Non-coding RNAs in schistosomes: an unexplored world

Non-coding RNAs (ncRNAs) were recently given much higher attention due to technical advances in sequencing which expanded the characterization of transcriptomes in different organisms. ncRNAs have different lengths (22 nt to >1, 000 nt) and mechanisms of action that essentially comprise a sophisticated gene expression regulation network. Recent publication of schistosome genomes and transcriptomes has increased the description and characterization of a large number of parasite genes. Here we review the number of predicted genes and the coverage of genomic bases in face of the public ESTs dataset available, including a critical appraisal of the evidence and characterization of ncRNAs in schistosomes. We show expression data for ncRNAs in Schistosoma mansoni. We analyze three different microarray experiment datasets: (1) adult worms' large-scale expression measurements; (2) differentially expressed S. mansoni genes regulated by a human cytokine (TNF-α) in a parasite culture; and (3) a stage-specific expression of ncRNAs. All these data point to ncRNAs involved in different biological processes and physiological responses that suggest functionality of these new players in the parasite's biology. Exploring this world is a challenge for the scientists under a new molecular perspective of host-parasite interactions and parasite development.

Migração lateral da desembocadura do Rio Itapocú, SC, Brasil: evolução morfológica e condicionantes físicas

Desembocaduras são ambientes bastante dinâmicos e sujeitos à complexa interação entre fatores estabilizadores e desestabilizadores. Dependendo dessa interação, desembocaduras podem apresentar a tendência de migração ao longo de barreiras arenosas. Um dos mecanismos mais eficientes de transporte de sedimento paralelo à costa, e consequentemente migração de canais, são as correntes longitudinais geradas pelas ondas se aproximando obliquamente à costa. A motivação do presente trabalho é entender o comportamento morfodinâmico do sistema de desembocadura do rio Itapocú, localizado no centro-norte de Santa Catarina (SC), frente aos processos forçantes que atuam na sua migração ao longo da linha de costa. A morfologia dos pontais arenosos foi obtida a partir de levantamentos morfológicos com o uso de DGPS. Para analisar a refração de ondas foi utilizado o modelo numérico MIKE 21 SW, sendo considerados como condições de contorno os dados de ondas referentes ao ano de 2002 e os dados de ondas previstos referentes ao período de coleta. Os dados de saída do modelo foram utilizados para estimar a deriva litorânea potencial na região. Os resultados morfológicos obtidos demonstraram uma migração da desembocadura para o norte durante o período analisado, sendo mais intenso durante o inverno e o verão. Ondas incidentes do quadrante sul sofreram mais o fenômeno da refração e as ondas de leste apresentaram menor variação angular ao se aproximarem à costa. A deriva litorânea potencial anual para os dados de ondas de 2002 apresentou sentido norte-sul, com inversão de sentido durante o outono. Utilizando os dados de ondas previstas para o período dos levantamentos, a deriva litorânea potencial estimada apresentou sentido sul-norte, concordando com a migração observada. Na região próxima a desembocadura, nos pontais arenosos, a deriva potencial apresentou direção para o norte durante todas as estações. Os dados de descarga fluvial não apresentaram influência na migração do canal, porém apresentaram uma relação com a largura do mesmo sazonalmente.Os dados de morfologia juntamente com os dados de deriva litorânea referentes às ondas de 2004/2005 mostraram claramente a migração do canal para o norte sendo a deriva a principal contribuinte para a migração da desembocadura.

Body trunk fat and insulin resistance in post-pubertal obese adolescents

CONTEXT AND OBJECTIVE: Insulin resistance is a metabolic disorder commonly associated with excess body fat accumulation that may increase chronic disease risk. The present study was undertaken to evaluate the relationship between body composition and insulin resistance among obese adolescents. DESIGN AND SETTING: Cross-sectional study, at the Adolescence Center, Pediatric Department, Universidade Federal de São Paulo. METHODS: Body composition was assessed using dual-energy X-ray absorptiometry. Dietary intake was evaluated using a three-day dietary record. The biochemical evaluation comprised glucose, insulin, serum lipid, leptin and ghrelin measurements. Insulin resistance was calculated by means of the homeostasis model assessment of insulin resistance (HOMA-IR). RESULTS: Forty-nine post-pubertal obese adolescents participated in the study: 12 boys and 37 girls of mean age 16.6 (1.4) years and mean body mass index (BMI) of 35.0 (3.9) kg/m². The mean glucose, insulin and HOMA values were 90.3 (6.4) mg/dl, 16.6 (8.1) µIU/ml and 3.7 (1.9), respectively. Hyperinsulinemia and insulin resistance were observed in 40.2% and 57.1% of the subjects, respectively. Adolescents with insulin resistance had higher BMI and body trunk fat. There was a trend towards higher leptin concentration in obese individuals with insulin resistance. Insulin resistance was positively correlated with body trunk fat, BMI, body fat mass (kg), leptin and body fat percentage. Furthermore, there was a negative correlation between HOMA-IR and lean body mass. The body composition predicted 30% of the HOMA-IR levels, according to linear regression models. CONCLUSION: Body trunk fat was significantly associated with insulin resistance, demonstrating the clinical importance of abdominal obesity during adolescence.

Shwachman-Kulczycki score still useful to monitor cystic fibrosis severity

INTRODUCTION: The Shwachman-Kulczycki score was the first scoring system used in cystic fibrosis to assess disease severity. Despite its subjectivity, it is still widely used. OBJECTIVE: To study correlations among forced expiratory volume in one second (FEV1), chest radiography, chest computed tomography, 6-minute walk test, and Shwachman-Kulczycki score in patients with cystic fibrosis and to test whether the Shwachman-Kulczycki score is still useful in monitoring the severity of the disease. METHODS: A cross-sectional prospective study was performed to analyze the correlations (Spearman). Patients with clinically stable cystic fibrosis, aged 3-21 years, were included. RESULTS: 43 patients, 19F/24M, mean age 10.5 + 4.7 years, with a median Shwachman-Kulczycki score of 70 were studied. The median Brasfield and Bhalla scores were 17 and 10, respectively. The mean Z score for the 6-minute walk test was -1.1 + 1.106 and the mean FEV1 was 59 + 26 (as percentage of predicted values). The following significant correlations versus the Shwachman-Kulczycki score were found: FEV1 (r = 0.76), 6-minute walk test (r = 0.71), chest radiography (r = 0.71) and chest computed tomography (r = -0.78). When patients were divided according to FEV1, a statistically significantly correlation with the Shwachman-Kulczycki score was found only in patients with FEV1 <70% (r = 0.67). CONCLUSIONS: The Shwachman-Kulczycki score remains an useful tool for monitoring the severity of cystic fibrosis, adequately reflecting the functional impairment and chest radiography and tomography changes, especially in patients with greater impairment of lung function. When assessing patients with mild lung disease its limitations should be considered and its usefulness in such patients should be evaluated in larger populations.

Rapid detection of bovine coronavirus by a semi-nested RT-PCR

Bovine coronavirus (BCoV) is a member of the group 2 of the Coronavirus (Nidovirales: Coronaviridae) and the causative agent of enteritis in both calves and adult bovine, as well as respiratory disease in calves. The present study aimed to develop a semi-nested RT-PCR for the detection of BCoV based on representative up-to-date sequences of the nucleocapsid gene, a conserved region of coronavirus genome. Three primers were designed, the first round with a 463bp and the second (semi-nested) with a 306bp predicted fragment. The analytical sensitivity was determined by 10-fold serial dilutions of the BCoV Kakegawa strain (HA titre: 256) in DEPC treated ultra-pure water, in fetal bovine serum (FBS) and in a BCoV-free fecal suspension, when positive results were found up to the 10-2, 10-3 and 10-7 dilutions, respectively, which suggests that the total amount of RNA in the sample influence the precipitation of pellets by the method of extraction used. When fecal samples was used, a large quantity of total RNA serves as carrier of BCoV RNA, demonstrating a high analytical sensitivity and lack of possible substances inhibiting the PCR. The final semi-nested RT-PCR protocol was applied to 25 fecal samples from adult cows, previously tested by a nested RT-PCR RdRp used as a reference test, resulting in 20 and 17 positives for the first and second tests, respectively, and a substantial agreement was found by kappa statistics (0.694). The high sensitivity and specificity of the new proposed method and the fact that primers were designed based on current BCoV sequences give basis to a more accurate diagnosis of BCoV-caused diseases, as well as to further insights on protocols for the detection of other Coronavirus representatives of both Animal and Public Health importance.

Acurácia, precisão e robustez das estimativas da digestibilidade aparente da matéria seca determinada com o uso de indicadores em ovinos

O objetivo foi avaliar a acurácia, precisão e robustez das estimativas da digestibilidade aparente da matéria seca obtidas utilizando-se como indicadores fibra em detergente ácido indigestível (FDAi), fibra em detergente neutro (FDNi) indigestível, lignina em detergente ácido (LDA), LDA indigestível (LDAi) e óxido crômico em comparação ao método de coleta total de fezes. Dezoito ovinos (56,5 ± 4,6 kg PV) foram designados aleatoriamente a dietas compostas de 25, 50 ou 75% de concentrado e feno de Coast cross por 25 dias. As fezes foram coletadas por cinco dias para determinação da digestibilidade aparente da MS. As amostras de alimentos e fezes foram incubadas no rúmen de três bovinos por 144 horas, para obtenção das frações indigestíveis. Óxido crômico foi administrado a 4,0 g/animal/dia. A acurácia foi avaliada pela comparação do viés médio (DAMS predito - DAMS observado) entre os indicadores; a precisão, por meio da raiz quadrada do erro de predição e do erro residual; e a robustez, pelo estudo da regressão entre o viés e o consumo de matéria seca, o nível de concentrado e o peso vivo. A recuperação fecal e a acurácia das estimativas da digestibilidade aparente da MS foram maiores para FDAi, seguida pela FDNi, LDAi, pelo óxido crômico e depois pela lignina em detergente ácido. O viés linear foi significativo apenas para FDAi, FDNi e LDAi. O uso de óxido crômico permitiu estimativas mais precisas da digestibilidade aparente da MS. Todos os indicadores foram robustos quanto à variação no consumo de matéria seca e apenas LDAi e óxido crômico foram robustos quanto aos níveis de concentrado na dieta. O óxido crômico não foi robusto quando houve variação no peso vivo animal. Assim, a FDAi é o indicador mais recomendado na estimativa da digestibilidade aparente da MS em ovinos quando o objetivo é comparar aos dados da literatura, enquanto o óxido crômico é mais recomendado quando o objetivo é comparar tratamentos dentro de um mesmo experimento.

Uso da cutina na estimativa da digestibilidade aparente de dietas para equinos

Avaliaram-se a acurácia, a precisão e a robustez dos indicadores cutina, lignina em detergente ácido, óxido crômico e coleta total de fezes na estimativa da digestibilidade aparente da matéria orgânica de dietas para equinos. Para tal, foram utilizados quatro equinos machos, com idade aproximada de 10 meses e média de peso de 197kg (170 a 216kg). O experimento foi realizado em quatro períodos, com duração de 11 dias cada, sendo os oito primeiros usados para adaptação às dietas e os três subsequentes, para colheita de material. O delineamento experimental foi em quadrado latino 4X4. A ponderação dos coeficientes de digestibilidade da matéria orgânica pelos indicadores foi efetuada por meio do viés. A acurácia e a precisão foram determinadas pela comparação entre os dados preditos e observados, e a robustez pela comparação dos vieses com outros fatores estudados. A cutina não se mostrou eficiente como indicador interno, pois superestimou a digestibilidade aparente da matéria orgânica e resultou em menor acurácia e precisão. O oxido crômico apresentou baixa recuperação fecal e subestimou a digestibilidade aparente da matéria orgânica, embora tenha sido o mais preciso. A lignina em detergente ácido foi o indicador que obteve a melhor recuperação fecal e foi o mais acurado, portanto, o indicador mais eficiente.

Effect of fructans-based fat replacer on chemical composition, starch digestibility and sensory acceptability of corn snacks

To develop a convenience healthy food snack the partially hydrogenated vegetable fat, used as the flavour fixative agent, was replaced by a non-fat-flavouring solution enriched with inulin and oligofructose. The effects of this replacement on chemical composition, in vitro rate of starch digestion and sensory acceptability were assessed. The new snack presented low-fat levels (0.1 per cent) and around a sevenfold increase in dietary fibre (15.3 per cent of dietary fibre, being 13.3 per cent of fructans) when compared with the traditional ones. The enrichment with fructans reduced the predicted Glycaemic Index by 25 per cent, thus indicating that this dietary fibre contributes effectively towards delaying the in vitro glycaemic response. Fructans-enriched snack presented overall acceptability score (6.6 ± 1.7) similar to the traditional one, flavoured with fatty fixative agent (7.4 ± 1.4). The healthy low-fat fibre-enriched snack produced presented the high sensory acceptability typical for this food product type

Impactos das atividades humanas sobre a dinâmica do fósforo no meio ambiente e seus reflexos na saúde pública

O fósforo é um nutriente com fontes finitas e não renováveis, cuja velocidade de exploração é atualmente muito superior às suas taxas de retorno ao seu ciclo natural, sendo que já existem previsões a respeito de um provável colapso nas suas fontes disponíveis e conhecidas, com impactos econômicos, sociais e ambientais graves e irreversíveis. Diante desse cenário, o presente trabalho busca apresentar informações sobre a dinâmica do fósforo no meio ambiente, avaliando os impactos causados pelas atividades humanas e verificando as ações que podem auxiliar na preservação do ciclo do nutriente. Visando contribuir para uma melhor visualização do assunto, foi analisada a evolução dos dados relativos à concentração populacional, número de industriais e extensão das áreas cultivadas em uma bacia hidrográfica, em relação às concentrações de fósforo nos compartimentos água e sedimento, ao longo de 22 anos. Para tanto, utilizou-se o rio Tietê como estudo de caso. Os resultados obtidos indicam que o controle das fontes domésticas, principalmente da quantidade de tripolifosfato de sódio (STPP) utilizada nos detergentes, é de grande importância para melhoria da qualidade das águas, proteção ao meio ambiente e garantia da saúde pública

Quasinormal modes of black holes in anti-de Sitter space: A numerical study of the eikonal limit

Using series solutions and time-domain evolutions, we probe the eikonal limit of the gravitational and scalar-field quasinormal modes of large black holes and black branes in anti-de Sitter backgrounds. These results are particularly relevant for the AdS/CFT correspondence, since the eikonal regime is characterized by the existence of long-lived modes which (presumably) dominate the decay time scale of the perturbations. We confirm all the main qualitative features of these slowly damped modes as predicted by Festuccia and Liu [G. Festuccia and H. Liu, arXiv:0811.1033.] for the scalar-field (tensor-type gravitational) fluctuations. However, quantitatively we find dimensional-dependent correction factors. We also investigate the dependence of the quasinormal mode frequencies on the horizon radius of the black hole (brane) and the angular momentum (wave number) of vector- and scalar-type gravitational perturbations.

The full Bayesian significance test for mixture models: results in gene expression clustering

Gene clustering is a useful exploratory technique to group together genes with similar expression levels under distinct cell cycle phases or distinct conditions. It helps the biologist to identify potentially meaningful relationships between genes. In this study, we propose a clustering method based on multivariate normal mixture models, where the number of clusters is predicted via sequential hypothesis tests: at each step, the method considers a mixture model of m components (m = 2 in the first step) and tests if in fact it should be m - 1. If the hypothesis is rejected, m is increased and a new test is carried out. The method continues (increasing m) until the hypothesis is accepted. The theoretical core of the method is the full Bayesian significance test, an intuitive Bayesian approach, which needs no model complexity penalization nor positive probabilities for sharp hypotheses. Numerical experiments were based on a cDNA microarray dataset consisting of expression levels of 205 genes belonging to four functional categories, for 10 distinct strains of Saccharomyces cerevisiae. To analyze the method's sensitivity to data dimension, we performed principal components analysis on the original dataset and predicted the number of classes using 2 to 10 principal components. Compared to Mclust (model-based clustering), our method shows more consistent results.

Aging and fluctuation-dissipation ratio in a nonequilibrium q-state lattice model

A generalized version of the nonequilibrium linear Glauber model with q states in d dimensions is introduced and analyzed. The model is fully symmetric, its dynamics being invariant under all permutations of the q states. Exact expressions for the two-time autocorrelation and response functions on a d-dimensional lattice are obtained. In the stationary regime, the fluctuation-dissipation theorem holds, while in the transient the aging is observed with the fluctuation-dissipation ratio leading to the value predicted for the linear Glauber model.

NEAR INFRARED SPECTROSCOPY FOR ESTIMATING SUGARCANE BAGASSE CONTENT IN MEDIUM DENSITY FIBERBOARD

Medium density fiberboard (MDF) is an engineered wood product formed by breaking down selected lignin-cellulosic material residuals into fibers, combining it with wax and a resin binder, and then forming panels by applying high temperature and pressure. Because the raw material in the industrial process is ever-changing, the panel industry requires methods for monitoring the composition of their products. The aim of this study was to estimate the ratio of sugarcane (SC) bagasse to Eucalyptus wood in MDF panels using near infrared (NIR) spectroscopy. Principal component analysis (PCA) and partial least square (PLS) regressions were performed. MDF panels having different bagasse contents were easily distinguished from each other by the PCA of their NIR spectra with clearly different patterns of response. The PLS-R models for SC content of these MDF samples presented a strong coefficient of determination (0.96) between the NIR-predicted and Lab-determined values and a low standard error of prediction (similar to 1.5%) in the cross-validations. A key role of resins (adhesives), cellulose, and lignin for such PLS-R calibrations was shown. PLS-DA model correctly classified ninety-four percent of MDF samples by cross-validations and ninety-eight percent of the panels by independent test set. These NIR-based models can be useful to quickly estimate sugarcane bagasse vs. Eucalyptus wood content ratio in unknown MDF samples and to verify the quality of these engineered wood products in an online process.

AtPIN: Arabidopsis thaliana Protein Interaction Network

Background: Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description: All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C(3)) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions: AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in Genome Differentiation

Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1), and in two candidate molecules (Ann1 and Dixon) were assessed. Based on comparative best bidirectional hit analyses, the majority (51%) of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.