Showing papers by "Universidade Federal Rural do Rio de Janeiro published in 2014"

SoilGrids1km--global soil information based on automated mapping.

Abstract: Background: Soils are widely recognized as a non-renewable natural resource and as biophysical carbon sinks. As such, there is a growing requirement for global soil information. Although several global soil information systems already exist, these tend to suffer from inconsistencies and limited spatial detail. Methodology/Principal Findings: We present SoilGrids1km — a global 3D soil information system at 1 km resolution — containing spatial predictions for a selection of soil properties (at six standard depths): soil organic carbon (g kg21), soil pH, sand, silt and clay fractions (%), bulk density (kg m23), cation-exchange capacity (cmol+/kg), coarse fragments (%), soil organic carbon stock (t ha21), depth to bedrock (cm), World Reference Base soil groups, and USDA Soil Taxonomy suborders. Our predictions are based on global spatial prediction models which we fitted, per soil variable, using a compilation of major international soil profile databases (ca. 110,000 soil profiles), and a selection of ca. 75 global environmental covariates representing soil forming factors. Results of regression modeling indicate that the most useful covariates for modeling soils at the global scale are climatic and biomass indices (based on MODIS images), lithology, and taxonomic mapping units derived from conventional soil survey (Harmonized World Soil Database). Prediction accuracies assessed using 5–fold cross-validation were between 23–51%. Conclusions/Significance: SoilGrids1km provide an initial set of examples of soil spatial data for input into global models at a resolution and consistency not previously available. Some of the main limitations of the current version of SoilGrids1km are: (1) weak relationships between soil properties/classes and explanatory variables due to scale mismatches, (2) difficulty to obtain covariates that capture soil forming factors, (3) low sampling density and spatial clustering of soil profile locations. However, as the SoilGrids system is highly automated and flexible, increasingly accurate predictions can be generated as new input data become available. SoilGrids1km are available for download via http://soilgrids.org under a Creative Commons Non Commercial license.

Reassessment of the potential economic impact of cattle parasites in Brazil

Abstract: The profitability of livestock activities can be diminished significantly by the effects of parasites. Economic losses caused by cattle parasites in Brazil were estimated on an annual basis, considering the total number of animals at risk and the potential detrimental effects of parasitism on cattle productivity. Estimates in U.S. dollars (USD) were based on reported yield losses among untreated animals and reflected some of the effects of parasitic diseases. Relevant parasites that affect cattle productivity in Brazil, and their economic impact in USD billions include: gastrointestinal nematodes - $7.11; cattle tick (Rhipicephalus (Boophilus) microplus) - $3.24; horn fly ( Haematobia irritans) - $2.56; cattle grub (Dermatobia hominis) - $0.38; New World screwworm fly ( Cochliomyia hominivorax) - $0.34; and stable fly (Stomoxys calcitrans) - $0.34. The combined annual economic loss due to internal and external parasites of cattle in Brazil considered here was estimated to be at least USD 13.96 billion. These findings are discussed in the context of methodologies and research that are required in order to improve the accuracy of these economic impact assessments. This information needs to be taken into consideration when developing sustainable policies for mitigating the impact of parasitism on the profitability of Brazilian cattle producers.

Receptor–ligand molecular docking

Abstract: Docking methodology aims to predict the experimental binding modes and affinities of small molecules within the binding site of particular receptor targets and is currently used as a standard computational tool in drug design for lead compound optimisation and in virtual screening studies to find novel biologically active molecules. The basic tools of a docking methodology include a search algorithm and an energy scoring function for generating and evaluating ligand poses. In this review, we present the search algorithms and scoring functions most commonly used in current molecular docking methods that focus on protein–ligand applications. We summarise the main topics and recent computational and methodological advances in protein–ligand docking. Protein flexibility, multiple ligand binding modes and the free-energy landscape profile for binding affinity prediction are important and interconnected challenges to be overcome by further methodological developments in the docking field.

Checklist of Brazilian bats, with comments on original records

Abstract: Lists of Brazilian bats have been compiled since the late 19th century, with remarkable variation in the criteria for species inclusion and use of nomenclature. To update the list of extant bat species that occur in Brazil, the Brazilian Bat Research Society created the Committee of the List of Brazilian Bats. Here we report the first result of the work of this Committee: a list with nine families, 68 genera, and 178 species with documented occurrence in Brazil, including nomenclatural comments. We also present two additional species lists: one with doubtful records (10 species) and other with erroneous records (six species). Since the beginning of the 21st century, 35 new bat species have been recorded for Brazil, and we anticipate that more species will be uncovered over the next years.

Prospective study of leptospirosis transmission in an urban slum community: role of poor environment in repeated exposures to the leptospira agent

Abstract: Background: Leptospirosis has emerged as an urban health problem as slum settlements have rapidly spread worldwide and created conditions for rat-borne transmission. Prospective studies have not been performed to determine the disease burden, identify risk factors for infection and provide information needed to guide interventions in these marginalized communities. Methodology/Principal Findings: We enrolled and followed a cohort of 2,003 residents from a slum community in the city of Salvador, Brazil. Baseline and one-year serosurveys were performed to identify primary and secondary Leptospira infections, defined as respectively, seroconversion and four-fold rise in microscopic agglutination titers. We used multinomial logistic regression models to evaluate risk exposures for acquiring primary and secondary infection. A total of 51 Leptospira infections were identified among 1,585 (79%) participants who completed the one-year follow-up protocol. The crude infection rate was 37.8 per 1,000 person-years. The secondary infection rate was 2.3 times higher than that of primary infection rate (71.7 and 31.1 infections per 1,000 person-years, respectively). Male gender (OR 2.88; 95% CI 1.40– 5.91) and lower per capita household income (OR 0.54; 95% CI, 0.30–0.98 for an increase of $1 per person per day) were independent risk factors for primary infection. In contrast, the 15–34 year age group (OR 10.82, 95% CI 1.38–85.08), and proximity of residence to an open sewer (OR 0.95; 0.91–0.99 for an increase of 1 m distance) were significant risk factors for secondary infection. Conclusions/Significance: This study found that slum residents had high risk (.3% per year) for acquiring a Leptospira infection. Re-infection is a frequent event and occurs in regions of slum settlements that are in proximity to open sewers. Effective prevention of leptospirosis will therefore require interventions that address the infrastructure deficiencies that contribute to repeated exposures among slum inhabitants.

NDVI time series for monitoring RUSLE cover management factor in a tropical watershed

Abstract: Land cover, an important factor for monitoring changes in land use and erosion risk, has been widely monitored and evaluated by vegetation indices. However, a study that associates normalized difference vegetation index NDVI time series to climate parameters to determine soil cover has yet to be conducted in the Atlantic Rainforest of Brazil, where anthropogenic activities have been carried out for centuries. The objective of this paper is to evaluate soil cover in a Brazilian Atlantic rainforest watershed using NDVI time series from Thematic Mapper TM Landsat 5 imagery from 1986 to 2009, and to introduce a new method for calculating the cover management factor C-factor of the Revised Universal Soil Loss Equation RUSLE model. Twenty-two TM Landsat 5 images were corrected for atmospheric effects using the 6S model, georeferenced using control points collected in the field and imported to a GIS database. Contour lines and elevation points were extracted from a 1:50,000-scale topographic map and used to construct a digital elevation model that defined watershed boundaries. NDVI and RUSLE C-factor values derived from this model were calculated within watershed limits with 1 km buffers. Rainfall data from a local weather station were used to verify NDVI and C-factor patterns in response to seasonal rainfall variations. Our proposed method produced realistic values for RUSLE C-factor using rescaled NDVIs, which highly correlated with other methods, and were applicable to tropical areas exhibiting high rainfall intensity. C-factor values were used to classify soil cover into different classes, which varied throughout the time-series period, and indicated that values attributed to each land cover cannot be fixed. Depending on seasonal rainfall distribution, low precipitation rates in the rainy season significantly affect the C-factor in the following year. In conclusion, NDVI time series obtained from satellite images, such as from Landsat 5, are useful for estimating the cover management factor and monitoring watershed erosion. These estimates may replace table values developed for specific land covers, thereby avoiding the cumbersome field measurements of these factors. The method proposed is recommended for estimating the RUSLE C-factor in tropical areas with high rainfall intensity.

Cluster analysis applied to the spatial and temporal variability of monthly rainfall in Alagoas state, Northeast of Brazil

Abstract: Rainfall over the northeast part of Brazil is highly influenced by several weather systems such as trade winds, the Intertropical Convergence Zone, Easterly Wave Disturbances, Bolivia High and Atlantic Sub-tropical Anticyclone. The objectives of this work were to identify, using cluster analysis, spatial and temporal rainfall patterns for the northeastern Brazilian state of Alagoas, and to relate those patterns with the weather systems that occur over that region, which is the most populated area of semiarid climate in the world. The dataset consists of 30-years long time series of rainfall from 36 stations located on the state. Hierarchical clustering using Ward's algorithm was used to classify the sites into five groups. The stations were grouped according to the distance to the coast and orography. Rainfall is not uniformly distributed in space and time in all regions, such as in two groups within the arid zone, where more than 60% of annual precipitation occurs in a period of 5 months (March to July). Rainfall was highest in the coastal regions and over areas of the state with high altitude, due to orographic rainfall. Overall, rainfall over the state of Alagoas is characterized by strong gradients from the coast to the continent and from north to south due to the physiography of the region and the influence of weather systems with different time scales.

Studies on coccidian oocysts (Apicomplexa: Eucoccidiorida)

Abstract: The oocysts of the coccidia are robust structures, frequently isolated from the feces or urine of their hosts, which provide resistance to mechanical damage and allow the parasites to survive and remain infective for prolonged periods. The diagnosis of coccidiosis, species description and systematics, are all dependent upon characterization of the oocyst. Therefore, this review aimed to the provide a critical overview of the methodologies, advantages and limitations of the currently available morphological, morphometrical and molecular biology based approaches that may be utilized for characterization of these important structures. It has become apparent that no single methodology is sufficient to fully characterize these structures and the majority of researchers favor the use of combinational or polyphasic approaches.

Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil.

Abstract: 16S rRNA gene sequence analysis of eight strains (BR 3299T, BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected from a semi-arid region of Brazil showed 97 % similarity to sequences of recently described rhizobial species of the genus Microvirga . Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA–DNA relatedness and AFLP further indicated that these strains belong to a novel species within the genus Microvirga . Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to those found in members of the genera Rhizobium and Mesorhizobium , which are not immediate relatives of the genus Microvirga , as shown by 16S rRNA gene sequence analysis. Phenotypic traits, such as host range and carbon utilization, differentiate the novel strains from the most closely related species, Microvirga lotononidis , Microvirga zambiensis and Microvirga lupini . Therefore, these symbiotic nitrogen-fixing bacteria are proposed to be representatives of a novel species, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299T ( = HAMBI 3457T).

Humic Substances and Plant Defense Metabolism

Abstract: Humic substances (HS) affect most plant metabolic processes. Regardless of their source, HS help regulate enzymatic systems related to primary, secondary, and defense metabolisms in response to environmental stress. Morphologically, the HS–plant interaction results in increased root length and the emanation of lateral roots. These morphological changes occur in response to complex regulatory and stress response processes activated by the application of HS and similar chemical fractions. Given that the roots are the main plant organs that interact with HS, HS–root interaction mechanisms are one of the most important topics in HS–plant research. Specifically, there is a known biochemical relationship between humic compounds and major plant metabolic processes. New findings about the modes of metabolite action in plants have increased our understanding of how HS help to optimize plant metabolism. Advanced technologies, such as large-scale and spectroscopy, have also increased our understanding of the modes of action of HS. The application of techniques such as amplified fragment length polymorphism (AFLP) and microarray analysis in study of HS-treated plants has demonstrated that approximately 6.1–9 % of differentially expressed genes correspond to metabolic pathways that are associated with defense mechanisms in response to stimuli. These results suggest that HS induce plant adaptive responses to environmental stress. In this study, we discuss how HS contribute to improved plant performance through complex metabolic mechanisms. We apply new findings about the modes of action of metabolites related to antioxidant mechanisms to understand HS modes of action and examine HS effects in plants by using spectroscopic techniques to study root interactions. We also propose a framework for investigating the use of HS in agriculture to improve the growth of food plants grown in high-stress environments.

New Families of Hetero-tri-spin 2p−3d−4f Complexes: Synthesis, Crystal Structures, and Magnetic Properties

Abstract: In this work we report the synthesis, crystal structures, and magnetic behavior of 2p–3d–4f heterospin systems containing the nitroxide radical 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl radical (N3tempo). These compounds were synthesized through a one-pot reaction by using [Cu(hfac)2], [Ln(hfac)3] (hfac = hexafluoroacetylacetonate, Ln = DyIII, TbIII or GdIII), and the N3tempo radical. Depending on the stoichiometric ratio used, the synthesis leads to penta- or trimetallic compounds, with molecular formulas [Cu3Ln2(hfac)8(OH)4(N3tempo)] (Ln = Gd, Tb, Dy) and [CuLn2(hfac)8(N3tempo)2(H2O)2] (Ln = Gd, Dy). The magnetic properties of all compounds were investigated by direct current (dc) and alternating current (ac) measurements. The ac magnetic susceptibility measurements of TbIII- and DyIII-containing compounds of both families revealed slow relaxation of the magnetization, with magnetic quantum tunneling in zero field.

Correlation of Total Phenolic and Flavonoid Contents of Brazilian Honeys with Colour and Antioxidant Capacity

Abstract: Sixty Brazilian honey samples were analysed for their total phenolic content with the Folin-Denis reagent, total flavonoid content by aluminium chloride method, and antioxidant activity by reaction with 2,2-diphenyl-1-picrylhydrazyl radical. Colour was also classified according to visual analysis and Pfund scale. Linear relationships were observed between colour and flavonoid content, total phenolics and antioxidant capacity, and total flavonoid and phenolic contents. The white-coloured Citrus honey showed the lowest antioxidant activity, while the light ambar Verbenaceae honey showed the highest total phenolics and antioxidant activity. Dark-coloured and polyfloral honeys, though less popularized among consumers, showed average to high antioxidant capacity.

Multi-Level Policy Dialogues, Processes, and Actions: Challenges and Opportunities for National REDD+ Safeguards Measurement, Reporting, and Verification (MRV)

Abstract: REDD+ social safeguards have gained increasing attention in numerous forums. This paper reviews the evolution of multi-level policy dialogues, processes, and actions related to REDD+ social safeguards (e.g., Cancun Safeguards 1-5) among policy makers, civil society organizations, and within the media in Brazil, Indonesia and Tanzania, three countries with well advanced REDD+ programs. We find that progress on core aspects of social safeguards is uneven across the three countries. Brazil is by far the most advanced having drafted a REDD+ social safeguards policy. Both Brazil and Indonesia have benefited from progress made by strong sub-national entities in the operationalization of REDD+ safeguards including free prior and informed consent (FPIC), participation, and benefit sharing. Tanzania has weakly articulated how social safeguards will be operationalized and has a more top-down approach. We conclude that in all three countries, measuring, reporting and verifying progress on social safeguards is likely to be a complex issue.

Much beyond Mantel: Bringing Procrustes Association Metric to the Plant and Soil Ecologist’s Toolbox

Abstract: The correlation of multivariate data is a common task in investigations of soil biology and in ecology in general. Procrustes analysis and the Mantel test are two approaches that often meet this objective and are considered analogous in many situations especially when used as a statistical test to assess the statistical significance between multivariate data tables. Here we call the attention of ecologists to the advantages of a less familiar application of the Procrustean framework, namely the Procrustean association metric (a vector of Procrustean residuals). These residuals represent differences in fit between multivariate data tables regarding homologous observations (e.g., sampling sites) that can be used to estimate local levels of association (e.g., some groups of sites are more similar in their association between biotic and environmental features than other groups of sites). Given that in the Mantel framework, multivariate information is translated into a pairwise distance matrix, we lose the ability to contrast homologous data points across dimensions and data matrices after their fit. In this paper, we attempt to familiarize ecologists with the benefits of using these Procrustean residual differences to further gain insights about the processes underlying the association among multivariate data tables using real and hypothetical examples.

Social isolation disrupts hippocampal neurogenesis in young non-human primates.

Abstract: Social relationships are crucial for the development and maintenance of normal behavior in non-human primates. Animals that are raised in isolation develop abnormal patterns of behavior that persist even when they are later reunited with their parents. In rodents, social isolation is a stressful event and is associated with a decrease in hippocampal neurogenesis but considerably less is known about the effects of social isolation in non-human primates during the transition from adolescence to adulthood. To investigate how social isolation affects young marmosets, these were isolated from other members of the colony for one or three weeks and evaluated for alterations in their behavior and hippocampal cell proliferation. We found that anxiety-related behaviors like scent-marking and locomotor activity increased after social isolation when compared to baseline levels. In agreement, grooming - an indicative of attenuation of tension - was reduced among isolated marmosets. These results were consistent with increased cortisol levels after one and three weeks of isolation. After social isolation (one or three weeks), reduced proliferation of neural cells in the subgranular zone of dentate granule cell layer was identified and a smaller proportion of BrdU-positive cells underwent neuronal fate (doublecortin labeling). Our data is consistent with the notion that social deprivation during the transition from adolescence to adulthood leads to stress and produces anxiety-like behaviors that in turn might affect neurogenesis and contribute to the deleterious consequences of prolonged stressful conditions.

Candidatus Rickettsia andeanae, a spotted fever group agent infecting Amblyomma parvum ticks in two Brazilian biomes

Abstract: Adult ticks of the species Amblyomma parvum were collected from the vegetation in the Pantanal biome (state of Mato Grosso do Sul) and from horses in the Cerrado biome (state of Piaui) in Brazil. The ticks were individually tested for rickettsial infection via polymerase chain reaction (PCR) targeting three rickettsial genes, gltA, ompA and ompB. Overall, 63.5% (40/63) and 66.7% (2/3) of A. parvum ticks from Pantanal and Cerrado, respectively, contained rickettsial DNA, which were all confirmed by DNA sequencing to be 100% identical to the corresponding fragments of the gltA, ompA and ompB genes of Candidatus Rickettsia andeanae. This report is the first to describe Ca. R. andeanae in Brazil.

Docking, Synthesis and Antiproliferative Activity of N-Acylhydrazone Derivatives Designed as Combretastatin A4 Analogues

Abstract: Cancer is the second most common cause of death in the USA. Among the known classes of anticancer agents, the microtubule-targeted antimitotic drugs are considered to be one of the most important. They are usually classified into microtubule-destabilizing (e.g., Vinca alkaloids) and microtubule-stabilizing (e.g., paclitaxel) agents. Combretastatin A4 (CA-4), which is a natural stilbene isolated from Combretum caffrum, is a microtubule-destabilizing agent that binds to the colchicine domain on β-tubulin and exhibits a lower toxicity profile than paclitaxel or the Vinca alkaloids. In this paper, we describe the docking study, synthesis, antiproliferative activity and selectivity index of the N-acylhydrazone derivatives (5a–r) designed as CA-4 analogues. The essential structural requirements for molecular recognition by the colchicine binding site of β-tubulin were recognized, and several compounds with moderate to high antiproliferative potency (IC50 values ≤18 µM and ≥4 nM) were identified. Among these active compounds, LASSBio-1586 (5b) emerged as a simple antitumor drug candidate, which is capable of inhibiting microtubule polymerization and possesses a broad in vitro and in vivo antiproliferative profile, as well as a better selectivity index than the prototype CA-4, indicating improved selective cytotoxicity toward cancer cells.

Medicinal plants traded in the open-air markets in the State of Rio de Janeiro, Brazil: an overview on their botanical diversity and toxicological potential

Abstract: Medicinal plants have been used for many years and are the source of new active substances and new drugs of pharmaceutical interest. The popular knowledge contained in the open- air markets is studied through urban ethnobotany, and is a good source of information for ethnobotanical research. In this context, we surveyed the literature on works concerning open-air markets in the State of Rio de Janeiro to gather knowledge of the commercialized plants therein. A literature search resulted in ten studies with 376 listed species, distributed in 94 families and 273 genera. Asteraceae family had the greater representation, followed by Lamiaceae and Fabaceae. Solanum was the most frequent genus. Two hundred and twenty four species could be considered potentially toxic or potentially interact with other drugs/medicines. Eighteen species are referred as “not for use during pregnancy”, and 3 “not for use while nursing”. These results are a source of concern since in Brazil, as it is worldwide, there is the notion that plants can never be harmful. The results for the Sorensen Coefficient showed greater similarity between works performed in very close study areas. Other studies presented low similarity, mainly because of the difficulty in plant identification or a very specific focus in methodology.

Supplementation with olive oil, but not fish oil, improves cutaneous wound healing in stressed mice.

Abstract: Supplementation with olive and fish oils reverses the effects of stress on behavioral activities and adrenal activation. However, previous studies have not shown whether supplementation with olive and fish oil could inhibit the effects of stress on cutaneous wound healing. Thus, this study investigated the effects of supplementation with fish or olive oil on cutaneous healing in stressed mice. Mice were subjected to rotational stress and treated with olive or fish oil daily until euthanasia. An excisional lesion was created on each mouse, and 14 days later, the lesions were analyzed. In addition, murine skin fibroblasts were exposed to elevated epinephrine levels plus olive oil, and fibroblast activity was evaluated. In the in vivo studies, administration of olive oil, but not fish oil, inhibited stress-induced reduction in wound contraction, reepithelialization, hydroxyproline levels, and blood vessel density. Stress-induced increases in vascular endothelial growth factor expression and the numbers of macrophages and neutrophils were reversed only by olive oil. Both oils reversed stress-induced increase in catecholamine levels and oxidative damage. In in vitro studies, olive oil treatment reversed the reduction in fibroblast migration and collagen deposition and the increase in lipid peroxidation induced by epinephrine. In conclusion, supplementation with olive oil, but not fish oil, improves cutaneous wound healing in chronically stressed mice.