First Identification of Culex flavivirus (Flaviviridae) in Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Strains of Xylella fastidiosa rapidly distinguished by arbitrarily primed-PCR

Genomic DNAs isolated from strains of Xylella fastidiosa that caused citrus variegated chlorosis, coffee leaf scorch, Pierce's Disease of grapevine, and plum leaf scorch were analyzed by arbitrarily primed polymerase chain reaction. Purified DNA was amplified under nonstringent conditions with single primers 21 nucleotides (nt) long. Thirty-nine amplification products were observed that were useful to distinguish among the strains and to derive a similarity matrix and construct a phenogram showing possible relationships among the strains. Strains isolated from diseased coffee and citrus in Brazil were closely related to each other (coefficient of similarity of 0.872), but only distantly related to a strain isolated from diseased grapevine in the USA (coefficient of similarity of 0.650). Strains of Xylella fastidiosa isolated from diseased plums in the USA and Brazil clustered with strains from different hosts isolated from their respective countries of origin. Thus, there may be two quite dissimilar clusters of strains of Xylella fastidiosa, one in North America and the other in South America. Each cluster contains strains that can cause disease in plum. The methods described provide a convenient and rapid method to distinguish between strains of Xylella fastidiosa that cause diseases of coffee and citrus in the same region of Brazil. This has not been possible previously. This will potentially enable the two strains to be distinguished in alternate hosts or in insect vectors.

Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set

The taxonomy of the N(2)-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradryrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses Clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster. (C) 2008 Elsevier B.V. All rights reserved.

Extração de DNA de materiais de arquivo e fontes escassas para utilização em reação de polimerização em cadeia (PCR)

Este trabalho visou a comparação de cinco métodos diferentes de extração de DNA de materiais de arquivo (tecidos incluídos em parafina, esfregaços de sangue periférico - corados e não corados com Leishman, lâminas com mielogramas, gotas de sangue em Guthrie Card) e de fontes escassas (células bucais, um e três bulbos capilares e 2 mL de urina), para que fossem avaliadas a facilidade de aplicação e a facilidade de amplificação deste DNA pela técnica da reação de polimerização em cadeia (PCR). Os métodos incluíram digestão por proteinase K, seguida ou não por purificação com fenol/clorofórmio; Chelex 100® (BioRad); Insta Gene® (BioRad) e fervura em água estéril. O DNA obtido foi testado para amplificação de três fragmentos gênicos: Brain-derived neutrophic factor (764 pb), Factor V Leiden (220 pb) e Abelson (106 pb). de acordo com o comprimento do fragmento gênico estudado, da fonte potencial de DNA e do método de extração utilizado, os resultados caracterizaram o melhor caminho para padronização de procedimentos técnicos a serem incluídos no manual de Procedimentos Operacionais Padrão do Laboratório de Biologia Molecular do Hemocentro - HC - Unesp - Botucatu.

Comparação entre a relação PCR/albumina e o índice prognóstico inflamatório nutricional (IPIN)

Objetivo: Simplificar o cálculo do índice prognóstico inflamatório nutricional (IPIN) empregando número menor de variáveis com conseqüente redução do custo da análise. Materiais e métodos: Foram estudados 54 pacientes e 12 indivíduos-controle com 48 ± 20 (média ± dp) anos de idade. As principais patologias dos pacientes eram: doença arterial periférica (22), pênfigo foliáceo (7), doença inflamatória intestinal (7), trauma (6) e pós-operatório de ortognatia (3). Foram obtidas amostras de sangue periférico, colhidas em jejum para dosagens de proteínas positivas (+) e negativas (-) de fase aguda (PFA) pelo método nefelométrico. Proteína C reativa (PCR), alfa-1-glicoproteína-ácida (alfa-1-GA), alfa-1-antitripsina (alfa-1-AT) e ceruloplasmina (CER) foram as PFA+ e albumina (Alb), transtiretina (TTR), transferrina (TF) e proteína ligadora do retinol (RBP) foram as representantes das PFA-. Esses valores foram analisados quanto à associação de correlação isolada ou associadamente na fórmula do índice prognóstico inflamatório e nutricional (IPIN = PCR + alfa-1-GA / Alb + TTR). de acordo com o índice prognóstico inflamatório e nutricional, os pacientes foram classificados em grupo-controle (G1); pacientes sem infecção/inflamação (IPIN < 1, G2) ou com risco de inflamação/infecção (IPIN > 1, G3). em seguida os pacientes do G3 foram subdivididos em baixo risco (G3A, n = 16); médio risco ( G3B, n = 10); alto risco (G3C, n = 6) e com risco de morte (G3D, n = 11). Os resultados foram correlacionados entre si (teste de Spearman) ou submetidos às comparações entre grupos (teste de Kruskall-Wallis). Resultados: Houve relação significativa entre as variáveis PCR ´ alfa-1-GA (r = 0,49), Alb ´ TTR (r = 0,60), Alb ´ RBP (r = 0,58), Alb ´ TF (r = 0,39), TTR ´ RBP (r = 0,56) e TTR´ TF (r = 0,43) e as melhores relações encontradas entre PFA+ e PFA- foram: PCR ´ Alb (r = - 0,71), PCR ´ TTR (r = - 0,54), PCR ´ TF (r = - 0,39) e alfa-1-GA ´ Alb (r = - 0,35). Os valores do IPIN mostraram a diferenciação G3 > (G1 = G2) e G3 > G3A. Entre todas as proteínas dosadas apenas PCR, Alb e TTR discriminaram os grupos: sendo G3 > (G1= G2) para PCR e G3< (G1= G2) para Alb e TTR. Apenas PCR, TTR e TF discriminaram a morbimortalidade com G3D > G3A (para PCR) e G3D < G3A (para TTR e TF). PCR/Alb e IPIN apresentaram concordância de valores para os riscos de complicações. Conclusão: Assim, conclui-se pela possibilidade de substituição do IPIN pela relação PCR/albumina, mais simples e de menor custo, mantendo-se o mesmo poder e sensibilidade para diagnóstico dos graus de risco de complicações.

Assessment of cytokine values in serum by RT-PCR in HIV-1 infected individuals with and without highly active anti-retroviral therapy (HAART)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Inflammatory cytokine mRNA detection by real time PCR in chorioamniotic membranes from pregnant women with preterm premature rupture of membranes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Development of a real-time PCR method for rapid sexing of human preimplantation embryos

Genes on the X chromosome are known to be responsible for more than 200 hereditary diseases. After IVF, the simple selection of embryo sex before uterine transfer can prevent the occurrence of affected offspring among couples at risk for these genetic disorders. The aim of this investigation was to develop a rapid method of preimplantation genetic diagnosis (PGD) using real-time polymerase chain reaction (PCR) for the sexing of human embryos, and to compare it to the fluorescence in-situ hybridization technique, considered to be the gold standard. After biopsies were obtained from 40 surplus non-viable embryos for transfer, a total of 98 blastomeres were analysed. It was possible to analyse 24 embryos (60%) by both techniques, generating a total of 70 blastomeres (35 per technique), white 28 blastomeres from 16 embryos (40%) were analysed only by real-time PCR. A rapid and safe method was developed in the present study for the sexual diagnosis of a single human cell (blastomere and buccal cell) using the emerging technology of real-time PCR. (C) 2009, Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Typing class I HLA-A gene using a nested PCR-RFLP procedure

In order to detect several new HLA-A class I alleles that have been described since 1998, the original PCR-RFLP method developed to identify the 78 alleles recognized at that time at high resolution level was adapted by us for low and medium resolution levels using a nested PCR-RFLP approach. The results obtained from blood samples of 23 subjects using both the PCR-RFLP method and a commercial kit (MicroSSP1A®, One Lambda Inc.) showed an agreement higher than 95%. The PCR-RFLP adapted method was effective in low and medium resolution histocompatibility evaluations.

Quantitative real-time RT-PCR and chromogenic in situ hybridization: precise methods to detect HER-2 status in breast carcinoma

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The heminested RT-PCR for the study of rabies virus pathogenesis

The aim of the present trial was to evaluate the heminested RT-PCR for the study of rabies virus distribution in mice inoculated experimentally. Inoculation was by the intramuscular route in 150 mice, using the dog street rabies virus. Groups of five animals were killed at different times. Fragments of different organs were collected and the material was tested by Fluorescent Antibody Test (FAT) and heminested RT-PCR (hn RT-PCR). Positive results were obtained beginning on the 10th day after inoculation in the brain, spinal cord, salivary gland, limbs, lungs, liver, spleen, urinary bladder, tongue and right kidney. Hn RT-PCR was shown to be more efficient for the study of rabies virus distribution in different tissues and organs. (C) 2004 Elsevier B.V.. All rights reserved.

Cloning, sequencing and expression analysis of the equine hepcidin gene by real-time PCR

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Direct Detection of Mycobacterium bovis in Bovine Lymph Nodes by PCR

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Species-specific nested PCR as a diagnostic tool for Brucella ovis infection in rams

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

First identification of Sarcocystis tenella (Railliet, 1886) Moule, 1886 (Protozoa: Apicomplexa) by PCR in naturally infected sheep from Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)