Key locations for soybean genotype assessment in Central Brazil

The objective of this work was to identify key locations for the establishment of soybean (Glycine max) genetic breeding programs, in the Central Region of Brazil. Grain yield data of three maturity groups of soybean genotypes, from regional trials conducted over three years, at 18 locations in Brazilian Cerrado were used. A key location for the early phases of the breeding program was defined as the site that best classifies the winning genotypes in the region. Key locations for the final phases were defined as those sites that best represent each environmental stratum, in relation to the adaptability of the respective winning genotype. This adaptability was estimated by additive main effects and multiplicative interaction (AMMI) model analysis, using the distance between the score of each location in a stratum and the score of the winning genotype, which characterizes such stratum in an AMMI biplot. The locations that best classified the winning genotypes over space and time were Mineiros, Placas and Rio Verde. For the final phases of genotype selection, with data from the three maturity group, the recommended locations were: Buritis, Chapadão do Céu, Iraí, Pamplona, Placas, Planaltina, Rio Verde, Sacramento, Senador Canedo, Uberaba, and Uberlândia.

Occurrence of Symphyla (Myriapoda) in the region of the Upper Solimões River, Amazonas, Brazil

The present work aimed at identifying the Symphyla species diversity and abundance in various land-use systems under different degrees of intensification in western Amazonia. This is the first inventory of Symphyla in primary and secondary forest, crops, agroforestry systems and pastures which was carried out in Benjamin Constant municipality, in the region of the Upper Solimões River, Brazil. Samples (n = 101) were collected using a metal corer, and the symphylan extraction was carried out using Berlese-Tullgren funnels. Two genera and three species of symphylans were encountered. Considering the diversity encountered in Amazonian inventories, with only four genera and five known species overall, the three species found in the present study are considered a reasonable representation of the regional diversity. Two of the Hanseniella species found have been known to cause plant damage.

The earthworm fauna of regenerating forests and anthropogenic habitats in the coastal region of Paraná

The aim of this study was to evaluate abundance, biomass and diversity of earthworms in the southern coast region of the Mata Atlântica biodiversity hotspot. A total of 51 study sites in pastures, banana monocultures, mixed agroforestry systems, secondary forests in succession and old-growth forests near the coast of Paraná, Brazil, were evaluated. Each site was sampled once. Species richness of the earthworms was generally low and varied little between sites. At all sites except for one, the peregrine species Pontoscolex corethrurus (Glossoscolecidae) strongly dominated. Three other peregrine species, Amynthas corticis, Amynthas gracilis (Megascolecidae) and Ocnerodrilus occidentalis (Ocnerodrilidae), were frequent in moist sites. No autochthonous species were found. Abundance and biomass of earthworms varied strongly within and between sites (0-338 individuals m-2, 0-96 g m-2 fresh weight). Pastures had significantly lower abundance than all other sites. The forest sites had similar earthworm abundance and biomass, with a tendency to be higher in younger succession stages. The coastal plain region has been strongly altered by human activities. Reasons for the lack of any autochthonous species and the dominance of one peregrine species require further investigation.

Energy balance measurements over a banana orchard in the Semiarid region in the Northeast of Brazil

The objective of this work was to evaluate the reliability of eddy covariance measurements, analyzing the energy balance components, evapotranspiration and energy balance closure in dry and wet growing seasons, in a banana orchard. The experiment was carried out at a farm located within the irrigation district of Quixeré, in the Lower Jaguaribe basin, in Ceará state, Brazil. An eddy covariance system was used to measure the turbulent flux. An automatic weather station was installed in a grass field to obtain the reference evapotranspiration (ET0) from the combined FAO-Penman-Monteith method. Wind speed and vapor pressure deficit are the most important variables on the evaporative process in both growing seasons. In the dry season, the heat fluxes have a similar order of magnitude, and during the wet season the latent heat flux is the largest. The eddy covariance system had acceptable reliability in measuring heat flux, with actual evapotranspiration results comparing well with those obtained by using the water balance method. The energy balance closure had good results for the study area, with mean values of 0.93 and 0.86 for the dry and wet growing seasons respectively.

GacS sensor domains pertinent to the regulation of exoproduct formation and to the biocontrol potential of Pseudomonas fluorescens CHA0.

In the root-colonizing biocontrol strain CHA0 of Pseudomonas fluorescens, cell density-dependent synthesis of extracellular, plant-beneficial secondary metabolites and enzymes is positively regulated by the GacS/GacA two-component system. Mutational analysis of the GacS sensor kinase using improved single-copy vectors showed that inactivation of each of the three conserved phosphate acceptor sites caused an exoproduct null phenotype (GacS-), whereas deletion of the periplasmic loop domain had no significant effect on the expression of exoproduct genes. Strain CHA0 is known to synthesize a solvent-extractable extracellular signal that advances and enhances the expression of exoproduct genes during the transition from exponential to stationary growth phase when maximal exoproduct formation occurs. Mutational inactivation of either GacS or its cognate response regulator GacA abolished the strain's response to added signal. Deletion of the linker domain of the GacS sensor kinase caused signal-independent, strongly elevated expression of exoproduct genes at low cell densities. In contrast to the wild-type strain CHA0, the gacS linker mutant and a gacS null mutant were unable to protect tomato plants from crown and root rot caused by Fusarium oxysporum f. sp. radicis-lycopersici in a soil-less microcosm, indicating that, at least in this plant-pathogen system, there is no advantage in using a signal-independent biocontrol strain.

Hot spots for diversity of Magnaporthe oryzae physiological races in irrigated rice fields in Brazil

The objective of this work was to evaluate the Magnaporthe oryzae pathotype diversity in new commercial irrigated rice fields in the Araguaia River Valley, state of Tocantins, Brazil. The causal agent of rice blast has heavily affected rice production in the region. Despite the efforts of breeding programs, blast resistance breakdown has been recorded shortly after the release of new resistant cultivars developed for the region. Among the causes of resistance breakage is the capacity of the fungus to rapidly develop new pathotypes. A sample of 479 M. oryzae monosporic isolates was obtained and tested using the international rice blast differential set. Isolate collections were made in small areas designed as trap nurseries and in scattered sites in their vicinity. Analysis of 250 M. oryzae isolates from three trap nurseries indicated the presence of 45 international M. oryzae races belonging to seven pathotype groups (IA-IG). In the isolates tested, 61 M. oryzae pathotypes belonging to all but the IH group were detected. The new areas of irrigated rice in the Araguaia River Valley have the highest diversity of M. oryzae pathotypes reported so far in Brazil.

Simulating maize yield in sub‑tropical conditions of southern Brazil using Glam model

The objective of this work was to evaluate the feasibility of simulating maize yield in a sub‑tropical region of southern Brazil using the general large area model (Glam). A 16‑year time series of daily weather data were used. The model was adjusted and tested as an alternative for simulating maize yield at small and large spatial scales. Simulated and observed grain yields were highly correlated (r above 0.8; p<0.01) at large scales (greater than 100,000 km²), with variable and mostly lower correlations (r from 0.65 to 0.87; p<0.1) at small spatial scales (lower than 10,000 km²). Large area models can contribute to monitoring or forecasting regional patterns of variability in maize production in the region, providing a basis for agricultural decision making, and Glam‑Maize is one of the alternatives.

Climatic potential for wine grape production in the tropical north region of Minas Gerais State, Brazil

The tropical north region of Minas Gerais State is one of the least developed of Brazil and viticulture could be an alternative to develop its agriculture zone. The objective of this work was to evaluate the climatic potential of that region for wine grape production. The evaluations were carried out applying the Multicriteria Climatic Classification System (Geoviticulture MCC System), that utilizes three reference climatic indexes (Dryness Index - DI, Heliothermal Index - HI and Cool Night Index - CI). Three locations - Pirapora (17º 21'S, 44º56'W, 489m), Montes Claros (16º43'S, 43º52'W, 647m) and Diamantina (18º15'S, 43º36'W, 1297m) - and two potential production cycles along the year - October to March (spring-summer period) and April to September (autumn-winter period) - were evaluated. The results showed that in the spring-summer period (SS period) Pirapora and Montes Claros presented a 'humid, very warm and with warm nights' of viticultural climate, according to MCC System. For the autumn-winter period (AW period), those two regions presented a 'moderately dry, warm and with temperate nights' according to MCC System. Otherwise, the Diamantina SS period presented a 'humid, temperate warm and with temperate nights' viticultural climate. In the AW period, the Diamantina climatic condition values represent a 'subhumid, temperate and with cool nights' viticultural climate. Based on those results it can be concluded that the North Region of Minas Gerais State has a great climatic potential to became a grape-growing region for wine-making, specially in the autumn-winter period.

Hidrogenionic potential (pH) of the attractant, trap density and control threshold for Ceratitis capitata (DIPTERA: TEPHRITIDAE) on Hamlin oranges in São Paulo central region, Brazil

This study evaluated the effect of initial pH values of 4.5, 6.5 and 8.5 of the attractant (protein bait) Milhocina® and borax (sodium borate) in the field, on the capture of fruit flies in McPhail traps, using 1, 2, 4 and 8 traps per hectare, in order to estimate control thresholds in a Hamlin orange grove in the central region of the state of São Paulo. The most abundant fruit fly species was Ceratitis capitata, comprising almost 99% of the fruit flies captured, of which 80% were females. The largest captures of C. capitata were found in traps baited with Milhocina® and borax at pH 8.5. Captures per trap for the four densities were similar, indicating that the population can be estimated with one trap per hectare in areas with high populations. It was found positive relationships between captures of C. capitata and the number of Hamlin oranges damaged, 2 and 3 weeks after capture. It was obtained equations that correlate captures and damage levels which can be used to estimate control thresholds. The average loss caused in Hamlin orange fruits by C. capitata was 2.5 tons per hectare or 7.5% of production.

Analysis of SKI-1/S1P prodomain provides insight on maturation and activation of SKI-1/S1P zymogen

SKI-l/SlP protease is a member of the proprotein convertase family, with several functions in cellular metabolism and homeostasis. It is responsible for the processing of several cellular substrates, including ATF6, SREBPs, and GlcNAc-1- phosphotranspherase. Furthermore, SKI-1/SlP is also responsible for maturation of arenavirus surface glycoprotein into GP1 and GP2 subunits. This processing is a strict requirement in order to achieve fully mature and fusion-competent virions. Furthermore, SKI-1/SlP itself is synthesized as an inactive zymogen, requiring sequential autocatalytic processing at several sites (B'/B and C) in its prodomain in order to mature and become fully active. Our project focused on the analysis of SKI- 1/S1P prodomain in the biogenesis of the active enzyme. In this context we have additionally developed and characterized a novel cell-based sensor for assessment of cellular activity of the enzyme, with a potential application in screening for novel SKI- 1/S1P inhibitors. In a first aim we have analysed the relevance of cleavage motifs found in the enzyme prodomain. Using molecular and biochemistry tools we have identified and characterized a novel C' maturation site. Furthermore, we found that SKI-1/SlP autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. Contrasting with other proprotein convertases, incompletely matured intermediates of SKI-1/SlP exhibit full catalytic activity toward selected substrates. In a second aim, we turned our attention to the structural basis of SKI-1/SlP N- terminus assisted folding. Studying the folding and activity of prodomain-truncated forms of the enzyme we found that a minimal folding unit is contained in the AB region. Deletion of the BC sequence affected auto-maturation but not folding, and partial activity was retained. However, the BC region seemed required for complete and full activity. Phylogenetic analyses showed that the AB sequence is highly conserved, while the BC fragment is variable in sequence and length. Specifically, replacement of the human prodomain with that of Drosophila, resulted in a fully mature and active chimeric enzyme, suggesting an evolution process of SKI-1/SlP prodomain towards a more complex arrangement and steps of activation. Overall, the additional data we have produced might provide fundamental knowledge crucial for the development of novel SKI-1/SlP inhibitors while also providing new SKI- 1/S1P variants with potential use in crystallization purpose. -- SKI-l/SlP est une protéase membre de la famille des proprotéines convertases (PCs), avec plusieurs fonctions dans le métabolisme cellulaire et de l'homéostasie. Il est responsable pour la maturation de plusieurs substrats cellulaires, y compris ATF6, SREBPs et GlcNAc-1-phosphotranspherase. SKI-l/SlP est également responsable pour la maturation de la glycoprotéine des arénavirus, une exigence stricte pour atteindre des virions infectieuse. Synthétisé comme un zymogène inactif, SKI-l/SlP nécessite d'un traitement autocatalytique séquentiel sur plusieurs sites (B'/B et C) de son prodomaine afin de devenir pleinement active. Notre projet était axé sur l'analyse de SKI-l/SlP prodomaine dans la biogenèse de l'enzyme. Dans ce contexte, nous avons développé un nouveau senseur-cellulaire pour l'évaluation de l'activité de l'enzyme. Ce dernier pourrait avoir une potentielle application dans l'identification de nouveaux inhibiteurs de SKI-l/SlP. Premièrement, nous avons analysé la pertinence des motifs de clivage trouvés dans le prodomaine de l'enzyme. En utilisant des outils moléculaires et biochimiques, nous avons identifié et caractérisé un nouveau site de maturation (C'). Aussi, nous avons constaté que la maturation de SKI-l/SlP a des intermédiaires dont le domaine catalytique reste associé à des fragments du prodomaine de différentes longueurs. Contrastant avec d'autres PCs, les intermédiaires partiellement matures de SKI-1 / SIP présentent une activité catalytique complète envers des substrats spécifiques. Dans un deuxième but nous avons tourné notre attention sur la base structurelle du pliage de SKI-l/SlP assisté par son N-terminus: En étudiant l'activité et pliage des formes tronquées dans le prodomaine de l'enzyme, nous avons constaté qu'une unité de pliage minimale est contenue dans la région de l'AB. La suppression de la séquence d'auto-BC affecte la maturation mais pas le pliage, et l'activité partielle est maintenue. Cependant, la région BC semble nécessaire pour une activité complète. Les analyses phylogénétiques ont montré que la séquence AB est fortement conservée, tandis que le fragment de BC est variable en longueur et en séquence. En particulier, le remplacement du prodomaine humain avec celui de la drosophile, a donné lieu à une enzyme chimérique complètement mature et active. Suggérant un processus d'évolution du prodomaine vers un arrangement et des mesures d'activation plus complexe. Globalement, ces donnees supplémentaires augment les connaissances fondamentales cruciales pour le développement de nouveaux inhibiteurs de SKI-1/ SIP, tout en offrant de nouvelles variantes SKI-1 / SIP dans le but d'obtenir la structure cristallographique de l'enzyme.

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes.

Background: Information about the composition of regulatory regions is of great value for designing experiments to functionally characterize gene expression. The multiplicity of available applications to predict transcription factor binding sites in a particular locus contrasts with the substantial computational expertise that is demanded to manipulate them, which may constitute a potential barrier for the experimental community. Results: CBS (Conserved regulatory Binding Sites, http://compfly.bio.ub.es/CBS) is a public platform of evolutionarily conserved binding sites and enhancers predicted in multiple Drosophila genomes that is furnished with published chromatin signatures associated to transcriptionally active regions and other experimental sources of information. The rapid access to this novel body of knowledge through a user-friendly web interface enables non-expert users to identify the binding sequences available for any particular gene, transcription factor, or genome region. Conclusions: The CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings in Drosophila.

Inhalable particulate matter characterization in a medium-sized urban region in Brazil (São José dos Campos Town) - Part I: Morphology

In this study, the concentration and morphological characteristics of inhalable particulate material (PM10) were evaluated and associated with climatic conditions. The mean annual concentration was 11.0 µg m−3, varying between 0,647 µg m−3 and 36.8 µg m−3. Wind speed has a higher influence on PM10 dispersion, but direction was associated with particle source. During the wet period, wind speed is the main dispersion factor, while speed and direction both are important during the dry period. Based on the morphological characteristics, it is concluded that biogenic particles prevail during the rainy season and terrigenous particles during the dry period, depending on the wind direction and intensity.

Genetic analyses of Rhizoctonia solani isolates from Phaseolus vulgaris grown in the Atlantic Rainforest Region of São Paulo, Brazil

Rhizoctonia solani isolates obtained from common beans (Phaseolus vulgaris) grown in the mountainous Atlantic Rainforest (Mata Atlântica) region of São Paulo, Brazil, were analyzed to determine their genetic diversity using internal transcribed spacer (ITS), microsatellite and telomere sequence-based PCR primers. Restriction digestion of the ITS1/5.8S/ITS2 ribosomal regions yielded unique banding patterns specific for AG4 and its subgroups. The ITS restriction digestion (ITS/RFLP), telomere and microsatellite primers identified five to 11 genotypes within the isolates of R. solani. While all isolates were pathogenic on beans, there was no correlation found between genotypic differences and pathogenicity. The different PCR primers revealed a number of isolates that were genetically similar. Some of these genetic groups were supported by more than one of the primers utilized in this study, thus confirming their relationship.

Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences

The aim of this study was to identify isolates of Rhizoctonia solani causing hypocotyl rot and foliar blight in soybean (Glycine max) in Brazil by the nucleotide sequences of ITS-5.8S regions of rDNA. The 5.8S rDNA gene sequence (155 bp) was highly conserved among all isolates but differences in length and nucleotide sequence of the ITS1 and ITS2 regions were observed between soybean isolates and AG testers. The similarity of the nucleotide sequence among AG-1 IA isolates, causing foliar blight, was 95.1-100% and 98.5-100% in the ITS1 and ITS2 regions, respectively. The nucleotide sequence similarity among subgroups IA, IB and IC ranged from 84.3 to 89% in ITS1 and from 93.3 to 95.6% in ITS2. Nucleotide sequence similarity of 99.1% and 99.3-100% for ITS1 and ITS2, respectively, was observed between AG-4 soybean isolates causing hypocotyl rots and the AG-4 HGI tester. The similarity of the nucleotide sequence of the ITS-5.8S rDNA region confirmed that the R. solani Brazilian isolates causing foliar blight are AG-1 IA and isolates causing hypocotyl rot symptoms are AG-4 HGI. The ITS-5.8S rDNA sequence was not determinant for the identification of the AG-2-2 IIIB R. solani soybean isolate.