Otimização da diagnose molecular de vírus, bactéria e fungo em cana-de-açúcar.

RESUMO: Visando à otimização da diagnose molecular de plântulas de cana-de-açúcar, tentou-se desenvolver iniciadores específicos para escaldadura e ferrugem alaranjada, assim como a comparação da PCR comum e a PCR em Tempo Real (PCR/TR) de maior resolução, importante para doenças com grande período de latência, como as causadas por: 1- Bactérias, (a) raquitismo-da-soqueira (Leifsonina xyli subsp. Xyli) e (b) escaldadura (Xanthomonas aibilineans); 2- Vírus, (a) amarelinho (Sugarcane Yellow Leaf Vírus); (b) mosaico (Sugarcane Mosaic Vírus) e (c) fijivirus (Fiji disease vírus); 3- fungo, (a) carvão (Sporisorium scitamineum) e (b) ferrugem alaranjada (Puccinia kuehnii). As plântulas foram obtidas do quarentenário do IAC. Os iniciadores da literatura para cana-de-açúcar detectaram especificamente o raquitismo, amarelinho, mosaico e fijivirus, enquanto os desenvolvidos para PCR/TR para as mesmas doenças, incluindo a escaldadura e ferrugem alaranjada, possibilitaram a detecção com maior diluição das amostras. Os iniciadores da ferrugem alaranjada, além de não detectarem a ferrugem marrom, também diferenciaram a ferrugem branca do milho. Os da escaldadura não foram específicos somente para o gênero Erwinia, enquanto que os da literatura não diferenciaram também outras espécies dos gêneros Kanthomonas, Pseudomonas, Enwinia, Stenotrophomona e Pantoea. A otimização das diluições para PCR/TR a partir de cDNA foi de apenas lOX. Porém, para extratos de DNA de planta, foi maior, de lOOX a lOOOX,indicando a maior sensibilidade do método. Dos 28 pares de iniciadores testados, os melhores para o agente causal de cada doença e curvas de diluições (com eficiência de PCR de 1,05 a 1,28) são apresentados

The Critical Behaviour of the Spin-3/2 Blume-Capel Model in Two Dimensions

The phase diagram of the spin-3/2 Blume-Capel model in two dimensions is explored by conventional finite-size scaling, conformal invariance and Monte Carlo simulations. The model in its $\tau$-continuum Hamiltonian version is also considered and compared with others spin-3/2 quantum chains. Our results indicate that differently from the standard spin-1 Blume-Capel model there is no multicritical point along the order-disorder transition line. This is in qualitative agreement with mean field prediction but in disagreement with previous approximate renormalization group calculations. We also presented new results for the spin-1 Blume-Capel model.Comment: latex 18 pages, 4 figure

Análises moleculares de bactérias e fungo em cana-de-açúcar.

RESUMO: A cana-de-açúcar é uma das principais culturas do Brasil, que é o maior produtor mundial de açúcar e álcool. A cultura da cana-de-açucar é extremamente vulnerável a doenças devido ao sistema de propagação por toletes facilitar a disseminação dos patógenos, uma vez que os colmos mesmo infectados podem não apresentar sintomas. A propagação dessas doenças em monoculturas em grandes áreas facilita as epidemias, sendo importante para o plantio de mudas sadias, métodos para a detecção precoce de doenças. Dentre as doenças mais importantes em cana-de-açúcar, são conhecidas as causadas por bactérias como a Leifsonia xyli subsp.xyli, agente causal do Raquitismo-da-soqueira ou ?ratoon stunting disease? (RSD) e a Xanthomonas albilineans, responsável pela Escaldadura das folhas ou ?sugarcarne leaf scald? (Ashby); por fungo como o do carvão (Ustilago scitaminea) que é uma doença considerada em todos os programas de melhoramento genético, com longo período de latência. Foram utilizadas como amostras folhas de plântulas de cana-açúcar desenvolvidas de cultura de tecido com cerca de 2 meses de transplante. Foram utilizados iniciadores de literatura para raquitismo e escaldadura ou desenvolvido pelo laboratório para carvão. Os fragmentos amplificados de cada doença foram clonados e a identidade confirmada por BLAST. O DNA dos controles positivos das reações foi obtido de clones dos fragmentos amplificados de plantas infectadas. Os iniciadores desenvolvidos para carvão mostraram especificidade em amostras de folhas de plântulas de cana-de-açúcar. A detecção de infecção confirma a eficácia da metodologia em plântulas com 2 meses de transplante, assim como o uso de clones como controle positivo, a maior facilidade para diagnostico de infecção em plântulas de cana-de-açúcar

Applied immuno-epidemiological research: an approach for integrating existing knowledge into the statistical analysis of multiple immune markers.

BACKGROUND: Immunologists often measure several correlated immunological markers, such as concentrations of different cytokines produced by different immune cells and/or measured under different conditions, to draw insights from complex immunological mechanisms. Although there have been recent methodological efforts to improve the statistical analysis of immunological data, a framework is still needed for the simultaneous analysis of multiple, often correlated, immune markers. This framework would allow the immunologists' hypotheses about the underlying biological mechanisms to be integrated. RESULTS: We present an analytical approach for statistical analysis of correlated immune markers, such as those commonly collected in modern immuno-epidemiological studies. We demonstrate i) how to deal with interdependencies among multiple measurements of the same immune marker, ii) how to analyse association patterns among different markers, iii) how to aggregate different measures and/or markers to immunological summary scores, iv) how to model the inter-relationships among these scores, and v) how to use these scores in epidemiological association analyses. We illustrate the application of our approach to multiple cytokine measurements from 818 children enrolled in a large immuno-epidemiological study (SCAALA Salvador), which aimed to quantify the major immunological mechanisms underlying atopic diseases or asthma. We demonstrate how to aggregate systematically the information captured in multiple cytokine measurements to immunological summary scores aimed at reflecting the presumed underlying immunological mechanisms (Th1/Th2 balance and immune regulatory network). We show how these aggregated immune scores can be used as predictors in regression models with outcomes of immunological studies (e.g. specific IgE) and compare the results to those obtained by a traditional multivariate regression approach. CONCLUSION: The proposed analytical approach may be especially useful to quantify complex immune responses in immuno-epidemiological studies, where investigators examine the relationship among epidemiological patterns, immune response, and disease outcomes

Risk factors for asthma and allergy associated with urban migration: background and methodology of a cross-sectional study in Afro-Ecuadorian school children in Northeastern Ecuador (Esmeraldas-SCAALA Study)

BACKGROUND: Asthma and allergic diseases are becoming increasingly frequent in children in urban centres of Latin America although the prevalence of allergic disease is still low in rural areas. Understanding better why the prevalence of asthma is greater in urban migrant populations and the role of risk factors such as life style and environmental exposures, may be key to understand what is behind this trend. METHODS/DESIGN: The Esmeraldas-SCAALA (Social Changes, Asthma and Allergy in Latin America) study consists of cross-sectional and nested case-control studies of school children in rural and urban areas of Esmeraldas Province in Ecuador. The cross-sectional study will investigate risk factors for atopy and allergic disease in rural and migrant urban Afro-Ecuadorian school children and the nested case-control study will examine environmental, biologic and social risk factors for asthma among asthma cases and non-asthmatic controls from the cross-sectional study. Data will be collected through standardised questionnaires, skin prick testing to relevant aeroallergen extracts, stool examinations for parasites, blood sampling (for measurement of IgE, interleukins and other immunological parameters), anthropometric measurements for assessment of nutritional status, exercise testing for assessment of exercise-induced bronchospasm and dust sampling for measurement of household endotoxin and allergen levels. DISCUSSION: The information will be used to identify the factors associated with an increased risk of asthma and allergies in migrant and urbanizing populations, to improve the understanding of the causes of the increase in asthma prevalence and to identify potentially modifiable factors to inform the design of prevention programmes to reduce the risk of allergy in urban populations in Latin America

Impact of a Citywide Sanitation Program in Northeast Brazil on Intestinal Parasites Infection in Young Children

BACKGROUND: Sanitation affects health, especially that of young children. Residents of Salvador, in Northeast Brazil, have had a high prevalence of intestinal parasites. A citywide sanitation intervention started in 1996 aimed to raise the level of sewer coverage from 26% to 80% of households. OBJECTIVES: We evaluated the impact of this intervention on the prevalence of Ascaris lumbricoides, Trichuris trichuria, and Giardia duodenalis infections in preschool children. METHODS: The evaluation was composed of two cross-sectional studies (1998 and 2003-2004), each of a sample of 681 and 976 children 1-4 years of age, respectively. Children were sampled from 24 sentinel areas chosen to represent the range of environmental conditions in the study site. Data were collected using an individual/household questionnaire, and an environmental survey was conducted in each area before and after the intervention to assess basic household and neighborhood sanitation conditions. Stool samples were examined for the presence of intestinal parasites. The effect of the intervention was estimated by hierarchical modeling, fitting a sequence of multivariate regression models. FINDINGS: The prevalence ofA. lumbricoides infection was reduced from 24.4% to 12.0%, T. trichuria from 18.0% to 5.0%, and G. duodenalis from 14.1% to 5.3%. Most of this reduction appeared to be explained by the increased coverage in each neighborhood by the sewage system constructed during the intervention. The key explanatory variable was thus an ecological measure of exposure and not household-based, suggesting that the parasite transmission prevented by the program was mainly in the public (vs. the domestic) domain. CONCLUSION: This study, using advanced statistical modeling to control for individual and ecological potential confounders, demonstrates the impact on intestinal parasites of sanitation improvements implemented at the scale of a large population

Biomassa sustentável de juvenis de pirarucu em tanques-rede de pequeno volume

The objective of this work was to estimate the sustainable biomass of pirarucu Arapaima gigas (Cuvier, 1829) juveniles kept in small volume net cages. During 200 days four 1-m3 net cages were stocked with 21 fish/cage and had an initial total biomass of 0.84±0.14 kg (21 fish/cage). The net cages were placed in a 50-m2 pond with constant water flow. Conditioning factor, feed conversion, specific growth rate and gain showed that the sustainable biomass of pirarucu juveniles for intensive rearing in 1-m 3 net cages was approximately 29 kg. Fish length at the end of the trial, in relation to the reduced net cage space, was a limiting factor to obtain good biological indices

Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil

The dengue virus has a single-stranded positive-sense RNA genome of ∼10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1–4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000–2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R0 = 1.53 and values for lineage 2 of R0 = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area