Genetic diversity of NS3 protease from Brazilian HCV isolates and possible implications for therapy with direct-acting antiviral drugs

The hepatitis C virus (HCV) NS3 protease has been one of the molecular targets of new therapeutic approaches. Its genomic sequence variability in Brazilian HCV isolates is poorly documented. To obtain more information on the magnitude of its genetic diversity, 114 Brazilian HCV samples were sequenced and analysed together with global reference sequences. Genetic distance (d) analyses revealed that subtype 1b had a higher degree of heterogeneity (d = 0.098) than subtypes 1a (d = 0.060) and 3a (d = 0.062). Brazilian isolates of subtype 1b were distributed in the phylogenetic tree among sequences from other countries, whereas most subtype 1a and 3a sequences clustered into a single branch. Additional characterisation of subtype 1a in clades 1 and 2 revealed that all but two Brazilian subtype 1a sequences formed a distinct and strongly supported (approximate likelihood-ratio test = 93) group of sequences inside clade 1. Moreover, this subcluster inside clade 1 presented an unusual phenotypic characteristic in relation to the presence of resistance mutations for macrocyclic inhibitors. In particular, the mutation Q80K was found in the majority of clade 1 sequences, but not in the Brazilian isolates. These data demonstrate that Brazilian HCV subtypes display a distinct pattern of genetic diversity and reinforce the importance of sequence information in future therapeutic approaches.

Trypanosoma rangeli protein tyrosine phosphatase is associated with the parasite's flagellum

Protein tyrosine phosphatases (PTPs) play an essential role in the regulation of cell differentiation in pathogenic trypanosomatids. In this study, we describe a PTP expressed by the non-pathogenic protozoan Trypanosoma rangeli (TrPTP2). The gene for this PTP is orthologous to the T. brucei TbPTP1 and Trypanosoma cruzi (TcPTP2) genes. Cloning and expression of the TrPTP2 and TcPTP2 proteins allowed anti-PTP2 monoclonal antibodies to be generated in BALB/c mice. When expressed by T. rangeli epimastigotes and trypomastigotes, native TrPTP2 is detected as a ~65 kDa protein associated with the parasite's flagellum. Given that the flagellum is an important structure for cell differentiation in trypanosomatids, the presence of a protein responsible for tyrosine dephosphorylation in the T. rangeli flagellum could represent an interesting mechanism of regulation in this structure.

Prevalence of hepatitis C virus infection among recyclable waste collectors in Central-West Brazil

The prevalence of hepatitis C virus (HCV) in a population of recyclable waste collectors (n = 431) was assessed using a cross-sectional survey in all 15 cooperatives in the city of Goiânia, Central-West Brazil. The HCV prevalence was 1.6% (95% confidence interval: 0.6-3.6) and a history of sexually transmitted infections was independently associated with this infection. HCV RNA (corresponding to genotype 1; subtypes 1a and 1b) was detected in five/seven anti-HCV-positive samples. Although the study population reported a high rate (47.3%) of sharps and needle accidents, HCV infection was not more frequent in recyclable waste collectors than in the general Brazilian population.

Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic

Typical human immunodeficiency virus-1 subtype B (HIV-1B) sequences present a GPGR signature at the tip of the variable region 3 (V3) loop; however, unusual motifs harbouring a GWGR signature have also been isolated. Although epidemiological studies have detected this variant in approximately 17-50% of the total infections in Brazil, the prevalence of B"-GWGR in the southernmost region of Brazil is not yet clear. This study aimed to investigate the C2-V3 molecular diversity of the HIV-1B epidemic in southernmost Brazil. HIV-1 seropositive patients were ana-lysed at two distinct time points in the state of Rio Grande do Sul (RS98 and RS08) and at one time point in the state of Santa Catarina (SC08). Phylogenetic analysis classified 46 individuals in the RS98 group as HIV-1B and their molecular signatures were as follows: 26% B"-GWGR, 54% B-GPGR and 20% other motifs. In the RS08 group, HIV-1B was present in 32 samples: 22% B"-GWGR, 59% B-GPGR and 19% other motifs. In the SC08 group, 32 HIV-1B samples were found: 28% B"-GWGR, 59% B-GPGR and 13% other motifs. No association could be established between the HIV-1B V3 signatures and exposure categories in the HIV-1B epidemic in RS. However, B-GPGR seemed to be related to heterosexual individuals in the SC08 group. Our results suggest that the established B"-GWGR epidemics in both cities have similar patterns, which is likely due to their geographical proximity and cultural relationship.

Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India

Klebsiella pneumoniae U25 is a multidrug resistant strain isolated from a tertiary care hospital in Chennai, India. Here, we report the complete annotated genome sequence of strain U25 obtained using PacBio RSII. This is the first report of the whole genome of K. pneumoniaespecies from Chennai. It consists of a single circular chromosome of size 5,491,870-bp and two plasmids of size 211,813 and 172,619-bp. The genes associated with multidrug resistance were identified. The chromosome of U25 was found to have eight antibiotic resistant genes [blaOXA-1,blaSHV-28, aac(6’)1b-cr,catB3, oqxAB, dfrA1]. The plasmid pMGRU25-001 was found to have only one resistant gene (catA1) while plasmid pMGRU25-002 had 20 resistant genes [strAB, aadA1,aac(6’)-Ib, aac(3)-IId,sul1,2, blaTEM-1A,1B,blaOXA-9, blaCTX-M-15,blaSHV-11, cmlA1, erm(B),mph(A)]. A mutation in the porin OmpK36 was identified which is likely to be associated with the intermediate resistance to carbapenems in the absence of carbapenemase genes. U25 is one of the few K. pneumoniaestrains to harbour clustered regularly interspaced short palindromic repeats (CRISPR) systems. Two CRISPR arrays corresponding to Cas3 family helicase were identified in the genome. When compared to K. pneumoniaeNTUHK2044, a transposase gene InsH of IS5-13 was found inserted.

Genetic associations in the detection of QTLs for wheat spike-related traits

The objective of this work was to assess the genetic diversity and population structure of wheat genotypes, to detect significant and stable genetic associations, as well as to evaluate the efficiency of statistical models to identify chromosome regions responsible for the expression of spike-related traits. Eight important spike characteristics were measured during five growing seasons in Serbia. A set of 30 microsatellite markers positioned near important agronomic loci was used to evaluate genetic diversity, resulting in a total of 349 alleles. The marker-trait associations were analyzed using the general linear and mixed linear models. The results obtained for number of allelic variants per locus (11.5), average polymorphic information content value (0.68), and average gene diversity (0.722) showed that the exceptional level of polymorphism in the genotypes is the main requirement for association studies. The population structure estimated by model-based clustering distributed the genotypes into six subpopulations according to log probability of data. Significant and stable associations were detected on chromosomes 1B, 2A, 2B, 2D, and 6D, which explained from 4.7 to 40.7% of total phenotypic variations. The general linear model identified a significantly larger number of marker-trait associations (192) than the mixed linear model (76). The mixed linear model identified nine markers associated to six traits.

Ação antagônica de rizobactérias contra Phytophthora parasitica e p. citrophthora e seu efeito no desenvolvimento de plântulas de citros

O antagonismo de Pseudomonas putida biovar A (C1-1B), P. putida biovar B (Santa Bárbara), P. fluorescens (C2-8C e RA2), Bacillus subtilis (OG e RC2) e Flavobacterium sp. (CIS/NA) contra Phytophthora parasitica e P. citrophthora , agentes da podridão radicular dos citros, foi avaliado através da inibição do crescimento micelial (cultura pareada) e redução na percentagem de infecção da doença em mudas de citros (tratamento de sementes com rizobactérias). Na seleção preliminar, 33 isolados bacterianos foram testados. Sementes de citros pré-germinadas foram tratadas por imersão nas suspensões das bactérias (10(9) ufc/ml), e plantadas em tubetes contendo solo natural infestado com o fitopatógeno (50 ml de suspensão/ kg de solo). A avaliação da percentagem de infecção foi efetuada após 15 dias. In vitro, os isolados bacterianos RC2, OG, CIS/NA e C1-1B foram os mais ativos inibidores do crescimento micelial de Phytophthora. Em condições de casa de vegetação, todos os isolados proporcionaram redução na percentagem de infecção da doença em todos os ensaios realizados. Promoção de crescimento de plantas foi verificada pela inoculação de plântulas com as linhagens OG, RC2, CiS/Na e C1-1B.

Características agronômicas de seis genótipos de maracujazeiro-azedo cultivados no Distrito Federal

Este trabalho teve como objetivo avaliar as características agronômicas de seis genótipos de maracujazeiro-azedo cultivados no Distrito Federal. O experimento foi desenvolvido na área experimental da Fazenda Água Limpa da Universidade de Brasília, no DF. Utilizou-se o delineamento em blocos casualizados, com quatro repetições, seis tratamentos e sete plantas por parcela. Foram avaliados os genótipos: Rubi Gigante, EC-3-0, EC-L-7, RC-3, Redondão e Gigante Amarelo. Os parâmetros analisados, durante seis meses (17 colheitas), foram: produtividade total estimada, quantidade de frutos e coloração da casca. O genótipo Rubi Gigante teve a maior produtividade (16,69 t/ha-1), enquanto o RC-3 a menor (2,92 t/ha-1). Foram observados resultados semelhantes quanto às variáveis: produtividade total e quantidade de frutos de tamanho: primeira, 1B e 1A em relação aos seis genótipos. Não houve diferença significativa a 5%, pelo teste de Tukey, para: % de frutos de coloração amarela, rosa e roxa; massa fresca de frutos amarelos e rosas; quantidade de frutos rosas e roxos, e também quantidade de frutos de tamanho 2A e 3A em relação a todos os genótipos avaliados. Os genótipos Rubi Gigante, Redondão, EC-3-0 e EC-L-7 podem ser recomendados para o cultivo no DF e região geoeconômica, se confirmarem a superioridade quando avaliados por um maior período e em diferentes condições ambientais.

Populações, matrizes e idade da planta na expressão de variáveis físicas em frutos do pequizeiro

O pequi é uma espécie com ampla distribuição no cerrado brasileiro, tendo grande importância social e econômica para os habitantes desse bioma. O presente trabalho foi proposto em função da ausência de informações sobre os efeitos de fatores genéticos e ambientais na expressão de variáveis físicas em frutos dessa espécie. Informações dessa natureza facilitam as decisões em relação ao processo de domesticação e melhoramento dessa espécie. Para atender a este objetivo, colheram-se frutos nos municípios de Curvelo e São Gonçalo do Rio Preto, Minas Gerais, totalizando 15 matrizes por município, selecionadas através de características que refletem suas idades, sendo a principal o diâmetro do tronco rente ao solo (DAS). As variáveis físicas avaliadas foram: Peso Total do Fruto (PTF); Peso do Mesocarpo Externo (PME); Peso dos Putamens (PTP) por fruto; Nº de Putamens (NP) por fruto e Peso Total de Polpa (PTPL) por fruto. O efeito de matrizes foi altamente significativo para todas as variáveis avaliadas, enquanto o de populações foi apenas para NP. As estimativas das correlações entre as variáveis avaliadas foram todas positivas, algumas significativas. As estimativas das correlações entre DAS e as demais variáveis também foram todas positivas, algumas significativas. Os resultados permitem concluir que: há grandes expectativas de ganhos a partir da propagação vegetativa de matrizes selecionadas no campo para as características físicas de seus frutos; o peso de polpa por fruto, caráter de grande importância econômica, mas de avaliação trabalhosa, pode ser selecionado a partir da avaliação do peso de putamens por fruto; o efeito da idade da planta sobre a expressão de variáveis físicas em frutos de pequi é nulo ou positivo, podendo a seleção ser conduzida em plantas jovens.

Produtividade e qualidade de frutos de progênies de maracujazeiro-azedo cultivados no Distrito Federal

Este trabalho teve como objetivo avaliar a produtividade e a qualidade de frutos de progênies de maracujazeiro-azedo cultivados no Distrito Federal. Foi conduzido na Fazenda Água Limpa-UnB, utilizando-se de delineamento de blocos casualizados, com 14 tratamentos (progênies), 04 repetições, sendo a parcela útil de oito plantas. As progênies avaliadas foram: Vermelhão Ingaí, EC-RAM, AR01, AR02, mar20#36, mar20#46, AP1, FP01, FB200, RC3, GA2-A1*AG, mar20#03, mar20#23 e mar20#09. As características analisadas em 75 colheitas foram: produtividade (kg/ha), massa média de frutos (g), número de frutos por hectare, coloração da casca e classificação quanto ao tamanho. Houve maior rendimento em Vermelhão Ingaí, EC-RAM e AR01. O Vermelhão Ingaí produziu a maior quantidade de frutos por hectare, estatisticamente superior aos demais. O EC-RAM obteve o maior número de frutos rosa e roxo. Todas as progênies apresentaram maior produção de frutos de cor amarela. O peso médio total variou de 83 g em mar20#36 e 128 g em EC-RAM. A maior produtividade de frutos para fins industriais foi verificado em Vermelhão Ingaí com frutos de primeira e mar20#46 com frutos 1B. Já para consumo in natura foi observado em AR02 com frutos 1A e 2 A e em AR01 com frutos 3 A.

Nível de evidência e grau de recomendação dos artigos sobre a acurácia diagnóstica da ultrassonografia na síndrome do túnel do carpo

OBJETIVO: Este trabalho teve como objetivo avaliar a qualidade dos artigos relacionados com a acurácia diagnóstica da ultrassonografia na síndrome do túnel do carpo idiopática e relacionada com o trabalho. MATERIAIS E MÉTODOS: Realizou-se busca em bases de dados eletrônicas, selecionando-se relatórios de revisões sistemáticas, ensaios clínicos randomizados e estudos observacionais. Após quatro etapas de análise, desde a triagem inicial até a avaliação pelo instrumento elaborado pelo Critical Appraisal Skills Programme, os artigos foram classificados em níveis de evidência, com seus respectivos graus de recomendação. RESULTADOS: Dos 68 artigos inicialmente encontrados, apenas 4 preencheram os critérios de qualidade propostos neste estudo. A mensuração da área transversal do nervo mediano foi o critério mais importante para o diagnóstico de síndrome do túnel do carpo (ponto de corte entre 9 e 10 mm²: sensibilidade = 82-86,3%; especificidade = 48-87%). Os quatro artigos obtiveram nível de evidência "1b" e grau de recomendação "A". CONCLUSÃO: A avaliação ultrassonográfica em pacientes com suspeita clínica de síndrome do túnel do carpo pode ser realizada como teste de primeira linha, com boa relação custo-benefício, reduzindo a necessidade de exames eletrodiagnósticos.

Evaluation of preoperative computed tomography angiography in association with conventional angiography versus computed tomography angiography only, in the endovascular treatment of aortic diseases

Objective To evaluate the association of conventional angiography (AG) with computed tomography angiography (CTA) as compared with CTA only, preoperatively, in the treatment of aortic diseases. Materials and Methods Retrospective study involving patients submitted to endovascular treatment of aortic diseases, in the period from January 2009 to July 2010, with use of preoperative CTA + conventional AG or CTA only. The patients were divided into two groups, namely: G1 – thoracic aortic diseases; and G2 – abdominal aortic diseases. G1 was subdivided into 1A (preoperative AG + CTA) and 1B (preoperative CTA). G2 was subdivided into 2C (CTA + AG) and 2D (CTA only). Results The authors evaluated 156 patients. In subgroups 1A and 1B, the rate of technical success was, respectively, 100% and 94.7% (p = 1.0); and the rate of therapeutic success was, respectively, 81% and 58% (p = 0.13). A higher number of complications were observed in subgroup 1B (p = 0.057). The accuracy in the calculation of the prosthesis was higher in subgroup 1A (p = 0.065). In their turn, the rate of technical success in subgroups 2C and 2D was, respectively, 92.3% and 98.6% (p = 0.17). The rate of therapeutic success was 73% and 98.6% (p = 0.79). Conclusion Preoperative conventional AG should be reserved for cases where CTA cannot provide all the information in the planning of a therapeutic intervention.

Esfoliação e hidratação da caulinita após intercalação com uréia

Well-ordered Georgia kaolinite (Kga-1b) obtained from the source Clay Repository of the Clay Minerals Society (USA) was intercalated with urea using grinding procedures. To achieve complete intercalation 20% of urea (in weight) was used, producing Al2Si2O5(OH)4 (N2H4CO)0,86 with an interplanar basal spacing of 1,08nm. After washing with water under ultrasound stirring at 363K, urea was completely removed and kaolinite was partially exfoliated. After drying under air, the material was converted to hydrated kaolinite with the composition Al2Si2O5(OH)4 (H2O)0,64 and an interplanar basal spacing of 0,84nm. In this compound, water molecules positioned between the layers of the silicate can be removed after calcination at 573K, regenerating structurally disordered kaolinite.

NMR investigation and theoretical calculations of the effect of solvent on the conformational analysis of 4',7-di-hydroxy-8-prenylflavan

The NMR conformational study of 4',7-di-hydroxy-8-prenylflavan 1 was carried out in acetone-d6, DMSO-d6 and CDCl3 which enabled the proposition of three conformations, namely 1a, 1b and 1c, differing in the position of the prenyl group. Geometry optimizations performed using AM1 method showed that 1a (deltaHf = -86.2 kcal/mol) is as stable as 1b (deltaHf = -85.1 kcal/mol) and 1c (deltaHf = -85.4 kcal/mol). When the solvent was included, the calculations showed that the solute-solvent interactions could be explained either in the light of the electronic intermolecular delocalization or the electrostatic character between solute and solvent. Theoretical calculations (HF/6-31G*, deltaFT/BLYP/6-31G*, and deltaFT/B3LYP/6-31G*) showed that the combination of these types of interactions present in each solute-solvent system, dependent on the chemical properties of the solvent, lead to different spatial arrangements of the prenyl group, which in turn determined the conformation of 1.

Phytochemical investigation of Wissadula periplocifolia (L.) C. Presl and evaluation of its antibacterial activity

A phytochemical study on the aerial parts of Wissadula periplocifolia using chromatographic techniques has led to the isolation of sitosterol (1a), stigmasterol (1b), sitosterol 3-O-β-D-glucopyranoside (2a), stigmasterol 3-O-β-D-glucopyranoside (2b), phaeophytin A (3), 13²-hydroxy-(13²-S)-phaeophytin A (4), phaeophytin B (5), 17³-ethoxyphaeophorbide (6), 3,4-seco-urs-4(23),20(30)-dien-3-oic acid (7), 3-oxo-21β-H-hop-22(29)-ene (8), dammaradienone (9a), and taraxastenone (9b). The isolated compounds were characterised by spectroscopic analysis. A preliminary assay to evaluate the antibacterial activity of W. periplocifolia extracts and fractions showed that the dichloromethane, ethyl acetate, and n-butanol fractions were active against Enterococcus faecalis.