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A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil BJID
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
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Analysis of 31 STR loci in the genetic isolate of Carloforte (Sardinia, Italy) Genet. Mol. Biol.
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
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Analysis of apolipoprotein E genetic polymorphism in a large ethnic Hakka population in southern China Genet. Mol. Biol.
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
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Analysis of bovine rotavirus strains circulating in diarrheic dairy calves in Uberaba, Minas Gerais, Brazil, during 2008-2009 Arq. Bras. Med. Vet. Zootec.
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
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Application of Oligonucleotide Microarray for the Detection and Genotyping of cry Genes in Bacillu thuringiensis Chilean J. Agric. Res.
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
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ATG genes, new playerson early Fe toxicity response in rice (Oryza sativa). Repositório Alice
MALTZAHN, L. E.; VIANA, V. E.; BUSANELLO, C.; VENSKE, E.; GIRARDI, C. L.; OLIVEIRA, A. C. DE; PEGORARO, C..
Rice yield is frequently impaired by abiotic adverse conditions in several parts of the globe. One of these constraints is soil iron toxicity. Plants respond to adverse conditions by activating different mechanisms, some of which have already been elucidated. Recently, autophagy has been associated with plant tolerance to abiotic stresses, however, the involvement of this mechanism in the response to iron toxicity has never been studied. Autophagy is a process of recycling cellular components and involves approximately 30 genes in rice. Thus, the objective of this study was to characterise the regulation and transcriptional activation of OsATG genes in rice seedlings under iron toxicity. In this condition, OsATG genes were induced in the tolerant genotype...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Transcriptional regulation; Abiotic stress; Autophagy; Gene expression; Genotyping; Iron.
Ano: 2020 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124879
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Avaliação genética das vacinas contra a brucelose bovina comercializadas no Brasil. Repositório Alice
BASTOS, R.; SOARES, C. O.; ELISEI, C.; MUNHOZ, A. L. R.; BEZERRA, N. L.; CAITANO, M. A. B.; ROSINHA, G. M. S..
Objetivou-se com este estudo caracterizar genotipicamente as amostras vacinais B19 e RB51 comercializadas no Brasil.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Brucella abortus; Brucellosis; Vaccine; B19; RB51; Genotyping; Genetic quality.
Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/handle/doc/937237
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BDGF: a database and webbased information retrieval system for genotype and phenotype. Repositório Alice
VIEIRA, F. D.; MOURA, D. G. de; SILVA, D. F. da; HIGA, R. H.; ZERLOTINI NETO, A..
In order to get efficient storage and fast queries in this high volume of data, in this work we present the BDGF system (Genotypes and Phenotypes Database). It is based on a data model first proposed by (HIGA, 2015).
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Bioinformática; Polimorfismo de nucleotídeo único; Recuperação da informação; Bioinformatics; Single nucleotide polymorphism; Genotyping; Phenotype; Information retrieval.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1067543
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Biotyping and genotypic diversity among oral Candida albicans strains from caries-free and caries-active healthy children BJM
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
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Changes in epidemiology of rotavirus in the Triângulo Mineiro region of Brazil: lack of two consecutive rotavirus seasons BJMBR
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
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Characterization of mixed infections with different strains of bovine rotavirus in an outbreak of diarrhea in dairy herds in Goiás, Brazil BJM
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
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Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis Electron. J. Biotechnol.
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 µg 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
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Compilation of an informative microsatellite set for genetic characterisation of East African finger millet (Eleusine coracana) Electron. J. Biotechnol.
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
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DEFB1 gene polymorphisms and tuberculosis in a Northeastern Brazilian population BJM
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>A (rs1799946), -44C>G (rs1800972) and -20G>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
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Detection and characterization of human rotavirus in hospitalized patients in the cities of Ponta Grossa, Londrina and Assai - PR, Brazil BJID
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
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Dideoxy single allele-specific PCR - DSASP new method to discrimination allelic BABT
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 < 0.05). A comparative analysis of the data obtained from both methods did not differ significantly (χ2 = 0.08, P > 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
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Dissecting the genetic basis of wheat blast resistance in the Brazilian wheat cultivar BR 18-Terena. Repositório Alice
GOGGARD, R.; STEED, A.; CHINOY, C.; FERREIRA, J. R.; SCHEEREN, P. L.; MACIEL, J. L. N.; CAIERAO, E.; TORRES, G. A. M.; CONSOLI, L.; SANTANA, F. M.; FERNANDES, J. M. C.; SIMMONDS, J.; UAUY, C.; COCKRAM, J.; NICHOLSON, P..
Background: Wheat blast, caused by Magnaporthe oryzae Triticum (MoT) pathotype, is a global threat to wheat (Triticum aestivum L.) production. Few blast resistance (R) genes have been identified to date, therefore assessing potential sources of resistance in wheat is important. The Brazilian wheat cultivar BR 18-Terena is considered one of the best sources of resistance to blast and has been widely used in Brazilian breeding programmes, however the underlying genetics of this resistance are unknown. Results: BR 18-Terena was used as the common parent in the development of two recombinant inbred line (RIL) F6 populations with the Brazilian cultivars Anahuac 75 and BRS 179. Populations were phenotyped for resistance at the seedling and heading stage using...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Wheat blast; Seedling resistance; Head resistance; Single nucleotide polymorphism (SNP) genotyping; Triticum Aestivum; Magnaporthe oryzae; Quantitative trait loci; Genotyping.
Ano: 2020 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124870
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Diversity and uncommon HPV types in HIV seropositive and seronegative women attending an STI clinic BJM
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
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DNA from tissues of young mice is optimal for genotyping Electron. J. Biotechnol.
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
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ERIC-PCR genotypic characterization of Haemophilus parasuis isolated from Brazilian swine BJM
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
Registros recuperados: 77
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