Temporal Dynamics of Tomato Severe Rugose Virus and Bemisia tabaci in Tomato Fields in São Paulo,Brazil

Temporal progress of a begomovirus disease in tomato fields and the abundance of its whitefly vector, Bemisia tabaci biotype B, were evaluated during three consecutive tomato plantings in the municipality of Sumaré, state of São Paulo, Brazil, in 2006 and 2007. The incidence of symptomatic plants and the number of adult whiteflies were weekly monitored on experimental plots randomly chosen in tomato commercial fields. Tomato severe rugose virus (ToSRV) was identified as the causal agent of the disease, and its relationships with other Brazilian begomoviruses was confirmed by partial and complete nucleotide sequencing of the viral genome. The disease temporal progress was analysed by fitting different models to disease incidence. The monomolecular model showed the best fit, which is consistent with a predominant role of primary spread in the epidemiology of ToSRV. A higher number of adult whiteflies were observed at the borders of the plots, also suggesting primary spread of ToSRV from external sources of inoculum, which might be represented by weeds and volunteer tomato‐infected plants. In Brazil, since 2004, there is a legislative measure that mandates, for some regions of processing tomato plantings, a 2‐month crop‐free period during the year. Based on our results, we suggest the extension of this measure to all tomato‐producing regions, including fresh market tomato. We also suggest that growers emphasize the elimination of old plants from harvested fields that can serve as virus reservoirs several weeks prior to new plantings and weeds nearby the fields to limit the primary spread of ToSRV.     

Fatal toxoplasmosis in a southern muriqui (Brachyteles arachnoides) from São Paulo state,Brazil: Pathological,immunohistochemical, and molecular characterization

We report the pathological, immunohistochemical, and molecular features of fatal acute systemic toxoplasmosis in an adult, female, free‐living southern muriqui (Brachyteles arachnoides) from São Paulo state, Brazil. PCR‐RFLP genotyping analysis identified the #21 genotype of Toxoplasma gondii. This represents the first report of acute toxoplasmosis involving this genotype in humans and animals.     

DNA barcodes identify marine fishes of São Paulo State,Brazil

Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centres, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, this study aims to assemble a DNA barcode reference sequence library for marine fishes from the coastal region of São Paulo State, Brazil. The standard 652 bp ‘barcode’ fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bidirectionally sequenced from 678 individuals belonging to 135 species. A neighbour‐joining analysis revealed that this approach can unambiguously discriminate 97% of the species surveyed. Most species exhibited low intraspecific genetic distances (0.31%), about 43‐fold less than the distance among species within a genus. Four species showed higher intraspecific divergences ranging from 2.2% to 7.6%, suggesting overlooked diversity. Notably, just one species‐pair exhibited barcode divergences of <1%. This library is a first step to better know the molecular diversity of marine fish species from São Paulo, providing a basis for further studies of this fauna – extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating the estimations about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation.     

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

Combinations of histones carrying different covalent modifications are a major component of epigenetic variation. We have mapped nine modified histones in the barley seedling epigenome by chromatin immunoprecipitation next‐generation sequencing (ChIP‐seq). The chromosomal distributions of the modifications group them into four different classes, and members of a given class also tend to coincide at the local DNA level, suggesting that global distribution patterns reflect local epigenetic environments. We used this peak sharing to define 10 chromatin states representing local epigenetic environments in the barley genome. Five states map mainly to genes and five to intergenic regions. Two genic states involving H3K36me3 are preferentially associated with constitutive gene expression, while an H3K27me3‐containing genic state is associated with differentially expressed genes. The 10 states display striking distribution patterns that divide barley chromosomes into three distinct global environments. First, telomere‐proximal regions contain high densities of H3K27me3 covering both genes and intergenic DNA, together with very low levels of the repressive H3K27me1 modification. Flanking these are gene‐rich interior regions that are rich in active chromatin states and have greatly decreased levels of H3K27me3 and increasing amounts of H3K27me1 and H3K9me2. Lastly, H3K27me3‐depleted pericentromeric regions contain gene islands with active chromatin states separated by extensive retrotransposon‐rich regions that are associated with abundant H3K27me1 and H3K9me2 modifications. We propose an epigenomic framework for barley whereby intergenic H3K27me3 specifies facultative heterochromatin in the telomere‐proximal regions and H3K27me1 is diagnostic for constitutive heterochromatin elsewhere in the barley genome.     

Plant‐mediated effects of drought on aphid population structure and parasitoid attack

The effects of predicted climate change on aphid–natural enemy interactions have principally considered the effects of elevated carbon dioxide concentration and air temperature. However, increased incidence of summer droughts are also predicted in Northern Europe, which could affect aphid–plant interactions and aphid antagonists. We investigated how simulated summer drought affected the bird cherry–oat aphid, Rhopalosiphum padi L., and its natural enemy the parasitoid wasp Aphidius ervi. Drought and, to a greater extent, aphids reduced barley ( Hordeum vulgare) dry mass by 33% and 39%, respectively. Drought reduced leaf and root nitrogen concentrations by 13% and 28%, respectively, but foliar amino acid concentrations and composition remained similar. Aphid numbers were unaffected by drought, but population demography changed significantly; adults constituted 41% of the population on drought‐treated plants, but only 26% on those receiving ambient irrigation. Nymphs constituted 56% and 69% of the population on these plants, respectively, suggesting altered aphid development rates on drought‐stressed plants. Parasitism rates were significantly lower on drought‐stressed plants (9 attacks h^?1 compared with 35 attacks h^?1 on ambient‐irrigated plants), most likely because of lower incidence of nymphs and more adults, the latter being more difficult to parasitize. Any physiological changes in individual aphids did not affect parasitoid preferences, suggesting that attacks were postponed because of drought‐induced changes in aphid demography. This study demonstrates the potential for sporadic climate change events, such as summer drought, to be disruptive to herbivore–antagonist interactions.     

Seasonal population dynamics and the genetic structure of the mosquito vector Aedes aegypti in São Paulo,Brazil

Population genetic studies of insect vectors can generate knowledge to improve epidemiological studies focused on the decrease of pathogen transmission. In this study, we used nine SNPs across the Aedes aegypti genome to characterize seasonal population variations of this important dengue vector. Mosquito samples were obtained by ovitraps placed over Botucatu SP from 2005 to 2010. Our data show that, regardless of the large variation in mosquito abundance (deduced from the number of eggs obtained from ovitraps), the effective population size remained stable over the years. These results suggest that Ae. aegypti is able to maintain a sufficiently large active breeding population during the dry season to keep genetic frequencies stable. These results open new perspectives on mosquito survey and control methods.     

Application of nontargeted metabolite profiling to discover novel markers of quality traits in an advanced population of malting barley

The process of breeding superior varieties for the agricultural industry is lengthy and expensive. Plant metabolites may act as markers of quality traits, potentially expediting the appraisal of experimental lines during breeding. Here, we evaluated the utility of metabolites as markers by assessing metabolic variation influenced by genetic and environmental factors in an advanced breeding setting and in relation to the phenotypic distribution of 20 quality traits. Nontargeted liquid chromatography–mass spectrometry metabolite profiling was performed on barley (Hordeum vulgare L.) grain and malt from 72 advanced malting barley lines grown at two distinct but climatically similar locations, with 2‐row and 6‐row barley as the main genetic factors. 27 420 molecular features were detected, and the metabolite and quality trait profiles were similarly influenced by genotype and environment; however, malt was more influenced by genotype compared with barley. An O2PLS model characterized molecular features and quality traits that covaried, and 1319 features associated with at least one of 20 quality traits. An indiscriminant MS/MS acquisition and novel data analysis method facilitated the identification of metabolites. The analysis described 216 primary and secondary metabolites that correlated with multiple quality traits and included amines, amino acids, alkaloids, polyphenolics and lipids. The mechanisms governing quality trait–metabolite associations were interpreted based on colocalization to genetic markers and their gene annotations. The results of this study support the hypothesis that metabolism and quality traits are co‐influenced by relatively narrow genetic and environmental factors and illustrate the utility of grain metabolites as functional markers of quality traits.     

Genetic Structure and Aggressiveness of Rhizoctonia solani AG1‐IA,the Cause of Sheath Blight of Rice in Southern China

One hundred and eighty isolates of Rhizoctonia solani AG1‐IA, the causal agent of rice sheath blight, were obtained from six locations in southern China. The genetic structure of R. solani isolates was investigated using random amplified polymorphic DNA (RAPD) markers, and a considerable genetic variation among R. solani isolates was observed. Most of the genetic diversity was distributed within populations, rather than among them. The distribution pattern of the genetic variation of R. solani appears to be the result of high gene flow (Nm) and low‐genetic differentiation among populations. The aggressiveness of R. solani was visually assessed by rice seedlings of five different cultivars in the glasshouse. All isolates tested were found to induce significantly different levels of disease severity, reflecting considerable variation in aggressiveness. The isolates were divided into highly virulent, moderately virulent and weakly virulent groups, and the moderately virulent isolates were dominant in R. solani population. No significant correlation was observed among the genetic similarity, pathogenic aggressiveness and geographical origins of the isolates. Information obtained from this study may be useful for breeding for improved resistance to sheath blight.     

Arabinoxylan, β‐glucan and pectin in barley and malt endosperm cell walls: a microstructure study using CLSM and cryo‐SEM

The architecture of endosperm cell walls in Hordeum vulgare (barley) differs remarkably from that of other grass species and is affected by germination or malting. Here, the cell wall microstructure is investigated using (bio)chemical analyses, cryogenic scanning electron microscopy (cryo‐SEM) and confocal laser scanning microscopy (CLSM) as the main techniques. The relative proportions of β‐glucan, arabinoxylan and pectin in cell walls were 61, 34 and 5%, respectively. The average thickness of a single endosperm cell wall was 0.30 µm, as estimated by the cryo‐SEM analysis of barley seeds, which was reduced to 0.16 µm after malting. After fluorescent staining, 3D confocal multiphoton microscopy (multiphoton CLSM) imaging revealed the complex cell wall architecture. The endosperm cell wall is composed of a structure in which arabinoxylan and pectin are colocalized on the outside, with β‐glucan depositions on the inside. During germination, arabinoxylan and β‐glucan are hydrolysed, but unlike β‐glucan, arabinoxylan remains present in defined cell walls in malt. Integrating the results, an enhanced model for the endosperm cell walls in barley is proposed.     

Obesity and Malnutrition in a Shantytown Population in the City of São Paulo,Brazil

To investigate the prevalence of obesity and malnutrition in the poor Brazilian population we conducted a survey on the socioeconomic and nutritional status of 535 families (comprising 2 411 individuals) living in shanty towns in the city of São Paulo. There was a 30% prevalence of malnutrition in the children, with chronic malnutrition as the most predominant problem. The prevalence of obesity was 6.4% in boys and 8.7% in girls. Overweight and obesity associated with stunting was found in 5.8% of boys and 6.8% girls. Adolescents showed a higher prevalence of malnutrition when weight-for-age distribution was used (boys 46.4%, girls 40.2%), but a right deviation in the distribution was observed with an increase in obesity and a decrease of malnutrition was observed (obesity was 21% in girls and 8.8% in boys; malnutrition was 15.5% in boys and 12.6% in girls) when the weight-for-height adjustment was made. Stunting was the most predominant type of malnutrition in both sexes. Obesity associated with stunting was more common than obesity without stunting, both in younger children and adolescents. Adults had a higher prevalence of obesity than malnutrition according to both the Metropolitan Life Insurance tables (1.7% of undernutrition, 16.7% of overweight, and 14.1% of obesity) and Body Mass Index (8.5% of undernutrition, 21.9% of overweight, and 14.6% of obesity). There was an increase in the percentage of obese children when at least one adult in the family was obese and an increased percentage of malnourished children when undernourished adults were present in the family. Obesity among the adults of the family decreased the occurrence of malnutrition among the children. In 9% of families there was a coexistence of obesity in the adults and malnutrition in the children. These results demonstrate a coexistence of malnutrition and obesity in poor urban Brazilian communities.     

Blood meal sources of mosquitoes captured in municipal parks in São Paulo,Brazil

The aim of this study was to investigate blood meal sources of mosquitoes captured in municipal parks in the city of São Paulo, Brazil, and to identify possible associations between mosquito species and their food preferences. Fourteen species of blood hosts of 510 engorged adult female mosquitoes were identified using PCR assays with a vertebrate‐specific primer set based on cytochrome b mitochondrial DNA of the following vertebrates: birds, dogs, cats, rodents, humans, and other primates. Mosquitoes were captured using a manual aspirator, CDC traps in the canopy, CDC traps at ground level, and Shannon traps. With the exception of cats, all other vertebrates were used as hosts by mosquitoes in the parks. Statistical analysis failed to show any trend toward association between most culicid species captured and the sources of blood meals. Instead, they revealed random patterns, indicating that the mosquitoes fed on the most abundant or convenient blood meal sources. Although feeding preferences were observed in two species (birds in the case of Cx. nigripalpus and dogs in the case of Cx. quinquefasciatus), our results highlight the opportunistic feeding habits of the female mosquitoes in this study.     

Drought‐related secondary metabolites of barley (Hordeum vulgare L.) leaves and their metabolomic quantitative trait loci

Determining the role of plant secondary metabolites in stress conditions is problematic due to the diversity of their structures and the complexity of their interdependence with different biological pathways. Correlation of metabolomic data with the genetic background provides essential information about the features of metabolites. LC‐MS analysis of leaf metabolites from 100 barley recombinant inbred lines (RILs) revealed that 98 traits among 135 detected phenolic and terpenoid compounds significantly changed their level as a result of drought stress. Metabolites with similar patterns of change were grouped in modules, revealing differences among RILs and parental varieties at early and late stages of drought. The most significant changes in stress were observed for ferulic and sinapic acid derivatives as well as acylated glycosides of flavones. The tendency to accumulate methylated compounds was a major phenomenon in this set of samples. In addition, the polyamine derivatives hordatines as well as terpenoid blumenol C derivatives were observed to be drought related. The correlation of drought‐related compounds with molecular marker polymorphisms resulted in the definition of metabolomic quantitative trait loci in the genomic regions of single‐nucleotide polymorphism 3101‐111 and simple sequence repeat Bmag0692 with multiple linkages to metabolites. The associations pointed to genes related to the defence response and response to cold, heat and oxidative stress, but not to genes related to biosynthesis of the compounds. We postulate that the significant metabolites have a role as antioxidants, regulators of gene expression and modulators of protein function in barley during drought.     

Thermal Regime and Stability of Jurumirim Reservoir (Paranapanema River,São Paulo,Brazil)

Thermal regime and stability in Jurumirim Reservoir (São Paulo, Brazil) were studied for a year. Isothermy and thermal stratification were observed from June to September and from October to March, respectively. The annual heat budget was 14.0 Kcal · cm⁻² and average heat gain per day was 67.2 cal · cm⁻² · day⁻¹. Maximum stability and wind work reached 324.2 and 3,037.5 g · cm · cm⁻², respectively. According to thermal structure and heat content, Jurumirim Reservoir was classified as a warm tropical monomictic lake.