
Hiv 1

Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

Genetic characterization of novel polymorphic microsatellite markers for Epilobium nankotaizanense (Onagraceae), an endemic and threatened herb in Taiwan

2021 ◽  
pp. 1-4
Author(s):  
Yu-Wei Tseng ◽  
Chi-Chun Huang ◽  
Chih-Chiang Wang ◽  
Chiuan-Yu Li ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Natural Populations ◽  
Conservation Strategy ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
The Family ◽  
Conservation Genetic ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Abstract Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

scholarly journals Molecular Characterization of Giardia duodenalis in Children and Adults Sampled in Algeria

2020 ◽  
Vol 9 (1) ◽  
pp. 54
Author(s):  
Salem Belkessa ◽  
Daniel Thomas-Lopez ◽  
Karim Houali ◽  
Farida Ghalmi ◽  
Christen Rune Stensvold
Keyword(s):  
Real Time ◽  
Molecular Characterization ◽  
Real Time Pcr ◽  
Intestinal Parasites ◽  
Giardia Duodenalis ◽  
Specific Pcr ◽  
Stool Samples ◽  
Pcr Targeting ◽  
Assemblage B

The molecular epidemiology of giardiasis in Africa remains unclear. A study was carried out across four hospitals in Algeria. A total of 119 fecal samples from 55 children, 37 adults, and 27 individuals of undetermined age, all scored positive for intestinal parasites by microscopy, and were screened by real-time PCR for Giardia. Molecular characterization of Giardia was performed by assemblage-specific PCR and PCR targeting the triose phosphate isomerase gene (tpi). Of the 119 samples, 80 (67%) were Giardia-positive by real-time PCR. For 48 moderately-highly real-time PCR-positive samples, tpi genotyping assigned 22 samples to Assemblage A and 26 to Assemblage B. Contrary to Assemblage A, Assemblage B exhibited substantial genetic diversity and allelic heterozygosity. Assemblage-specific PCR proved to be specific for discriminating Assemblage A or B but not as sensitive as tpi genotyping. We confirmed that real-time PCR is more sensitive than microscopy for detecting Giardia in stool samples and that robust amplification and sequencing of the tpi gene is feasible when moderate-to-strongly real-time PCR-positive samples are used. This study is one of the few performed in Africa providing genotyping data on Giardia infections in humans. Both assemblages A and B were commonly seen and not associated with specific sociodemographic data.

scholarly journals Multiplex Real-Time PCR Method for Simultaneous Identification and Toxigenic Type Characterization of Clostridium difficile From Stool Samples

2015 ◽  
Vol 35 (3) ◽  
pp. 306-313 ◽  
Author(s):  
Abdullah Kilic ◽  
Mohammad J. Alam ◽  
Naradah L. Tisdel ◽  
Dhara N. Shah ◽  
Mehmet Yapar ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Real Time ◽  
Real Time Pcr ◽  
Stool Samples ◽  
Pcr Method ◽  
Simultaneous Identification

scholarly journals Haemoglobin polymorphism in selected farm animals: A review

2014 ◽  
Vol 30 (3) ◽  
pp. 377-390 ◽  
Author(s):  
S.S.A. Egena ◽  
R.O. Alao
Keyword(s):  
Genetic Improvement ◽  
Raw Materials ◽  
Farm Animals ◽  
Starch Gel Electrophoresis ◽  
Gene Frequencies ◽  
Starch Gel ◽  
And Performance ◽  
Polypeptide Chains ◽  
Degree Of Similarity

Biochemical diversity or polymorphism is the occurrence of varieties attributed to biochemical differences which are under genetic control. It has created a leeway for the genetic improvement of farm animals. This is because it can be used as a useful tool for the characterization of livestock breeds and population. This way, the degree of similarity or differences within and between breeds can be ascertained and this differences or similarity are important raw materials for genetic improvement of animals. Data obtained on gene frequencies and genotypes through polymorphism study makes it not only possible to compare the gene stocks of animals, the possible effects of the genes on reproductive and performance traits, but also study genetic variability under different environmental conditions of selection. This study was carried out to review haemoglobin (Hb) polymorphism in selected farm animals with the view of finding out the type of polymorphism observed by starch gel electrophoresis due to variation in the amino acid sequence in the polypeptide chains of Hb. The review showed clearly that there is a gene-controlled diversity in the different farm animals considered. This could serve as a reference point for future studies earmarked for the improvement of the animals possibly via marker-assisted selection.

scholarly journals Molecular characterization of hookworm spp. isolated from food handlers, Khartoum, Sudan: A cross-sectional study

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 662
Author(s):  
Tarig A. Gamar ◽  
Hassan H. Musa ◽  
Hisham N. Altayb ◽  
Mohamed H. Mohamed ◽  
Adam D. Abakar
Keyword(s):  
Public Health ◽  
Molecular Characterization ◽  
Molecular Probe ◽  
Hookworm Infection ◽  
Food Handlers ◽  
The Public ◽  
Necator Americanus ◽  
Link Type ◽  
Stool Samples

Background: Hookworms infect the intestines, cause an itchy rash, respiratory and gastrointestinal problems, and eventually iron deficiency (anaemia) due to the ongoing loss of blood. The objectives of this study were to assess the prevalence and molecular characterization of hookworms isolated from food handlers attending the Public Health Laboratories in Khartoum state, Sudan, for annual check-ups, and to assess the efficiency of PCR as molecular probe for hookworm infection. Methods: A total of 350 foods handlers’ participant's stool samples who were not suspected to be infected with hookworms were studied. Conventional methods were applied to make an early diagnosis. Stool samples were collected from public health laboratories (the public health lab in the Medical Commission) of Khartoum State; Omdurman locality, Khartoum North locality and Khartoum locality between October 2016 and April 2017. Specific identification was made by PCR on specimens identified as positive by Baermann’s technique, which were then sequence and genotyped Results: The prevalence of hookworms in the stool samples of food-handlers was 1.43%. One larval specimen recovered by Baermann’s technique was confirmed to be Necator americanus by PCR. PCR also confirmed that Necator americanus was the common species isolated from four further specimens. The results of DNA sequencing for Necator americanus were deposited in NCBI GenBank under the following accession numbers: sample 91, MH035824; sample 92, MH035825; sample 294, MH035826; and sample 319 MH035827. Conclusion: PCR was found to be effective for confirmation of the diagnosis of hookworm infection and can aid the clinician in initiating prompt and appropriate antiparasite therapy.

scholarly journals Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data

2018 ◽  
Author(s):  
Arghavan Bahadorinejad ◽  
Ivan Ivanov ◽  
Johanna W Lampe ◽  
Meredith AJ Hullar ◽  
Robert S Chapkin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sample Size ◽  
Microbial Communities ◽  
State Of The Art ◽  
Metagenomic Data ◽  
Data Sets ◽  
Sequencing Data ◽  
Sample Data

AbstractWe propose a Bayesian method for the classification of 16S rRNA metagenomic profiles of bacterial abundance, by introducing a Poisson-Dirichlet-Multinomial hierarchical model for the sequencing data, constructing a prior distribution from sample data, calculating the posterior distribution in closed form; and deriving an Optimal Bayesian Classifier (OBC). The proposed algorithm is compared to state-of-the-art classification methods for 16S rRNA metagenomic data, including Random Forests and the phylogeny-based Metaphyl algorithm, for varying sample size, classification difficulty, and dimensionality (number of OTUs), using both synthetic and real metagenomic data sets. The results demonstrate that the proposed OBC method, with either noninformative or constructed priors, is competitive or superior to the other methods. In particular, in the case where the ratio of sample size to dimensionality is small, it was observed that the proposed method can vastly outperform the others.Author summaryRecent studies have highlighted the interplay between host genetics, gut microbes, and colorectal tumor initiation/progression. The characterization of microbial communities using metagenomic profiling has therefore received renewed interest. In this paper, we propose a method for classification, i.e., prediction of different outcomes, based on 16S rRNA metagenomic data. The proposed method employs a Bayesian approach, which is suitable for data sets with small ration of number of available instances to the dimensionality. Results using both synthetic and real metagenomic data show that the proposed method can outperform other state-of-the-art metagenomic classification algorithms.

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