scholarly journals Molecular Characterization of Fasciola spp. from a Donkey (Equus asinus) Using Partial Sequencing of cox1 and nad1

2020 ◽  
Author(s):  
Mohammad ASADPOUR ◽  
Hassan SHARIFIYAZDI ◽  
Mohammad MOAZENI ◽  
Seyed Hossein MALEKPOUR
Keyword(s):  
Fasciola Hepatica ◽  
Sequence Data ◽  
Nucleotide Polymorphisms ◽  
Equus Asinus ◽  
The World ◽  
Mitochondrial Sequences ◽  
Southwestern Iran ◽  
Fasciola Spp ◽  
Important Parasite

Background: Fasciola hepatica as an important parasite affects health of humans and animals in some tropical and subtropical areas of the world, including Iran. Little is known about the molecular diversity of Fasciola in Equidae. Therefore, this study aimed to characterize the genetic polymorphisms among parasites. Methods: Eight adult Fasciola spp. isolates were collected from a working donkey after necropsy in Shiraz, southwestern Iran, in 2018. Primarily, various parameters were measured morphologically. Subsequently, DNA was extracted from each fluke and molecular markers of cytochrome C oxidase (cox1) and NADH dehydrogenase 1(nad1) from individual Fasciola isolates were amplified using PCR assay and sequence data were employed for molecular and phylogenetic analysis. Genetic diversity between isolates was evaluated by comparing the sequences of these two mitochondrial regions. Results: Based on the morphological and analyzed mitochondrial sequences, all of eight donkey isolates (100%) were identified as F. hepatica. Moreover, nine and five nucleotide polymorphisms were identified in the cox1and nad1 region sequences, respectively. Conclusion: Accordingly, phylogenetic data revealed five and four haplotypes among donkey isolates based on the cox1and nad1 markers. Similarly, some of these haplotypes have been previously reported from different host species in Iran as well as all around the world.

scholarly journals Characterization of a profilin-like protein from Fasciola hepatica

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10503
Author(s):  
Jessica Wilkie ◽  
Timothy C. Cameron ◽  
Travis Beddoe
Keyword(s):  
Fasciola Hepatica ◽  
Recombinant Expression ◽  
Tegument Proteins ◽  
Novel Treatments ◽  
The World ◽  
Eukaryotic Organisms ◽  
Novel Drug ◽  
First Time ◽  
Important Disease

Fasciola hepatica is the causative agent of fasciolosis, an important disease of humans and livestock around the world. There is an urgent requirement for novel treatments for F. hepatica due to increasing reports of drug resistance appearing around the world. The outer body covering of F. hepatica is referred to as the tegument membrane which is of crucial importance for the modulation of the host response and parasite survival; therefore, tegument proteins may represent novel drug or vaccine targets. Previous studies have identified a profilin-like protein in the tegument of F. hepatica. Profilin is a regulatory component of the actin cytoskeleton in all eukaryotic cells, and in some protozoan parasites, profilin has been shown to drive a potent IL-12 response. This study characterized the identified profilin form F. hepatica (termed FhProfilin) for the first time. Recombinant expression of FhProfilin resulted in a protein approximately 14 kDa in size which was determined to be dimeric like other profilins isolated from a range of eukaryotic organisms. FhProfilin was shown to bind poly-L-proline (pLp) and sequester actin monomers which is characteristic of the profilin family; however, there was no binding of FhProfilin to phosphatidylinositol lipids. Despite FhProfilin being a component of the tegument, it was shown not to generate an immune response in experimentally infected sheep or cattle.

scholarly journals Molecular Characterization of Fasciola and Dicrocoelium Species Isolated from Ruminant Livestock in Qazvin, Iran

2020 ◽  
Vol 20 (5) ◽  
pp. 737-742
Author(s):  
Mojtaba Shahnazi ◽  
Maryam Ebadi ◽  
Zahra Abbaspoor ◽  
Elham Hajialilo ◽  
Amir Javadi ◽  
...  
Keyword(s):  
Fasciola Hepatica ◽  
Pcr Amplification ◽  
Decisive Role ◽  
28S Rdna ◽  
Rdna Gene ◽  
Molecular Approaches ◽  
Infected Liver ◽  
Fasciola Spp ◽  
The City

Introduction: Fascioliasis and dicrocoeliasis are the most frequent zoonotic diseases with increasing human health problems in different parts of Iran. Two species, Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica), are spread in the country. Molecular approaches have a decisive role in identifying both the species. The aim of this study was to detect Fasciola spp. and Dicrocoelium spp. by amplifying the ITS-2 and 28S rDNA gene sequence. Methods: Overall, 30 infected liver samples were collected from the livestock of Qazvin, Iran. The adult flukes were collected from different livestock. DNA extraction and PCR amplification of ribosomal RNA gene region (ITS2) and 28S rDNA gene fragment were conducted and a phylogenetic tree was constructed. Results: All the isolates obtained from the cattle (No: 7) and 82.6% (No: 19) of sheep isolates were infected with F. hepatica species, whereas 17.4% (No: 4) of sheep isolates were infected with F. gigantica. It was also shown that F. hepatica was the predominant species of Fasciola present in the region. All the specimens were infected with Dicrocoelium dendriticum (D. dendriticum). Conclusion: Both the species of Fasciola were found in Qazvin. D. dendriticum was the sole infecting species of the Dicrocoelium genus in the livestock of the city of Qazvin. Further research studies are needed to determine the intermediate host of the parasites in the region.

Molecular Characterization of Fasciola spp. from Some Parts of Iran

2020 ◽  
Author(s):  
Hamid HASANPOUR ◽  
Reza FALAK ◽  
Saied Reza NADDAF ◽  
Santiago MAS-COMA ◽  
Mohammad Bagher ROKNI ◽  
...  
Keyword(s):  
East Asia ◽  
Fasciola Hepatica ◽  
Genetic Difference ◽  
Rflp Analysis ◽  
Restriction Fragment Polymorphism ◽  
Pcr Rflp ◽  
The World ◽  
Liver Flukes ◽  
Fasciola Spp ◽  
Different Parts

Background: Identification of liver flukes, Fasciola hepatica, and Fasciola gigantica by morphometric parameters is not always reliable due to the overlapping measurements. This study aimed to characterize the liver flukes of animals from different parts of Iran by the genetic markers, ITS1, and COXI. Methods: We collected flukes from infected livestock in six provinces of Iran from Sep to Nov 2016. The flukes were identified by amplification of a 680 bp sequence of ITS1 locus followed by a restriction fragment polymorphism (RFLP) assay. The genetic diversity among isolates was evaluated by amplification and sequencing of a 493 bp fragment of the COXI gene. Results: We obtained 38 specimens from Khuzestan, 22 from Tehran, 10 from Isfahan, 10 from Mazandaran, 4 from Kurdistan, and 3 from Ardabil provinces. PCR-RFLP analysis revealed two patterns, representing F. hepatica, and F. gigantica. Fifty specimens from cattle and sheep exhibited F. hepatica pattern and 37 from the cattle, sheep, buffalo, and goat that of F. gigantica. The phylogeny based on COXI revealed two distinct clades separating F. hepatica from F. gigantica. In our phylogeny, the Iranian F. gigantica isolates showed a distinct separation from the African flukes, while grouped with the East Asia specimens demonstrating a common ancestor. The F. hepatica isolates clustered with the flukes from different parts of the world, including East Asia, Europe, and South America. Conclusion: The present study revealed a substantial genetic difference between F. gigantica populations of Asia and Africa, while F. hepatica isolates from different parts of the world shared high similarities.

scholarly journals Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health

2020 ◽  
Vol 12 (s1) ◽  
Author(s):  
Rami Kantor ◽  
John P. Fulton ◽  
Jon Steingrimsson ◽  
Vladimir Novitsky ◽  
Mark Howison ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Hiv Transmission ◽  
Sequence Data ◽  
The United States ◽  
Viral Sequence ◽  
Transmission Networks ◽  
New Methods ◽  
Hiv Epidemic ◽  
The World

AbstractGreat efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks.

scholarly journals The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nathalie Raharimalala ◽  
Stephane Rombauts ◽  
Andrew McCarthy ◽  
Andréa Garavito ◽  
Simon Orozco-Arias ◽  
...  
Keyword(s):  
Wild Species ◽  
Illegitimate Recombination ◽  
Recombination Mechanism ◽  
Comparative Analyses ◽  
Robusta Coffee ◽  
Caffeine Synthase ◽  
The World ◽  
Decaffeinated Coffee ◽  
Chromosome Level

AbstractCaffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

2021 ◽  
Vol 7 (3) ◽  
pp. 47
Author(s):  
Marios Lange ◽  
Rodiola Begolli ◽  
Antonis Giakountis
Keyword(s):  
Disease Onset ◽  
Cancer Genome ◽  
Driver Mutations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Coding Regions ◽  
Functional Variants ◽  
Coding Variants ◽  
Clinical Potential

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.

scholarly journals Theoretical and Empirical Characterization of Water as a Factor: Examples and Related Issues with the World Trade Model

Water ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 459
Author(s):  
Ignacio Cazcarro ◽  
Albert E. Steenge
Keyword(s):  
World Trade ◽  
Low Cost ◽  
Virtual Water ◽  
Considerable Change ◽  
Water Research ◽  
Trade Model ◽  
The World ◽  
Main Model ◽  
Selection Of

This article originates from the theoretical and empirical characterization of factors in the World Trade Model (WTM). It first illustrates the usefulness of this type of model for water research to address policy questions related to virtual water trade, water constraints and water scarcity. It also illustrates the importance of certain key decisions regarding the heterogeneity of water and its relation to the technologies being employed and the prices obtained. With regard to WTM, the global economic input–output model in which multiple technologies can produce a “homogeneous output”, it was recently shown that two different mechanisms should be distinguished by which multiple technologies can arise, i.e., from “technology-specific” or from “shared” factors, which implies a mechanism-specific set of prices, quantities and rents. We discuss and extend these characterizations, notably in relation to the real-world characterization of water as a factor (for which we use the terms technology specific, fully shared and “mixed”). We propose that the presence of these separate mechanisms results in the models being sensitive to relatively small variations in specific numerical values. To address this sensitivity, we suggest a specific role for specific (sub)models or key choices to counter unrealistic model outcomes. To support our proposal we present a selection of simulations for aggregated world regions, and show how key results concerning quantities, prices and rents can be subject to considerable change depending on the precise definitions of resource endowments and the technology-specificity of the factors. For instance, depending on the adopted water heterogeneity level, outcomes can vary from relatively low-cost solutions to higher cost ones and can even reach infeasibility. In the main model discussed here (WTM) factor prices are exogenous, which also contributes to the overall numerical sensitivity of the model. All this affects to a large extent our interpretation of the water challenges, which preferably need to be assessed in integrated frameworks, to account for the main socioeconomic variables, technologies and resources.

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