Search results for " Phylogenetic analysis"

showing 10 items of 19 documents

Genetic structure and molecular variability of grapevine fanleaf virus in sicily

2021

Grapevine fanleaf virus (GFLV) is one of the main causes of grapevine fanleaf degeneration disease (GFDD) and is present in almost all areas where grapevine is cultivated. In this work, we ascertained the presence and spread of GFLV in different commercial vineyards in four Sicilian provinces (Italy), and its genetic structure and molecular variability were studied. In detail, a total of 617 grapevine samples of 11 autochthonous grapevine cultivars were collected in 20 commercial vineyards. Preliminary screening by serological (DAS-ELISA) and molecular (RT-PCR) analyses for ArMV (arabis mosaic virus) and GFLV detection were conducted. Results obtained showed the absence of ArMV in all the s…

0106 biological sciencesGFLVAgriculture (General)molecular variabilityGFLV; grapevine disease; molecular variability; DAS-ELISA; RT-PCR; phylogenetic analysisRT-PCRPlant Science01 natural sciencesS1-972Arabis mosaic virus03 medical and health sciencesCultivar030304 developmental biology0303 health sciencesPhylogenetic treebiologyphylogenetic analysisSettore AGR/12 - Patologia VegetaleGrapevine fanleaf virusbiology.organism_classificationlanguage.human_languageSettore AGR/03 - Arboricoltura Generale E Coltivazioni ArboreeHorticulturegrapevine diseaseGenetic structurelanguageDAS-ELISAAgronomy and Crop ScienceSicilian010606 plant biology & botanyFood Science
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High genetic stability of potato yellow mosaic Panama virus infecting tomato in Panama

2018

The relevant regions in Panama involved in commercial tomato production, including the Chiriqui, Veraguas, Herrera, Los Santos and Panama Oeste provinces, were surveyed for the distribution and genetic diversity of potato yellow mosaic Panama virus (PYMPV) in the growing seasons of 2011 and 2012. A total of 28 tomato plots were surveyed and 314 individual tomato plants were sampled. DNA was extracted from each plant for a subsequent rolling circle amplification (RCA) analysis, to confirm the presence of begomovirus infections. The samples displaying a positive RCA reaction were subsequently analysed by PCR with a specific primer pair to identify PYMPV. This virus was detected in samples col…

0301 basic medicineCloningGenetic diversityVeterinary medicinePanamaBegomovirusfood and beveragesBegomovirus . Rolling circle amplification . Single-strand conformation polymorphism . Phylogenetic analysis . Solanum lycopersicumSettore AGR/12 - Patologia VegetaleSingle-strand conformation polymorphismPlant ScienceBiologybiology.organism_classificationVirus03 medical and health sciences030104 developmental biologyRolling circle replicationPotato yellow mosaic Panama virus
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Evaluation of HIV transmission clusters among natives and foreigners living in Italy

2020

We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2&ndash

0301 basic medicineMalelcsh:QR1-502SubtypeHIV InfectionsmigrantsBioinformatics; Cluster detection; Drug resistance testing; Human immunodeficiency virus (HIV); Migrants; Molecular epidemiology; Phylogenetic analysis; Risk factors; Subtypes; Transmission networks and clusters; Adult; Cohort Studies; Female; Genotype; HIV Infections; HIV-1; Humans; Italy; Male; Middle Aged; Sexual and Gender Minorities; pol Gene Products Human Immunodeficiency Virus; Emigrants and Immigrants; Phylogenylcsh:MicrobiologyMen who have sex with menCohort StudiesSexual and Gender Minorities0302 clinical medicineGenotypehuman immunodeficiency virus (HIV); molecular epidemiology; phylogenetic analysis; migrants; cluster detection; transmission networks and clusters; subtypes; drug resistance testing; risk factors; bioinformaticsMedicinerisk factors030212 general & internal medicinepol Gene ProductsHiv transmissionPhylogenySubtypesPhylogenetic analysisTransmission (medicine)subtypesvirus diseasesHuman immunodeficiency virus (HIV)bioinformaticsMiddle AgedTransmission networks and clustersCluster detectionInfectious DiseasesItalyMolecular epidemiologyCohortFemaleHuman Immunodeficiency VirusCohort studyAdultmedicine.medical_specialtyGenotypeBioinformaticsEmigrants and ImmigrantsMigrantsArticleNO03 medical and health sciencesPhylogenetic analysiVirologyHumansBioinformaticMolecular epidemiologybusiness.industryPublic healthphylogenetic analysisMigrantDrug resistance testingSettore MED/17030104 developmental biologyRisk factorspol Gene Products Human Immunodeficiency Virustransmission networks and clustersTransmission networks and clusters.HIV-1Risk factorbusinessDemography
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Yeasts vectored by migratory birds collected in the Mediterranean island of Ustica and description of Phaffomyces usticensis f.a. sp. nov., a new spe…

2014

Nine yeast species belonging to genera Candida , Cryptococcus , Phaffomyces , Rhodotorula and Wickerhamomyces , and one species of Aureobasidium genus were isolated from the cloaca of migratory birds. Candida glabrata and C. inconspicua were the species most frequently isolated and Wickerhamomyces sylviae , which has recently been described as a new species isolated from bird cloaca, was again found. The majority of isolates showed the ability to grow up to 40 °C and/or at pH 3.0, two environmental conditions typical of the digestive tract of birds. The phylogenetic analysis of the D1/D2 domain of 26S rRNA gene placed the cultures of Phaffomyces in a new lineage that differed from the close…

Cactaceaephenotypic characterizationMolecular Sequence DataCryptococcusAureobasidiumRhodotorulaApplied Microbiology and BiotechnologyMicrobiologyNew species Yeast birdsBirdscactus-yeastMediterranean IslandsWickerhamomycesAscomycotaGenusPhaffomyces usticensis sp. novBotanyAnimalsPhylogenyRibosomalPhylogenetic treebiologyCandida glabrataphylogenetic analysisGeneral Medicinebiology.organism_classificationnovel speciesDelichon urbicumSettore AGR/11 - Entomologia Generale E ApplicataPhenotypeRNA RibosomalCactusRNADelichon urbicum; Phaffomyces usticensis sp. nov.; cactus-yeast; novel species; phenotypic characterization; phylogenetic analysis; Animals; Ascomycota; Birds; Cactaceae; Mediterranean Islands; Molecular Sequence Data; Phenotype; Phylogeny; RNA RibosomalSettore AGR/16 - Microbiologia Agraria
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Generic revision of Cypricercinae McKenzie, 1971 (Crustacea, Ostracoda), with the description of three new genera and one new species and a phylogene…

2009

The Cypricercinae are one of the most speciose subfamilies of non-marine ostracods, with more than 170 described species, mostly from the tropics. Although the identity of the subfamily as such is clear, because of the presence of unifying characters such as the Triebel’s loop in the attachment of the caudal ramus, the supra-specific taxonomy of this group has long been confused because of lack of good generic and tribal characters. Here, the generic characters of the Cypricercinae are revised. Eleven genera are retained in this subfamily, including three new genera: Bradleytriebella n. gen., Nealecypris n. gen. and Pseudostrandesia n. gen. Tanycypris siamensis n. sp. is described from Thai…

Cypricercinae Ostracoda Taxonomy Generic revision Phylogenetic analysis
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Phylogenetic analyses of Fusarium graminearum strains from cereals in Italy, and characterisation of their molecular and chemical chemotypes

2014

The Fusarium graminearum species complex (FGSC) is a pathogen of durum wheat and other cereals worldwide. The complex consists of at least 15 species that can produce various mycotoxins, including trichothecenes, associated with human and animals toxicoses. In particular, deoxynivalenol (DON), nivalenol (NIV) and their different acetylated derivatives can be produced by the different chemotypes of the complex. In this study, 90 strains, isolated mainly from wheat in Italy and belonging to the FGSC, were assessed for their phylogeny and their chemotype and trichothecene genotype. Almost all strains of the FGSC belonged to F. graminearum sensu stricto, whereas two strains were F. cortaderiae…

FusariumSpecies complexbiologyPhylogenetic treeChemotypephylogenetic analysisTrichothecenePlant Sciencechemotype; F. graminearum complex; Italy; phylogenetic analysis.biology.organism_classificationF. graminearum complexchemistry.chemical_compoundGibberella zeaechemistryItalyPhylogeneticsBotanyMycotoxinAgronomy and Crop Sciencechemotype
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PHYLOGENETIC ANALYSIS OF HBV INFECTION IN SICILY: IS THE EPIDEMIOLOGY CHANGING?

2010

HCV Epidemiology Phylogenetic analysis
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Correction: Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns …

2020

The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic mult…

HeredityBiochemistryGeographical LocationsSongbirdsPleistocene EpochAfrica NorthernEnergy-Producing OrganellesPhylogenyData ManagementMultidisciplinaryQuaternary PeriodGeographyFossilsQRPhylogenetic AnalysisGeologyBiodiversityBiological EvolutionFossil CalibrationMitochondriaPhylogeneticsEuropeGenetic MappingPhylogeographyBiogeographyMedicineCellular Structures and OrganellesResearch ArticleGenetic MarkersComputer and Information SciencesMitochondria ; Fossil calibration ; Haplotypes ; Europe ; Phylogenetic analysis ; Phylogeography ; Paleogenetics ; Pleistocene epochScienceBioenergeticsDNA MitochondrialGeneticsAnimalsEvolutionary SystematicsTaxonomyEvolutionary BiologyPopulation BiologyEcology and Environmental SciencesBiology and Life SciencesPaleontologyCorrectionGenetic VariationGeologic TimeCell BiologyHaplotypesPeople and PlacesEarth SciencesCenozoic EraPaleogeneticsPopulation Genetics
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Viral Sequence Analysis of Occult HBV Infection and Its Reactivation in Immunosuppressed Patients

2012

Mechanisms associated with reactivation of hepatitis B virus (HBV) in patients with occult HBV infection (OBI) remain unclear. In some cases immunosuppression is an enhancer of viral replication. However, not all patients with OBI who undergo immunosuppression experience reactivation. This study explores the role of viral heterogeneity as a determinant of occult HBV reactivation. HBV genotype, mutation patterns and quasispecies were assessed by sequencing the PreS/S region of 16 patients with OBI undergoing chemotherapy, 3 of whom experienced a OBI reactivation. The latter were also assessed at the time of reactivation. Phylogenetic analysis identified low nucleotide and amino acid diversit…

MaleHepatitis B virusSettore MED/07 - Microbiologia E Microbiologia ClinicaSettore MED/12 - GastroenterologiaGenotypeoccult HBV HBV reactivation phylogenetic analysismolecular epidemiologyGenetic VariationSequence Analysis DNAHepatitis BImmunocompromised HostDNA ViralHumansFemaleRetrospective Studies
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Phylogenetic Analysis of isolates from new cases of HBV infection in Southern Italy.

2012

The level of endemicity of hepatitis B virus (HBV) infections in Italy is low and genotype D infections predominant. New HBV strains may however be introduced as a result of movements of people from regions of high endemicity. The aim of the present study was to determine whether strains from new cases of acute hepatitis B detected in southern Italy were due to endemic or new HBV strains. We studied 34 isolates from patients with acute hepatitis B infection, and 35 from chronic hepatitis B patients. A phylogenetic analysis of preS/S region was done by comparing the sequences from the acute and chronic cases with references sequences. The study showed that 44% of strain from acute hepatitis …

Microbiology (medical)AdultMalemedicine.medical_specialtyHepatitis B virusSettore MED/07 - Microbiologia E Microbiologia ClinicaGenotypeBiologymedicine.disease_causeMicrobiologyLiver diseaseEpidemiologyGenotypeGeneticsmedicineHumansMolecular BiologyEcology Evolution Behavior and SystematicsPhylogenyAgedHepatitis B virusAged 80 and overMolecular EpidemiologySettore MED/12 - GastroenterologiaMolecular epidemiologyPhylogenetic treeSequence Analysis DNAHepatitis BMiddle Agedmedicine.diseaseHepatitis BVirologyInfectious DiseasesItalyImmunologyDNA ViralFemaleViral hepatitisHBV genotypes molecular epidemiology Acute HBV infection phylogenetic analysis
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