Hibridização reversa e sequenciamento na genotipagem do vírus da hepatite C

INTRODUÇÃO: Os métodos de genotipagem do vírus da hepatite C têm sido muito discutidos. O objetivo deste trabalho foi comparar as metodologias de hibridização reversa e sequenciamento direto para a genotipagem do vírus da hepatite C. MÉTODOS: Noventa e uma amostras de plasma de pacientes assistidos na Faculdade de Medicina de Botucatu da Universidade Estadual Paulista foram utilizadas. A genotipagem por hibridização reversa foi realizada utilizando o kit comercial INNO-LiPA® v.1.0. O sequenciamento direto foi efetuado em sequenciador automático utilizando protocolos in house. RESULTADOS: A genotipagem por sequenciamento direto mostrou-se eficiente na resolução dos resultados inconclusivos pelo kit comercial. O kit mostrou resultados errôneos em relação à subtipagem viral. Além disso, a genotipagem por sequenciamento direto revelou um erro do kit com relação à determinação genotípica questionando a eficiência do método também para a identificação do genótipo viral. CONCLUSÕES: A genotipagem realizada por meio de sequenciamento direto permite uma maior acurácia na classificação viral quando comparada à hibridização reversa.

Análise comparativa das metodologias de hibridização reversa e sequenciamento direto para a genotipagem do vírus da hepatite C

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

Identificação e validação de genes diferencialmente expressos em carcinoma de pênis

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

Piezoelectric biosensors for real-time monitoring of hybridization and detection of hepatitis C virus

The piezoelectric quartz crystal resonators modified with oligonucleotide probes were used for detection of hepatitis C virus (HCV) in serum. The gold electrodes on either rough or smooth surface crystals were modified with a self-assembled monolayer of cystamine. After activation with glutaraldehyde, either avidin or streptavidin were immobilized and used for attachment of biotinylated DNA probes (four different sequences). Piezoelectric biosensors were used in a flow-through setup for direct monitoring of DNA resulting from the reverse transcriptase-linked polymerase chain reaction (RT-PCR) amplification of the original viral RNA. The samples of patients with hepatitis C were analyzed and the results were compared with the standard RT-PCR procedure (Amplicor test kit of Roche, microwell format with spectrophotometric evaluation). The piezoelectric hybridization assay was completed in 10 min and the same sensing surface was suitable for repeated use. (C) 2004 Elsevier B.V. All rights reserved.

Selection and validation of reference genes for gene expression studies by reverse transcription quantitative PCR in Xanthomonas citri subsp citri during infection of Citrus sinensis

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

Development of globular embryos from the hybridization between 'Pêra Rio' sweet orange and 'Poncã' mandarin

Objetivou-se estudar a influência de diversas concentrações do meio MT, sacarose, vitaminas, carvão ativado e ácido giberélico no cultivo de embriões imaturos oriundos do cruzamento entre laranjeira 'Pêra Rio' x tangerineira 'PONCÃ' . Os embriões foram excisados sob condições assépticas e inoculados em 15 mL do meio de cultura MT, de acordo com cada experimento a seguir: 1) concentrações do meio de cultura MT (0%, 50%, 100%, 150% e 200%) combinados com 0, 30, 60 e 90 g.L-1 de sacarose; 2) concentrações de vitaminas do meio MT (0%, 50%, 100%, 150% e 200%) combinados com 0, 30, 60 e 90 g.L-1 de sacarose e; 3) concentrações de carvão ativado (0; 0.5; 1; 1.5 e 2 g.L-1) combinados com GA3 (0; 0.01; 0.1; 1 e 10 mg.L-1). Após a inoculação, os embriões foram mantidos por 90 dias em sala de crescimento à temperatura de 27±1ºC, fotoperíodo de 16 horas e irradiância de 32 µmol.m-2.s-1. A utilização de 50% e 100% do meio MT associado a 60 e 90 g.L-1 de sacarose, respectivamente, acrescido de 0.01 mg.L-1 de GA3, proporcionou melhor desenvolvimento de embriões globulares. Não houve necessidade da adição de carvão ativado e vitaminas no meio MT para o cultivo de embriões globulares.

Comparative Studies of the (Anti) Mutagenicity of Baccharis dracunculifolia and Artepillin C by the Bacterial Reverse Mutation Test

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

Immobilization of streptavidin in sol-gel films: Application on the diagnosis of hepatitis C virus

Recent advances have accelerated the development of biosensors for the analysis of specific gene sequences. In this kind of biosensor, a DNA probe is immobilized on a transducer and the hybridization with the target DNA is monitored by suitable methodology. In the present work, the streptavidin (STA) was encapsulated in thin films siloxane-poly(propylene oxide) hybrids prepared by sol-gel method and deposited on the graphite electrode surface by dip-coating process. Biotinylated 18-mer probes were immobilized through STA and a novel amperometric DNA biosensor for the detection and genotyping of the hepatitis C virus (genotypes 1, 2A/C, 2B and 3) is described. The HCV RNA from serum was submitted to reverse transcriptase-linked polymerase chain reaction (RT-PCR) and biotin-labeled cDNA was obtained. Thus, the cDNA was hybridized to the target-specific oligonucleotide probe immobilized on the graphite electrode surface and following the avidin-peroxidase conjugate was added. The enzymatic response was investigated by constant potential amperometry at -0.45 V versus Ag/AgCl using H2O2 and KI solutions. HCV RNA negative and positive controls and positive samples of sera patients were analyzed and the results were compared to commercial kit. The proposed methodology appeared to be suitable and convenient tool for streptavidin immobilization and diagnose of HCV disease. (c) 2006 Elsevier B.V. All rights reserved.

Structural and functional evidence that a B chromosome in the characid fish Astyanax scabripinnis is an isochromosome

Astyanax scabripinnis possesses a widespread polymorphism for metacentric B chromosomes as large as the largest chromosome pair in the A complement. on the basis of C-banding pattern, it was hypothesized that these B chromosomes are isochromosomes that have arisen by means of centromere misdivision and chromatid nondisjunction. In the present paper we test this hypothesis by analysing (i) the localization of a repetitive DNA sequence on both B chromosome arms, and (ii) synaptonemal complex formation, in order to test the functional homology of both arms. Genomic DNA digested with KpnI and analysed by gel electrophoresis showed fragments in a ladder-like pattern typical of tandemly repetitive DNA. These fragments were cloned and their tandem organization in the genome was confirmed. A 51-bp long consensus sequence, which was AT-rich (59%) and contained a variable region and two imperfect reverse sequences, was obtained. Fluorescence in situ hybridization (FISH) localized this repetitive DNA into noncentromeric constitutive heterochromatin which encompasses the terminal region of some acrocentric chromosomes, the NOR region, and interstitial polymorphic heterochromatin in chromosome 24. Most remarkably, tandem repeats were almost symmetrically placed in the two arms of the B chromosome, with the exception of two additional small clusters proximally located on the slightly longer arm. Synaptonemal complex (SC) analysis showed 26 completely paired SCs in males with 1B. The ring configuration of the B univalent persisting until metaphase I suggests that the two arms formed chiasmata. All these data provided strong support for the hypothesis that the B chromosome is an isochromosome.

A new algorithm for Reverse Monte Carlo simulations

We present a new algorithm for Reverse Monte Carlo (RMC) simulations of liquids. During the simulations, we calculate energy, excess chemical potentials, bond-angle distributions and three-body correlations. This allows us to test the quality and physical meaning of RMC-generated results and its limitations. It also indicates the possibility to explore orientational correlations from simple scattering experiments. The new technique has been applied to bulk hard-sphere and Lennard-Jones systems and compared to standard Metropolis Monte Carlo results. (C) 1998 American Institute of Physics.

Indicator-free electrochemical DNA hybridization biosensor

A new electrochemical hybridization biosensor protocol without an external indicator is described. The biosensor format involves the immobilization of inosine-substituted (guanine-free) probe onto the carbon paste transducer, and a direct chronopotentiometric detection of the duplex formation by the appearance of the guanine oxidation peak of the target. Such a use of the intrinsic DNA electrochemical response for monitoring hybridization events offers several advantages (over the common use of external indicators), including the appearance of a new peak, a Aat background, or simplicity. A 4 min short hybridization period allows a detection limit around 120 ng/ml. Performance characteristics of the sensor are described along with future prospects. (C) 1998 Elsevier B.V. B.V. All rights reserved.

A study of reverse logistics flow management in vehicle battery industries in the midwest of the state of São Paulo (Brazil)

Having the objective of minimizing costs and improving their image in the consumer and export market, car battery industries began to seek environmental alternatives geared towards sustainable development. Reverse logistics flow represents an unprecedented tool for the economic and operational development of company activities, as well as a differential in the search for competitive advantages through environmentally correct practices. The aim of this paper is to describe the reverse logistics chain adopted by automotive battery industries in the midwest of the state of São Paulo, proposing a reverse logistics framework for small manufacturers that creates actions aimed at not harming the environment. (C) 2010 Elsevier Ltd. All rights reserved.

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)