Consulta: subjectFacets:"Genotyping"
Registros recuperados: 56
Data/hora: 09/06/2024 06:35:19

Genetic differentiation between Cinta Senese and commercial pig breeds using microsatellite
Provedor de dados: 69
Autores: Scali,Monica; Vignani,Rita; Bigliazzi,Jacopo; Paolucci,Elisa; Bernini,Andrea; Spiga,Ottavia; Niccolai,Neri; Cresti,Mauro.
Background: Cinta Senese (CS) is an autochthonous Tuscan breed, which risked extinction since the ‘60s. Results: Monitoring the genetic variability of the actual population by use of DNA molecular markers is essential to address a correct breeding policy, finalized to obtain the race preservation and its fitness in the future. 17 SSRs autosomal markers and 1 associated to the X chromosome were used to genotype 86 individuals belonging to the CS and 12 belonging to two main white races Landrace (L), Large White (LW) and crosses between LW and L and L and CS widespread in Tuscany and used in the recent past to obtain hybrids with the CS. Conclusions: A dendrogram of similarity measures the relative genetic distance between individuals in the population. Data...
Tipo: Journal article
Palavras-chave: Cinta Senese; Genetic diversity; Genotyping; Microsatellites; Sus scrofa.
Ano: 2012
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582012000200001

Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis
Provedor de dados: 69
Autores: Arias,Renée S; Stetina,Salliana R; Scheffler,Brian E.
Currently, a large number of microsatellites are available for Rotylenchulus reniformis (reniform nematode); however, two barriers exist for genotyping samples from different geographical areas. The limited amount of nucleic acids obtained from single nematodes which would require their multiplication to obtain enough DNA for testing; and the strictly regulated transport of live samples and multiplication in greenhouse for being a plant pathogen. Whole-genome amplification (WGA) of samples consisting of one and five dead gravid females with their associated egg masses was successfully performed on disrupted tissue using three commercial kits. DNA yield after WGA ranged from 0.5 to 8 Âµg and was used to test 96 microsatellite markers we previously developed...
Tipo: Journal article
Palavras-chave: Genotyping; Reniform nematode; SSR; STR; WGA.
Ano: 2011
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000300014

Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana)
Provedor de dados: 69
Autores: De Villiers,Santie M; Michael,Vincent N; Manyasa,Eric O; Saiyiorri,Annis N; Deshpande,Santosh.
Background Genetic diversity of finger millet (Eleusine coracana), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic diversity. The markers were evaluated to determine (1) how efficiently they amplified target loci during high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3) polymorphism and ability to discern genetic diversity within the tested finger millet germplasm. Results Across 88 samples, the 52...
Tipo: Journal article
Palavras-chave: Diversity analysis; SSR markers; Genotyping.
Ano: 2015
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000200003

DNA from tissues of young mice is optimal for genotyping
Provedor de dados: 69
Autores: Picazo,María G; García-Olmo,Dolores C.
Background Genotyping of mice is a common procedure in animal facilities. The aim of this study was to compare the quantity and quality of DNA extracted from samples obtained from young mice (YM; 10 d old) and adult mice (AM; 12 weeks old). We collected samples from the tail and ear of YM and AM. We also sampled blood, check cells (via buccal swabs), hair and fecal pellets of AM, and biopsied distal phalanx of YM. We isolated DNA using commercial kits and determined concentrations and purity by spectrophotometry. The integrity of DNA was evaluated by agarose-gel electrophoresis and polymerase chain reaction (PCR). Results DNA in all samples was amplified successfully but the intensities of bands after electrophoresis was heterogeneous. In general, tissues...
Tipo: Journal article
Palavras-chave: DNA extraction; Genotyping; Mouse.
Ano: 2015
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000200004

SSR genetic diversity assessment of popular pigeonpea varieties in Malawi reveals unique fingerprints
Provedor de dados: 69
Autores: Njung'e,Vincent; Deshpande,Santosh; Siambi,Moses; Jones,Richard; Silim,Said; De Villiers,Santie.
Background: Pigeonpea (Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family and the only cultivated species in the genus Cajanus. It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, it is grown as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant quality reduction and yield losses. In this study, 48 polymorphic SSR markers were used to assess the diversity among all pigeonpea varieties cultivated in Malawi to determine if a genetic fingerprint could be identified to distinguish the popular varieties. Results: A total of 212 alleles were observed with an average of 5.58 alleles...
Tipo: Journal article
Palavras-chave: Genetic variation; Genotyping; Microsatellites; Seed purity.
Ano: 2016
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300008

RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
Provedor de dados: 69
Autores: Wang,Jinpeng; Li,Li; Qi,Haigang; Du,Xuedi; Zhang,Guofan.
Background: Reduced-representation sequencing technology is widely used in genotyping for its economical and efficient features. A popular way to construct the reduced-representation sequencing libraries is to digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the restriction enzyme(s). But there are few computer programs which can evaluate the usability of restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as fragment number. But for linkage mapping analysis, enzyme loci distribution is also an important factor to evaluate the enzyme. For phylogenetic studies, comparison of...
Tipo: Journal article
Palavras-chave: Genotyping; Reduced-representation libraries; Reduced-representation sequencing.
Ano: 2016
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300003

Genetic polymorphisms and haplotypes of the organic cation transporter 1 gene (SLC22A1) in the Xhosa population of South Africa
Provedor de dados: 74
Autores: Jacobs,Clifford; Pearce,Brendon; Du Plessis,Mornè; Hoosain,Nisreen; Benjeddou,Mongi.
Human organic cation transporter 1 is primarily expressed in hepatocytes and mediates the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for human organic cation transporter 1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response to clinical drugs, which are substrates for this transporter. The genotypic and allelic distributions of 19 nonsynonymous and one intronic SLC22A1 single nucleotide polymorphisms were determined in 148 healthy Xhosa participants from South Africa, using a SNAPshot® multiplex assay. In addition, haplotype structure for SLC22A1 was inferred from the genotypic data. The minor allele...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Polymorphism; Haplotype; Population genetic structure; Genotyping; Genetic variability.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000300006

Analysis of 31 STR loci in the genetic isolate of Carloforte (Sardinia, Italy)
Provedor de dados: 74
Autores: Robledo,Renato; Piras,Ignazio; Beggs,William; Calò,Carla.
The genotypes of 31 autosomal short tandem repeat loci in the population of Carloforte were analyzed, these representing a linguistic and genetic isolate located on the island of Sardinia (Italy). The markers span the entire length of chromosomes 19, 20, 21 and 22. Allele frequencies and statistical parameters were presented for all loci. Observed heterozygosity ranged from 0.279 to 0.884, and polymorphism information content from 0.552 to 0.886. All but two loci showed Hardy-Weinberg equilibrium after Bonferroni correction. The 31 short tandem repeat loci examined in the present work provide additional data on the genetic structure of the Carloforte population.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Autosomal STRs; Population data; Genotyping; Carloforte; Sardinia.
Ano: 2009
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300006

Analysis of apolipoprotein E genetic polymorphism in a large ethnic Hakka population in southern China
Provedor de dados: 74
Autores: Zhong,Zhixiong; Wu,Heming; Wu,Hesen; Zhao,Pingsen.
Abstract There is currently no data about the genetic variations of APOE in Hakka population in China. The aim of this study was to analyze the allelic and genotypic frequencies of APOE gene polymorphisms in a large ethnic Hakka population in southern China. The APOE genes of 6,907 subjects were genotyped by the gene chip platform. The allele and genotype frequencies were analyzed. Results showed that the ∊3 allele had the greatest frequency (0.804) followed by ∊2 (0.102), and ∊4 (0.094), while genotype ∊3/∊3 accounted for 65.43% followed by ∊2/∊3 (15.85%), ∊3/∊4 (14.13%), ∊2/∊4 (3.01%), ∊4/∊4 (0.84%), and ∊2/∊2 (0.74%) in all subjects. The frequencies of the ∊4 allele in Chinese populations were lower than Mongolian and Javanese, while the frequencies of...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Apolipoprotein E; Genetic polymorphism; Hakka; Southern China; Genotyping.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000500742

Are there differences in heterozygosity of strains obtained from intercrossed and self-fertilized onion plants?
Provedor de dados: 75
Autores: Luz,José Magno Queiroz; Machado,Daniel Lucas Magalhães; Maciel,Gabriel Mascarenhas; Freitas,Joelson André de; Oliveira,Roberta Camargos de.
ABSTRACT The commercial use of onion hybrids is preferred by producers. In contrast, the production of hybrid onion seeds is extremely inefficient. This is due to the use of lineages obtained by successive self-fertilizations assuming the effect of inbreeding depression per se. Therefore, it is necessary to understand new alternatives to reduce the effect of inbreeding depression in the strains. The objective of this study was to evaluate possible differences in polymorphism and levels of heterozygosity of strains obtained from intercrossed and self-fertilized plants. Twelve onion populations belonging to Bayer’s breeding program (Granex, IPA-1, IPA-2 and IPA-3) were used, obtained by self-fertilization of one plant, intercrossing of two plants or...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Allium cepa; Hybrid; Onion polymorphism; Genotyping; Primers.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-05362020000300274

Genotipagem por meio de marcadores SNP em cevada (Hordeum vulgare): um estudo de caso em cultivares e populações resultantes de retrocruzamentos.
Provedor de dados: 14
Autores: MUDADU, M. de A.; LAU, E. Y.; PEREIRA, J. F.; MINELLA, E.
Este documento representa o primeiro passo no sentido de aumentar a utilização de marcadores SNP em cevada por grupos de pesquisa no Brasil. As formas de obtenção e análise dos dados são detalhadas utilizando-se estudo de caso sobre diversidade genética de cultivares e incorporação de um importante gene por meio de cruzamento e retrocruzamentos. Este relato aproveita a experiência de pesquisadores da Embrapa Trigo e da Embrapa Informática Agropecuária e abre a possibilidade para que milhares de marcadores SNP possam ser utilizados para diferentes finalidades, potencializando um melhoramento de cevada mais preciso e com maiores ganhos genéticos.
Tipo: Documentos (INFOTECA-E)
Palavras-chave: Marcador molecula; Chip SNP; Genotipagem; Melhoramento genético; Cevada; Hordeum Vulgare; Single nucleotide polymorphism; Genetic improvement; Genotyping.
Ano: 2019
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1116075

Imputação de genótipos em bovinos: um guia passo a passo.
Provedor de dados: 14
Autores: MUDADU, M. de A.; CARVALHO, H. G. de; YOKOO, M. J. I.; CARDOSO, F. F.
O programa de melhoramento genético no Brasil está implementando o uso de marcadores genéticos, um procedimento chamado seleção genômica (SG). SG consiste em genotipar uma população de referência com fenótipos conhecidos e na descoberta de marcadores genéticos associados. O efeito dos marcadores são estimados e validados de forma a tornar possível predizer os valores genéticos dos cadidatos à seleção baseado nos seus genótipos. A genotipagem de alta densidade tem custo elevado, de forma que usa-se genotipar a população de referência usando chips de alta densidade de marcadores e genotipar com menor custo os candidatos a seleção usando chips de baixa densidade de marcadores. A imputação de genótipos é então aplicada para expandir os dados de genotipagem dos...
Tipo: Documentos (INFOTECA-E)
Palavras-chave: Genotipagem em alta densidade; Imputação de genótipos; Bioinformática; Genotyping; Bioinformatics.
Ano: 2016
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1064163

Protocolo para identificação de híbridos de amendoim forrageiro utilizando marcador molecular microssatélite.
Provedor de dados: 14
Autores: CAMPOS, T. de; AZÊVEDO, H. S. F. da S.; OLIVEIRA, J. C. de; FERREIRA FILHO, J. A.; YOMURA, R. B. T.; SILVA, L. M. da.
A pecuária na Amazônia representa uma cadeia produtiva importante para pequenos, médios e grandes produtores, uma vez que mais de 80% das áreas desmatadas são ocupadas por pastagens e cerca da metade delas encontra-se degradada ou em vias de degradação. A utilização de pastagens consorciadas pode ser uma alternativa de recuperação, manutenção da produtividade por um período maior e redução do tempo dos animais no pasto. Essa tecnologia tem sido amplamente defendida e utilizada pelos pecuaristas. A utilização do amendoim forrageiro em consórcio com gramíneas em pastagens tem mostrado resultados bastante significativos em relação ao aumento na rentabilidade e melhoria das condições do pasto. No entanto, ainda há baixa oferta de cultivares no mercado. No...
Tipo: Fôlder / Folheto / Cartilha (INFOTECA-E)
Palavras-chave: Amendoim forrageiro; Forage peanut; Cacahuete forrajero; Marcador microssatélite; Genotipagem; Fitomejoramiento; Marcadores genéticos.; Genotipificación; Híbridos; Leguminosas forrajeras; Melhoramento genético vegetal; Leguminosa forrageira; Marcador molecular; Híbrido; Plant breeding; Forage legumes; Genetic markers; Hybrids; Genotyping; Arachis pintoi.
Ano: 2016
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1064915

Genetic differences for behaviour in juveniles from two strains of brown trout suggest an effect of domestication history
Provedor de dados: 5
Autores: Benhaim, David; Guyomard, Rene; Chatain, Beatrice; Quillet, Edwige; Begout, Marie-laure.
Because captivity constitutes a drastic environmental change, domestication is expected to induce a rapid genetic selection for behavioural traits. In this study, we searched for genetic differences in behaviour among brown trout juveniles from two strains differing for their domestication history, i.e. an almost pure native wild Mediterranean population (W) and an Atlantic domesticated strain (D). In order to assess pure genetic differences among strains, males from the two origins were mated with Mediterranean females to produce two experimental crosses (WW and WD). The swimming activity characteristics of individual WW and WD juveniles were compared before and after the application of a stress (light switched off suddenly, followed by a 5-min period of...
Tipo: Text
Palavras-chave: Domestication; Genotyping; Microsatellite; Swimming activity; Restocking.
Ano: 2013
URL: http://archimer.ifremer.fr/doc/00152/26301/24409.pdf

Runs of homozygosity for autozygosity estimation and genomic analysis in production animals
Provedor de dados: 86
Autores: Rebelato,Arnaldo Basso; Caetano,Alexandre Rodrigues.
Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Autozygosity; FROH; Genotyping; Selection signatures; Single nucleotide polymorphism; SNPs.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2018000900975

Genetic variability of Brazilian rice landraces determined by SSR markers
Provedor de dados: 86
Autores: Borba,Tereza Cristina de Oliveira; Mendes,Clistiane dos Anjos; Guimarães,Élcio Perpétuo; Brunes,Tuliana Oliveira; Fonseca,Jaime Roberto; Brondani,Rosana Vianello; Brondani,Claudio.
The objective of this study was to evaluate the genetic variability of rice (Oryza sativa) landraces collected in Brazilian small farms. Twelve simple sequence repeat (SSR) markers characterized 417 landraces collected in 1986, 1987 and 2003, in the state of Goiás, Brazil. The number of landraces with long and thin grain type increased in the evaluated period, probably due to market demand. Based on the molecular data, the genetic variability increased during this period and, as per to the factorial correspondence analysis, most of the accessions were grouped according to the year of collection. The incorporation of modern rice cultivars in landrace cultivation areas and the selection carried out by small farmers are the most probable factors responsible...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Oryza sativa; Genotyping; Microsatellites; Participatory breeding; Rice breeding.
Ano: 2009
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2009000700009

Genotypic profile of Pantanal creole sheep regarding susceptibility or resistance to scrapie
Provedor de dados: 86
Autores: Gonçalves,Aline Najara Domingos; Soares,Cleber Oliveira; Sanches,Simone Camargo; Reis,Fernando Alvarenga; Rosinha,Grácia Maria Soares.
Abstract: The objective of this work was to determine the genotypic profile specific to scrapie in codons 136, 154, and 171 of the PRNP gene of the Pantanal creole sheep. Genomic DNA was extracted from blood samples collected from 66 sheep, and the regions of interest on the DNA strand were amplified by PCR. Five haplotypes were identified: ARR, alanine, arginine, arginine; ARQ, alanine, arginine, glutamine; AHQ, alanine, histidine, glutamine; ARH, alanine, arginine, histidine; and VRQ, valine, arginine, glutamine. The most common genotypes were ARQ/ARQ (27%) and ARR/ARQ (24%). The genotypic profile of the Pantanal creole sheep shows low to moderate susceptibility.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genotyping; PRNP gene; Single nucleotide polymorphisms; Transmissible spongiform encephalopathies.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2016000500684

Infectious bronchitis in Brazilian chickens: current data and observations of field service personnel
Provedor de dados: 89
Autores: Silva,EN.
The infectious bronchitis virus (IBV) was detected for the first time in Brazil by Hipólito in 1957 in chickens sold life in the municipal market of Belo Horizonte, MG, when commercial poultry production was just starting in that country. The Massachusetts (Mass) serotype was identified. However, the clinical disease was only observed in 1975, when poultry production was intensely growing. The extensive outbreak produced the classical condition in layers and breeders, affecting egg production and quality, whereas broilers presented respiratory and "nephritis-nephrosis" signs. The disease rapidly spread to all poultry-producing regions in the country, and in 1979, both the imports and the manufacturing of live vaccines against IB strains Mass, H120 and H52,...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Chicken; Genotyping; Infectious Bronchitis; PCR; Vaccination; Variants.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2010000300009

Molecular studies of the Brazilian infectious bronchitis virus isolates
Provedor de dados: 89
Autores: Abreu,JT; Mourão,MM; Santos,CE; Veloso,CJM; Resende,JS; Flatschart,RB; Folgueras-Flatschart,AV; Júnior,SN; Santoro,MM; Mendes,ACR; Franco,GR; Silva,A; Campos,AB; Fernandez,S.
Avian infectious bronchitis virus (IBV) isolates have been widely characterized by reverse transcription followed by polymerase chain reaction and DNA sequencing. In present study, these techniques were applied to three viral genomic regions comprising the complete and/or a partial S1 segment, S2 and nucleocapsid genes. DNA sequences from viral isolates obtained from 1972 to 1989 and from 2006 to 2008 were compared. High similarity (&gt;90%) was observed among some of the genomic segments, including S1 hypervariable region, which could suggest a common origin or ancestry. DNA sequences from S2 and N protein genes obtained from different infected tissues of the same flock were analyzed, and a clear segregation between respiratory and intestinal tract was...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Infectious bronchitis virus; Genotyping; Spike glycoprotein; Nucleocapsid; Phylogenetic tree.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2010000200005

Polymorphism of alpha s1-casein gene in a dairy goat herd in the southeastern region of Brazil
Provedor de dados: 96
Autores: Soares,Maria Amélia Menck; Rodrigues,Marcelo Teixeira; Mognol,Giuliana Patrícia; Ribeiro,Lucinéia de Fátima Chasko; Silva,José Luis da Conceição; Brancalhão,Rose Meire Costa.
Three different regions of the alpha s1-casein gene (CSN1S1) were investigated to determine the frequencies of major alleles for null, low, intermediate and high milk protein expression in a herd of dairy goats raised in the southeastern region of Brazil. Genomic DNA samples were obtained from leukocytes of 145 dairy goats and regions of interest in the gene were amplified through Polymerase Chain Reaction (PCR), then evaluated in both agarose (O and E allele) and polyacrylamide gels (F allele). For better characterization of the F allele, a PCR-RFLP (PCR-Restriction Fragment Length Polymorphism) study was performed employing the endonuclease XmnI. The allelic frequencies in the herd of 62 Saanen goats studied were: CSN1S1E = 0.35; CSN1S1F = 0.30; CSN1S1O1...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Alpine; Capra hircus; CSN1S1; Genotyping; Milk proteins; Saanen.
Ano: 2009
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982009000600008

Validation of SSR-tetranucleotide multiplex panel for kinship evaluation in tilapia breeding programs
Provedor de dados: 124
Autores: Freitas,Suzane Fonseca; Moreira,Heden Luiz Marques; Souza,Daiane Machado; Moreira,Carla Giovane Ávila; Tavares,Rafael Aldrighi; Dionello,Nelson José Laurino.
ABSTRACT This study aimed to develop PCR assays, reaction combinations, and validation of tetranucleotide SSR loci for tilapia, to minimize the impact of erroneous allele inferences on genotype determination of this marker. Microsatellites containing tetranucleotide repeats were obtained from tilapia genome, version 2.1, avoiding loci in the same linking group. Primers were designed for different fragment sizes, and fluorescence added to each locus. A total of 10 loci were amplified, separately and in combination, and loaded into a single capillary sequencer panel. Alleles were amplified without stutters and easily interpreted. PCR amplifications of DNA repeatedly extracted from samples, and genotyping at different PCR rounds were performed to infer allele...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genetic variability; Genotyping; Microsatellite markers.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1806-66902020000400409

Phenotypic and molecular characterization of apple (Malus × domestica Borkh) genetic resources in Greece
Provedor de dados: 63
Autores: Ganopoulos,Ioannis; Tourvas,Nikolaos; Xanthopoulou,Aliki; Aravanopoulos,Filippos A.; Avramidou,Euaggelia; Zambounis,Antonios; Tsaftaris,Athanasios; Madesis,Panagiotis; Sotiropoulos,Thomas; Koutinas,Nikolaos.
ABSTRACT: The phenotypic and genetic analysis of apple (Malus × domestica Borkh) genotypes is essential for breeding species. Information on the morphology and genetic structure of apple offers significant help for germplasm maintenance and selection of suitable material to breed superior cultivars. This study shows the results of an investigation on the morphology and the genetic diversity for 19 apple cultivars, which are preserved in an ex situ collection in Naoussa, Central Macedonia, Greece. Information was recorded over a 5-year period for 47 traits describing plant morphology and phenotype, as well as leaf and fruit quality. Data were analyzed using the principal component analysis (PCA) method. The Euclidean distance metric and the Ward’s...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genetic diversity; Genotyping; Microsatellite markers; Multivariate analysis; Phenotyping.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162018000600509

Universal tail sequence-SSR applied to molecular characterization of tropical maize hybrids
Provedor de dados: 63
Autores: Ribeiro,Carlos Alexandre Gomes; Pinto,Marcos de Oliveira; Maciel,Talles Eduardo Ferreira; Pastina,Maria Marta; Barros,Everaldo Gonçalves de; Guimarães,Claudia Teixeira.
ABSTRACT The development of efficient and low-cost genotyping methods is essential to precise genetic characterization of cultivars. Here, we present a system based on fluorescently labeled universal tail sequence primers (UTSP) to resolve microsatellite (SSR) markers as an alternative for molecular fingerprinting of maize. A set of 20 SSRs using the UTSP presented an average polymorphic information content of 0.84, which provided a probability of random identity ranging from 10−7 to 10−14, and a minimum exclusion power of 99.99998 % in a group of 48 tropical maize single-cross hybrids traded in Brazil. The genetic diversity analysis based on multidimensional scaling explained approximately 28 % of the total variance for the first two coordinates, tending...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Zea mays; Fingerprinting; Genotyping; Cultivar protection.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162017000200163

Overview of genotypic and clinical profiles of human immunodeficiency virus type 1-infected children in Rio de Janeiro, Brazil
Provedor de dados: 42
Autores: Machado,Elizabeth S.; Lambert,John S.; Afonso,Adriana O.; Cunha,Silvia M.; Oliveira,Ricardo H.; Tanuri,Amilcar; Sill,Anne M.; Soares,Marcelo A.
Although mother-to-child HIV transmission prevention has slowed down pediatric HIV infection in developed countries, large numbers of infants still become infected in developing nations. Data on pediatric HIV infection is however largely scarce. In this study, we have overviewed clinical, laboratory and genotypic data from a large cohort of HIV-infected infants regularly followed at two pediatric HIV outpatient clinics in Rio de Janeiro, Brazil. Children on antiretroviral therapy, as well as drug-naïve, newly diagnosed infants were analyzed. Prevalence of drug resistance mutations, as well as immunological and virological responses to therapy were evaluated. Additionally, HIV-1 subtype frequencies and their distribution over the course of the epidemic were...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: HIV-1; Pediatric; Drug resistance; Clinical; Genotyping; Subtype.
Ano: 2004
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652004000400008

Unraveling the genetic complexity of a cultivated breeding population of “yerba mate” (Ilex paraguariensis St. Hil.)
Provedor de dados: 42
Autores: PAIVA,DANIELA IVANA; CASCALES,JIMENA; ROSETTI,MARÍA EVA NATALIA; SCHERER,RAFAEL ALEJANDRO; GAUCHAT,MARÍA ELENA; GOTTLIEB,ALEXANDRA MARINA.
Abstract  We report the first comprehensive multilocus molecular characterization of cultivated Ilex paraguariensis plants belonging to a breeding program. Using nuclear and homologous chloroplastidic molecular markers, we have genotyped 158 plants from four plantation sites. Analyses of the nuclear data (187 variable dominant loci) allowed detecting high diversity (0.569), the occurrence of four distinct genetic clusters, and a low but significant differentiation among sites. Additionally, 20 chloroplastidic alleles were identified applying five microsatellite polymorphic markers, and a high chloroplastidic diversity was recognized (0.505); two haplogroups were distinguished amongst the 63 haplotypes detected. Our results from both nuclear and plastidic...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Chloroplastidic microsatellites; Genetic diversity; Genotyping; ISSR markers.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652020000100717

Paraconsistents artificial neural networks applied to the study of mutational patterns of the F subtype of the viral strains of HIV-1 to antiretroviral therapy
Provedor de dados: 42
Autores: SANTOS,PAULO C.C. DOS; LOPES,HELDER F.S.; ALCALDE,ROSANA; GONSALEZ,CLÁUDIO R.; ABE,JAIR M.; LOPEZ,LUIS F.
ABSTRACT The high variability of HIV-1 as well as the lack of efficient repair mechanisms during the stages of viral replication, contribute to the rapid emergence of HIV-1 strains resistant to antiretroviral drugs. The selective pressure exerted by the drug leads to fixation of mutations capable of imparting varying degrees of resistance. The presence of these mutations is one of the most important factors in the failure of therapeutic response to medications. Thus, it is of critical to understand the resistance patterns and mechanisms associated with them, allowing the choice of an appropriate therapeutic scheme, which considers the frequency, and other characteristics of mutations. Utilizing Paraconsistents Artificial Neural Networks, seated in...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Artificial Neural Networks; HIV; Genotyping; Paraconsistent logic; Paraconsistents Artificial Neural Networks; Pattern recognition.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652016000100323

Genotyping of Toxoplasma gondii isolates from naturally infected Gallus domesticus in Santa Catarina state, Brazil
Provedor de dados: 45
Autores: Trevisani,N.; Barros,L.D.; Vieira-Neto,A.; Sartor,A.A.; Souza,A.P.; Garcia,J.L.; Moura,A.B.
ABSTRACT Toxoplasmosis is a widespread zoonosis that can infect warm-blooded animals including birds and humans, and chickens are considered to be indicators of environmental contamination. In Brazil, Toxoplasma gondii has a non-clonal population structure composed of three lineages (I, II, and III), presenting high recombination, and resulting in wide genetic diversity. This study aimed to genetically characterize T. gondii isolates from naturally infected chickens (Gallus domesticus) in Santa Catarina state, southern Brazil region. Sera from 133 free-range chickens were analyzed by an immunofluorescence assay (IFA) to detect IgG antibodies against T. gondii. Brain and heart from 30 positive animals, based on IFA (≥ 1:64), were used to isolate the...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Toxoplasma gondii; Gallus domesticus; Genotyping; Brazil.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352017000100139

Identification of SNP c.-22G&amp;gt;A in the melanophilin gene from a dog with color dilution alopecia: case report
Provedor de dados: 45
Autores: Santos,L.M.; Messas,N.B.; Palumbo,M.I.P.; Miyasato,L.A.; Leal,P.V.; Martins,T.B.; Ramos,C.A.N.
ABSTRACT Mutant color alopecia is an ectodermical defection of color dilution, characterized by partial alopecia, dry, shine-less hair, and peeling and papule. Melanization damages also occur on the cortical structure of the affected hair. The animals affected have big melanin grains with irregular shape on the basal keratinocytes, also on the hair matrix cells and rod. Therefore, there is not a specific treatment that makes any difference on the syndrome evolution. Although in some animals, it is possible to use weekly showers with benzyl peroxide to reduce seborrhea formation and secondary infections. There is evidence that the condition in dogs is caused by a single nucleotide polymorphism in the gene encoding the melanophilin protein. In the present...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genotyping; Dermatology; Skin diseases; Mendelian inheritance.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352017000601503

Analysis of bovine rotavirus strains circulating in diarrheic dairy calves in Uberaba, Minas Gerais, Brazil, during 2008-2009
Provedor de dados: 45
Autores: Dulgheroff,A.C.B.; Pereira,W.A.B.; Sarmento,R.R.; Silva,G.A.V.; Naveca,F.G.; Domingues,A.L.S.
RESUMO O objetivo deste estudo foi detectar rotavírus em fezes de bezerros com diarreia em Uberaba, MG, e caracterizar os genes VP7 e VP4 por meio da genotipagem e da análise filogenética. Setenta e quatro amostras foram coletadas entre novembro de 2008 e setembro de 2009. A detecção do vírus foi feita por teste de aglutinação e as amostras positivas foram submetidas à transcrição reversa, seguida de reação em cadeia da polimerase (RT-PCR), tipagem por PCR e sequenciamento. A taxa de detecção de rotavírus foi de 6,8% e todas as amostras apresentaram o genótipo G6P[5]. A análise filogenética mostrou que as amostras do genótipo G6 pertencem à linhagem IV e que, para ambos os genes (VP7 e VP4), as amostras deste estudo compõem um sub-cluster à parte daquele...
Tipo: Info:eu-repo/semantics/other
Palavras-chave: Bovine rotavirus; Genotyping; Genetic lineage.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352016000401090

Migratory connections among breeding grounds off the Eastern Pacific and feeding areas in the Antarctic Peninsula based on genotype matching
Provedor de dados: 50
Autores: Caballero,Susana; Steel,Debbie; Pallin,Logan; Botero-Acosta,Natalia; Felix,Fernando; Olavarría,Carlos; Diaz granados,Maria Claudia; Bessudo,Sandra; Friedlander,Ari; Scott Baker,C.
ABSTRACT We analysed 114 DNA samples collected in different locations within the stock G breeding grounds, including Ecuador and the northern and southern Pacific of Colombia. We genotyped 15 microsatellite loci, sexed all samples, and performed genotype comparisons. Genotype comparisons were done using a DNA register of previously genotyped individuals from the Colombian breeding ground and the Antarctic Peninsula feeding Area. We confirmed connectivity between feeding grounds in Antarctic Peninsula and breeding grounds in Colombia and Ecuador using microsatellite loci. We found recaptures within each sampling location in the same year, but we also found a few recaptures in the same locations between years both in breeding and feeding grounds....
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Megaptera novaeangliae; Southeastern Pacific; Genotyping; Microsatellite; Migratory connectivity.
Ano: 2021
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0122-97612021000300031

Dideoxy single allele-specific PCR - DSASP new method to discrimination allelic
Provedor de dados: 52
Autores: Lima,Eleonidas Moura; Lopes,Otávio Sérgio; Soares,Leonardo Ferreira; Arruda,Talitta Dantas; Gigek,Carolina Oliveira; Melo,Cynthia Germoglio Farias; Smith,Marilia Arruda Cardoso; Oliveira,João Ricardo Gonçalves; Medeiros,Arnaldo; Delatorre,Plínio; Burbano,Rommel Rodriguez.
Gastric cancer (GC) is a multifactorial disease with a high mortality rate in Brazil and worldwide. This work aimed to evaluate single nucleotide polymorphisms (SNP) rs1695, in the Glutathione S-Transferase Pi (GSTP1) gene in GC samples by comparative analysis Specific PCR - ASP and Dideoxy Single Allele-Specific PCR - DSASP methods. The DSASP is the proposed new method for allelic discrimination. This work analyzed 60 GC samples, 26 diffuse and 34 intestinal types. The SNP rs1695 of the GSTP1 gene was significantly associated with GC analyzed by DSASP method (χ2 = 9.7, P &lt; 0.05). A comparative analysis of the data obtained from both methods did not differ significantly (χ2 = 0.08, P &gt; 0.05). These results suggest that the SNP rs1695 of the GSTP1...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: DSASP method; Genotyping; Gastric Cancer.
Ano: 2015
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132015000300414

Treatment switch guided by HIV-1 genotyping in Brazil
Provedor de dados: 55
Autores: Tupinambás,Unaí; Ribeiro,Flávia Andrade; Aleixo,Agdemir; Greco,Dirceu.
We assessed the performance of HIV-1 genotyping tests in rescue therapy. Patients were divided into two groups: group 1 (genotyped), included those switching to new antiretroviral drugs based on HIV-1 genotyping data, and group 2 (standard of care -SOC), comprised those in rescue therapy who had not used this test. This was an open and non-randomized study, with 74 patients, followed up for a mean period of 12 months, from February 2002 to May 2003. The groups differed in the duration of antiretroviral use, experience with diverse drug classes (non-nucleoside reverse transcriptase inhibitors and protease inhibitors) and viral load &lt;2.6 log10 copies/mL at any time during treatment. In 23 patients (group 1), the switch in antiretroviral (ARV) regimen was...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: HIV-1; Genotyping; Antiretroviral resistance testing.
Ano: 2006
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702006000200003

Detection and characterization of human rotavirus in hospitalized patients in the cities of Ponta Grossa, Londrina and Assai - PR, Brazil
Provedor de dados: 55
Autores: Nozawa,Carlos M; Kerntopf,Gustavo Franthesco; Czernisz,Érika da Silva; Albuquerque,Daniele; Romanin,Priscila; Freitas,José Felipe Eliseu; Santos,Norma; Benati,Fabrício José; Pietruchinski,Eduardo; Linhares,Rosa Elisa Carvalho.
Acute diarrheal disease is still one of the major public health problems worldwide. Rotaviruses (RV) are the most important viral etiologic agents and children under five years of age are the target population. OBJECTIVE: To investigate the rate of RV infection in hospitalized patients due to acute diarrhea in the cities of Ponta Grossa, Londrina and Assai - Paraná. METHODS: Latex agglutination (LA); immunochromatography (ICG); polyacrylamide gel electrophoresis (PAGE) and negative staining electron microscopy (ME) tests were used to detect the virus. For the genotyping, RT-PCR and RT-PCR-ELISA were used, respectively, for NSP4 and VP4/VP7. RESULT: Out of 124 samples there were 69 positive stool samples for RV, for at least one of the used tests, 67 of...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Rotavirus; Determination; Hospitalized patients; Genotyping.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702010000600002

Trends and predictors of HIV-1 acquired drug resistance in Minas Gerais, Brazil: 2002–2012
Provedor de dados: 55
Autores: Duani,Helena; Aleixo,Agdemir Waleria; Tupinambás,Unaí.
Abstract Several studies show that the prevalence of multidrug-resistant HIV-1 virus is declining over time. A retrospective cohort study was carried out to evaluate the trends of drug resistance in antiretroviral treatment-exposed individuals in a state of a middle-income country, Minas Gerais, southeast region of Brazil. We analyzed 2115 HIV-1 sequences from 2002 up to 2012, from 52 cities of Minas Gerais. The groups were analyzed according to the definitions: "IAS – 3 class mutations", if ≥1 drug resistance mutation from IAS 2015 list (DRM) was present in each class; "No fully susceptible drugs" as the absence of any fully susceptible drug in Stanford algorithm; and "GSS ≥ 2″, when a maximum calculated GSS (genotypic susceptibility score) was ≥2 or ≥3,...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: HIV; Antiretroviral; Resistance; Genotyping; Epidemiology.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702017000200148

Microarray-based genotyping and detection of drug-resistant HBV mutations from 620 Chinese patients with chronic HBV infection
Provedor de dados: 55
Autores: Hua,Wenhao; Zhang,Guanbin; Guo,Shujun; Weijie,Li; Sun,Lanhua; Xiang,Guangxin.
Background: Research has shown that hepatitis B virus (HBV) genotypes are closely linked to the clinical manifestations, treatment, and prognosis of the disease.Objective: To study the association between genotype and drug-resistant HBV mutations in 620 Chinese patients with chronic HBV infection.Methods: HBV DNA levels were determined using real-time quantitative PCR in plasma samples. Microarrays were performed for the simultaneous detection of HBV genotypes (HBV/B, C, and D) and drug-resistance-related hotspot mutations. A portion of the samples analyzed using microarrays was selected randomly and the data were confirmed using direct DNA sequencing.Results: Most samples were genotype C (471/620; 76.0%), followed by genotype B (149/620; 24.0%). Among the...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Chronic HBV; Microarray; Genotyping; Drug-resistance mutations.
Ano: 2015
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702015000300291

Virological suppression in children and adolescents is not influenced by genotyping, but depends on optimal adherence to antiretroviral therapy
Provedor de dados: 55
Autores: Abreu,Juliana Costa de; Vaz,Sara Nunes; Martins Netto,Eduardo; Brites,Carlos.
ABSTRACT  Objective: To evaluate the virological outcomes in children and adolescents infected with HIV-1 in Salvador, Bahia according to genotyping results.  Methods: We retrospectively evaluated the rates of virological suppression of children and adolescents submitted to HIV-1 genotyping test from January/2008 to December/2012. The participants were followed in the two referral centers for pediatric AIDS care, in Salvador, Brazil. Resistance mutations, drug sensitivity profiles, and viral subtypes were analyzed using the Stanford HIV-1 Drug Resistance Database. Adherence was estimated by drugs withdrawal at pharmacies of the two sites.  Results: 101 subjects were included: 35 (34.6%) were drug-naïve, and the remaining 66 were failing ART. In drug-naïve...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Children; Virological suppression; Genotyping; Adherence.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702017000300219

A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil
Provedor de dados: 55
Autores: Duarte,Tonya Azevedo; Nery,Joilda Silva; Boechat,Neio; Pereira,Susan Martins; Simonsen,Vera; Oliveira,Martha; Gomes,Maria Gabriela Miranda; Penha-Gonçalves,Carlos; Barreto,Mauricio Lima; Barbosa,Theolis.
ABSTRACT  Introduction: The Mycobacterium tuberculosis East African-Indian (EAI) spoligotyping family (belonging to lineage 1, Indo-Oceanic, defined by the region of deletion RD239) is distributed worldwide, but is more prevalent in Southeast Asia, India, and East Africa. Studies in Latin America have rarely identified EAI. In this study, we describe the occurrence of the EAI family in Brazil.  Methods: EAI was identified in a systematic literature review of genetic diversity studies pertaining to M. tuberculosis in Brazil, as well as in a survey conducted in Salvador, Bahia, located in the northeastern region of this country.  Results: The EAI6-BGD1 spoligotyping family and the EAI5 Spoligotype International Type (SIT) 1983 clade were the most frequently...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Mycobacterium tuberculosis; Phylogeography; Genotyping; Epidemiology.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702017000300317

Molecular techniques for MRSA typing: current issues and perspectives
Provedor de dados: 55
Autores: Trindade,P. A.; McCulloch,J. A.; Oliveira,G. A.; Mamizuka,E. M.
Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA) as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include:...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Staphylococcus aureus; Molecular epidemiology; Genotyping; Methicillin resistance.
Ano: 2003
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702003000100005

Molecular characterization and epidemiology of cefoxitin resistance among Enterobacteriaceae lacking inducible chromosomal ampC genes from hospitalized and non-hospitalized patients in Algeria: description of new sequence type in Klebsiella pneumoniae isolates
Provedor de dados: 55
Autores: Gharout-Sait,Alima; Touati,Abdelaziz; Guillard,Thomas; Brasme,Lucien; Champs,Christophe de.
In this study, 922 consecutive non-duplicate clinical isolates of Enterobacteriaceae obtained from hospitalized and non-hospitalized patients at Bejaia, Algeria were analyzed for AmpC-type β-lactamases production. The ampC genes and their genetic environment were characterized using polymerase chain reaction (PCR) and sequencing. Plasmid incompatibility groups were determined by using PCR-based replicon typing. Phylogenetic grouping and multilocus sequence typing were determined for molecular typing of the plasmid-mediated AmpC (pAmpC) isolates.Of the isolates, 15 (1.6%) were identified as AmpC producers including 14 CMY-4- producing isolates and one DHA-1-producing Klebsiella pneumoniae . All AmpC-producing isolates co-expressed the broad-spectrum TEM-1...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Enterobacteriaceae; AmpC β-lactamases; Genotyping; Algeria.
Ano: 2015
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702015000200187

Molecular epidemiology of Acinetobacter baumannii in central intensive care unit in Kosova teaching hospital
Provedor de dados: 55
Autores: Raka,Lul; Kalenc,Smilja; Bošnjak,Zrinka; Budimir,Ana; Katić,Stjepan; Šijak,Dubravko; Mulliqi-Osmani,Gjyle; Zoutman,Dick; Jaka,Arbëresha.
Infections caused by bacteria of genus Acinetobacter pose a significant health care challenge worldwide. Information on molecular epidemiological investigation of outbreaks caused by Acinetobacter species in Kosova is lacking. The present investigation was carried out to enlight molecular epidemiology of Acinetobacterbaumannii in the Central Intensive Care Unit (CICU) of a University hospital in Kosova using pulse field gel electrophoresis (PFGE). During March - July 2006, A. baumannii was isolated from 30 patients, of whom 22 were infected and 8 were colonised. Twenty patients had ventilator-associated pneumonia, one patient had meningitis, and two had coinfection with bloodstream infection and surgical site infection. The most common diagnoses upon...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genotyping; Acinetobacter baumannii; Kosova; Intensive care unit.
Ano: 2009
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702009000600004

Molecular epidemiology and antimicrobial susceptibility of Enterococci recovered from Brazilian intensive care units
Provedor de dados: 55
Autores: Titze-de-Almeida,Ricardo; Rollo Filho,Maurício; Nogueira,Celeste A.; Rodrigues,Isabela P.; Eudes Filho,João; Nascimento,Rejane S. do; Ferreira II,Renato F.; Moraes,Lídia M. P.; Boelens,Hélène; Van Belkum,Alex; Felipe,Maria Sueli Soares.
We studied the antimicrobial resistance and the molecular epidemiology of 99 enterococcal surveillance isolates from two hospitals of Brasília, Brazil. Conventional biochemical tests were used to identify the enterococcal species and the disk diffusion method was used to determine their resistance profiles. Enterococcus faecalis (76%) and E. faecium (9%) were the most prevalent species. No enterococci showed the vanA or vanB vancomycin resistance phenotypes or genotypes. Only the intrinsically resistant species E. gallinarum (n=2) and E. casseliflavus (n=3) harbored the vancomycin-resistance genes vanC1 and vanC2/3, respectively. We found E. faecalis isolates with high-level resistance to gentamicin (22%) and streptomycin (8%) and both E. faecalis and E....
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Enterococci; Antimicrobial resistance; Genotyping.
Ano: 2004
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702004000300002

IS1245 restriction fragment length polymorphism typing of Mycobacterium avium from patients admitted to a reference hospital in Campinas, Brazil
Provedor de dados: 56
Autores: Panunto,A.C.; Villares,M.C.B.; Ramos,M.C.
Mycobacterium avium is an important pathogen among immunodeficient patients, especially patients with AIDS. The natural history of this disease is unclear. Several environmental sources have been implicated as the origin of this infection. Polyclonal infection with this species is observed, challenging the understanding of its pathogenesis and treatment. In the present study 45 M. avium strains were recovered from 39 patients admitted to a reference hospital between 1996 and 1998. Species identification was performed using a species-specific nucleic acid hybridization test (AccuProbe®) from Gen-Probe®. Strains were genotyped using IS1245 restriction fragment length polymorphism typing. Blood was the main source of the organism. In one patient with...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Mycobacterium avium; IS1245 RFLP; Mycobacteria; AIDS; Genotyping.
Ano: 2003
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2003001000017

Changes in epidemiology of rotavirus in the Triângulo Mineiro region of Brazil: lack of two consecutive rotavirus seasons
Provedor de dados: 56
Autores: Dulgheroff,A.C.B.; Figueiredo,E.F.; Gouvêa,V.S.; Domingues,A.L.S.
Rotaviruses are the main cause of infantile acute diarrhea, and a monovalent (G1P[8]) vaccine against the virus was introduced into the Brazilian National Immunization Program for all infants in March 2006. The objectives of this study were to determine the rate and genotype distribution of rotavirus causing infantile diarrhea in the Triângulo Mineiro region of Brazil during 2011-2012 and to assess the impact of local vaccination. Fecal specimens were analyzed for detection and characterization of rotavirus using polyacrylamide gel electrophoresis, reverse transcription followed by polymerase chain reaction (PCR), and PCR-genotyping assays. Overall, rotavirus was diagnosed in 1.7% (6/348) of cases. Rotavirus positivity rates decreased 88% [95% confidence...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Rotavirus; Infantile diarrhea; Surveillance; Genotyping.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2014001201091

PCR-based ribotyping of Staphylococcus aureus
Provedor de dados: 56
Autores: Oliveira,A.M.; Ramos,M.C.
Genotyping techniques are valuable tools for the epidemiologic study of Staphylococcus aureus infections in the hospital setting. Pulsed-field gel electrophoresis (PFGE) is the current method of choice for S. aureus strain typing. However, the method is laborious and requires expensive equipment. In the present study, we evaluated the natural polymorphism of the genomic 16S-23S rRNA region for genotyping purpose, by PCR-based ribotyping. Three primer pairs were tested to determine the size of amplicons produced and to obtain better discrimination with agar gel electrophoresis and ethidium bromide staining. The resolution of the typing system was determined using sets of bacteria obtained from clinical specimens from a large tertiary care hospital. These...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Staphylococcus aureus; PCR ribotyping; Genotyping; Methicillin-resistant Staphylococcus aureus.
Ano: 2002
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2002000200005

Typing of Pseudomonas aeruginosa from hospitalized patients: a comparison of susceptibility and biochemical profiles with genotype
Provedor de dados: 56
Autores: Freitas,A.L.; Barth,A.L.
Typing techniques are essential for understanding hospital epidemiology, permitting the elucidation of the source of infection and routes of bacterial transmission. Although DNA-based techniques are the "gold standard" for the epidemiological study of Pseudomonas aeruginosa, antibiotic profiles and biochemical results are used because they are easy to perform and to interpret and relatively inexpensive. Antibiotypes (susceptibility profiles) and biotypes (biochemical profiles) were compared to genotypes established by DNA restriction enzyme analysis in 81 clinical isolates of P. aeruginosa from three hospitals in Porto Alegre, Brazil. The epidemiological relationship among patients was also evaluated. Susceptibility and restriction profiles were discrepant...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Pseudomonas aeruginosa; Typing; Genotyping; Phenotypic markers.
Ano: 2004
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2004000100011

Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA
Provedor de dados: 58
Autores: Ashayeri-Panah,Mitra; Eftekhar,Fereshteh; Ghamsari,Maryam Mobarak; Parvin,Mahmood; Feizabadi,Mohammad Mehdi.
In this study, the discriminatory power of pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) methods for subtyping of 54 clinical isolates of Klebsiella pneumoniae were compared. All isolates were typeable by RAPD, while 3.6% of them were not typeable by PFGE. The repeatability of both typing methods were 100% with satisfying reproducibility (≥ 95%). Although the discriminatory power of PFGE was greater than RAPD, both methods showed sufficient discriminatory power (DI &gt; 0.95) which reflects the heterogeneity among the K. pneumoniae isolates. An optimized RAPD protocol is less technically demanding and time consuming that makes it a reliable typing method and competitive with PFGE.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Klebsiella pneumoniae; Pulsed field gel electrophoresis; Random amplified polymorphic DNA; Genotyping.
Ano: 2013
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822013000300024

Biotyping and genotypic diversity among oral Candida albicans strains from caries-free and caries-active healthy children
Provedor de dados: 58
Autores: Mardegan,Rita de Cássia; Klein,Marlise Inêz; Golvea,Magda Baglione; Rodrigues,Janaina Aparecida Oliveira; Gonçalves,Reginaldo Bruno; Höfling,José Francisco.
Candida albicans oral strains collected from caries-free and caries-active healthy children ranging from 24 to 36 months old, were studied. The aim of the study was to determine proteinase and phospholipase activities produced by Candida albicans in the two groups and to determine the phenotypic diversity of these enzymes based on genetic polymorphism using the AP-PCR method. Strains identified by morphological and fermentation tests as C. albicans were grown in proteinase and phospholipase agar media at 37ºC for 7 and 4 days, respectively. After the incubation period, the enzyme activity of the proteinase and phospholipase positive strains was measured. All strains were subjected to AP-PCR, using the arbitrary primer AP-3. The enzymatic analysis showed no...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Candida albicans; Genotyping; Proteinase; Phospholipase; Virulence.
Ano: 2006
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822006000100005

Molecular typing of Mycobacterium bovis isolates: a review
Provedor de dados: 58
Autores: Ramos,Daniela Fernandes; Tavares,Lucas; Silva,Pedro Eduardo Almeida da; Dellagostin,Odir Antônio.
Mycobacterium bovis is the main causative agent of animal tuberculosis (TB) and it may cause TB in humans. Molecular typing of M. bovis isolates provides precise epidemiological data on issues of inter- or intra-herd transmission and wildlife reservoirs. Techniques used for typing M. bovis have evolved over the last 2 decades, and PCR-based methods such as spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) have been extensively used. These techniques can provide epidemiological information about isolates of M. Bovis that may help control bovine TB by indicating possible links between diseased animals, detecting and sampling outbreaks, and even demonstrating cases of laboratory cross-contamination between...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Tuberculosis; Bovine; Diagnosis; Genotyping; Mycobacterium bovis.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000200001

Diversity and uncommon HPV types in HIV seropositive and seronegative women attending an STI clinic
Provedor de dados: 58
Autores: Mattos,Adriana Tonani de; Freitas,Luciana Bueno de; Lima,Bettina Moulin Coelho; Miranda,Angélica Espinosa; Spano,Liliana Cruz.
Given the causal relationship between specific types of HPV with cervical cancer and precursor lesions, it is important to identify the viral type involved. The aim of this study is to access the prevalence of HPV types in HIV seropositive and seronegative women. Accordingly, 77 HPV positive cervical samples were obtained from 284 women (seropositive (n=112) and seronegative (n=172) for HIV) who attended a Sexually Transmitted Infection clinic, in Vitoria, Southeastern Brazil. Viral DNA was amplified by PCR using MY09/MY11 degenerated primers and the genotyping was performed by Restriction Fragment Length Polymorphism. Seventy five out of the 77 HPV samples were genotyped: 6, 11, 13, 16, 18, 26, 31, 31b, 32, 33, 34, 35, 52, 53, 55, 56, 58, 59, 61, 62, 64,...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Human papillomavirus (HPV); HIV seropositive and seronegative women; RFLP; Genotyping; Cervical secretion.
Ano: 2011
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822011000200047

ERIC-PCR genotypic characterization of Haemophilus parasuis isolated from Brazilian swine
Provedor de dados: 58
Autores: Moreno,Luisa Zanolli; Castilla,Karina Salvagni; Gobbi,Débora Dirani Sena de; Coutinho,Tania Alen; Ferreira,Thais Sebastiana Porfida; Moreno,Andrea Micke.
Haemophilus parasuis infection, known as Glässer's disease, is characterized by fibrinous polyserositis, arthritis and meningitis in piglets. Although traditional diagnosis is based on herd history, clinical signs, bacterial isolation and serotyping, the molecular-based methods are alternatives for species-specific tests and epidemiologic study. The aim of this study was to characterize H. parasuis strains isolated from different states of Brazil by serotyping, PCR and ERIC-PCR. Serotyping revealed serovar 4 as the most prevalent (24 %), followed by serovars 14 (14 %), 5 (12 %), 13 (8 %) and 2 (2 %), whereas 40 % of the strains were considered as non-typeable. From 50 strains tested 43 (86%) were positive to Group 1 vtaA gene that have been related to...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Haemophilus parasuis; Glässer disease; Genotyping; ERIC-PCR.
Ano: 2011
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822011000400025

Teat papillomatosis associated with bovine papillomavirus types 6, 7, 9, and 10 in dairy cattle from Brazil
Provedor de dados: 58
Autores: Tozato,Claudia C.; Lunardi,Michele; Alfieri,Alice F.; Otonel,Rodrigo A.A.; Di Santis,Giovana W.; Alcântara,Brígida K. de; Headley,Selwyn A.; Alfieri,Amauri A.
This study describes the clinical, histopathological, and virological characterization of teat papillomatosis from Brazilian dairy cattle herds. Four types of bovine papillomavirus were identified (BPV6, 7, 9, and 10); one of these (BPV7) is being detected for the first time in Brazilian cattle.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Papilloma; BPV; Genotyping.
Ano: 2013
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822013000300039

Characterization of mixed infections with different strains of bovine rotavirus in an outbreak of diarrhea in dairy herds in Goiás, Brazil
Provedor de dados: 58
Autores: Brito,Wilia Marta Elsner Diederichsen de; Munford,Veridiana; Villaça,André Martins; Caruzo,Thabata Alessandra Ramos; Rácz,Maria-Lucia.
Ten faecal samples of bovine rotavirus from calves less than 30 days old from an outbreak of diarrhea in Hidrolândia, Goiás, Brazil were submitted to serological and molecular characterization, using enzyme immunoassay for subgrouping and serotyping, PAGE for determination of electropherotypes and PCR for genome typing. Nine samples belonged to group A/subgroup I rotavirus and one sample was group A / subgroup non-I/non-II. Four samples were characterized as G10P[11] (B223-like), four samples showed a mixture of two rotavirus strains (G6G10 and P[5]P[11]), one sample was characterized as G6P[11] and one sample was characterized only by G serotyping/genotyping, and did not react with any P primer used. Two electropherotypes were detected and both were...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Rotavirus; Diarrhea; Bovine; Genotyping; Serotyping.
Ano: 2000
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822000000200015

Ribotyping and increasing trend of antibiotic resistance of Pseudomonas aeruginosa isolated in Iran
Provedor de dados: 58
Autores: Pourshafie,Mohammad Reza; Mousavi,Sayed Fazlolah; Parzadeh,Masoumeh.
The trend of antibiotic resistance, ribotyping and serotyping patterns of Pseudomonas aeruginosa collected since 1987 in Iran were investigated. The results showed that among the aminoglycosides, amikacin was the most effective antibiotic against P. aeruginosa with 98.4% susceptibility rate followed by tobramycin (73%) and gentamicin (71%). Of the cephalosporins, susceptibility to ceftazidime was 93%. Among the antibiotics tested in vitro, ciproflaxacin was found to be the most effective against the strains, with 98.4% susceptibility rate. The most predominant monovalent serotype was O:11 (34%). Other dominant serotypes were O:5 (20%), O:1 (16%) and O:6 (15%). Thirteen percent of the isolates showed no agglutination with the tested sera. A high percent of...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Pseudomonas aeruginosa; Iran; Genotyping.
Ano: 2007
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822007000300010

Molecular typing of Mycobacterium bovis isolated in the south of Brazil
Provedor de dados: 58
Autores: Ramos,Daniela Fernandes; Silva,Ana Bárbara Scholante; Fagundes,Michel Quevedo; von Groll,Andrea; Silva,Pedro Eduardo Almeida da; Dellagostin,Odir Antônio.
Bovine tuberculosis is a major infectious disease of the cattle. In this study, 85 M. bovis isolates from 162 lymph nodes, obtained from a herd of cattle on a farm in southern Brazil, were evaluated using spoligotyping and VNTR. The strains were grouped into five clusters and five orphans, showing a heterogenic genetic profile, what could represent diverse geographic origins of the introduced cows and/or the frequent movement of cattle between different properties.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bovine tuberculosis; Mycobacterium bovis; Genotyping.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000200039

DEFB1 gene polymorphisms and tuberculosis in a Northeastern Brazilian population
Provedor de dados: 58
Autores: Silva,Ronaldo Celerino da; Cruz,Heidi Lacerda Alves da; Brandão,Lucas André Cavalcanti; Guimarães,Rafael Lima; Montenegro,Lilian Maria Lapa; Schindler,Haiana Charifker; Segat,Ludovica; Crovella,Sergio.
Abstract β-Defensin-1, an antimicrobial peptide encoded by the DEFB1 gene, is known to play an important role in lung mucosal immunity. In our association study we analyzed three DEFB1 functional polymorphisms -52G&gt;A (rs1799946), -44C&gt;G (rs1800972) and -20G&gt;A (rs11362) in 92 tuberculosis patients and 286 healthy controls, both from Northeast Brazil: no association was found between the studied DEFB1 polymorphisms and the disease. However we cannot exclude that this lack of association could be due to the low number of subjects analyzed, as suggested by the low statistical power achieved for the three analyzed SNPs (values between 0.16 and 0.50).
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Tuberculosis; Innate immunity; DEFB1; Genotyping; Polymorphism.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000200389

Application of Oligonucleotide Microarray for the Detection and Genotyping of cry Genes in Bacillu thuringiensis
Provedor de dados: 117
Autores: Xu-Guang,Liu; Fu-Ping,Song; Si-Yuan,Wen; Sheng-Qi,Wang; Da-Fang,Huang; Jie,Zhang.
We have developed a parallel, rapid, high-throughput oligonucleotide microarray-based assay for the reliable detection and genotyping of three cry genes (cry1, cry2 and cry9) in Bacillus thuringiensis (Bt). After the non-polymerase chain reaction (PCR), amplified Bt genomic DNA were fluorescent-labeled using a random primer.   The corresponding oligonucleotide probes were designed for the different cry genes that can hybridize Bt genomic DNA after cluster analysis and were printed on glass slides. This microarray has unambiguously detected and identified the cry genes in 10 isolates and reference Bt. Our data demonstrates that the microarray assay is simple and rapid for the detection and genotyping of genes. This type of assay is also a potentially...
Tipo: Journal article
Palavras-chave: Oligonucleotide microarray; Cry genes; Genotyping; Random primer labeling; Bioinformatics.
Ano: 2010
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392010000200004