Vírus da encefalite São Luis: primeiro isolamento de humano no Estado de São Paulo, Brasil

O presente estudo relata o isolamento do vírus da encefalite São Luis (SLEV) de um caso febril humano suspeito de dengue, em São Pedro, Estado de São Paulo. MAC-ELISA realizado com soros das fases aguda e convalescente foi inconclusivo e anticorpos IgG foram detectados por inibição da hemaglutinação para flavivirus. Imunofluorescência indireta com cultura de células C6/36 inoculadas com soro da fase aguda foi positivo para flavivirus mas negativo quando testado com anticorpos monoclonais para dengue. O RNA extraído de cultura de células infectadas foi amplificado na presença de primers universais para o gênero Flavivirus, deduzidos de uma região da proteína não estrutural 5 e diretamente sequenciado. Os resultados da pesquisa no BLAST indicaram que a seqüência apresenta 93% de similaridade de nucleotídeos com a seqüência de SLEV (cepa MS1.7), confirmado por RT-PCR, realizado com primers específicos para SLEV. O fato de SLEV ter sido identificado como a causa de doença humana indica a necessidade de aprimorar a vigilância a fim de detectar precocemente esse agente no Estado de São Paulo e no Brasil. Esse caso é também um alerta para os profissionais de saúde sobre a necessidade de investigações clínicas e epidemiológicas mais completas sobre doenças febris como no caso relatado. Infecções por SLEV podem não ser reconhecidas ou confundidas com outras causadas por arbovírus como a dengue.This paper reports the isolation of St. Louis encephalitis virus (SLEV) from a febrile human case suspected to be dengue, in São Pedro, São Paulo State. A MAC-ELISA done on the patient's acute and convalescent sera was inconclusive and hemagglutination inhibition test detected IgG antibody for flaviviruses. An indirect immunofluorescent assay done on the C6/36 cell culture inoculated with the acute serum was positive for flaviviruses but negative when tested with dengue monoclonal antibodies. RNA extracted from the infected cell culture supernatant was amplified by RT-PCR in the presence of NS5 universal flavivirus primers and directly sequenced. Results of BLAST search indicated that this sequence shares 93% nucleotide similarity with the sequence of SLEV (strain-MSI.7), confirmed by RT-PCR performed with SLEV specific primers. Since SLEV was identified as the cause of human disease, it is necessary to improve surveillance in order to achieve early detection of this agent in the state of São Paulo and in Brazil. This finding is also an alert to health professionals about the need for more complete clinical and epidemiological investigations of febrile illnesses as in the reported case. SLEV infections can be unrecognized or confused with other ones caused by an arbovirus, such as dengue

Habitat specialization and phylogenetic structure of tree species in a coastal Brazilian white-sand forest

Aims The coastal Brazilian rainforest on white-sand (restinga) ranks among the most fragmented forest types in the tropics, owing to both the patchy distribution of sandy soils and widespread coastal development activities. Here we study the environmental and evolutionary determinants of a forest tree assemblage at a single restinga forest in Southeastern Brazil. We also explore the ability of competing hypotheses to explain the maintenance of species diversity in this forest type, which includes contrasting extremes of edaphic conditions associated with flooding stress. Methods The study was conducted in a white-sand forest permanent plot of 10.24 ha on the coastal plain of Southeastern Brazil. This plot was divided into 256 quadrats of 20×20 m, which were classified into two main edaphic habitats (flooded and drained). Trees with a diameter ≥1cm at breast height were identified. We assembled DNA sequence data for each of the 116 morphospecies recognized using two chloroplast markers (rbcL and matK). A phylogenetic tree was obtained using the maximum likelihood method, and a phylogenetic distance matrix was produced from an ultrametric tree. We analyzed similarity in floristic composition and structure between habitats and related them to cross-plot distances using permutation procedures. Null model torus shift simulations were performed to obtain a statistical significance level for habitat association for each species. The phylogenetic structure for the two habitats and for each 20×20 m quadrat was calculated using the mean phylogenetic distance weighted by species abundance and checked for significance using the standardized effect size generated by 5000 randomizations of phylogenetic tip labels. Important Findings Our results indicate that partitioning among edaphic habitats is important for explaining species distributions and coexistence in restinga forests. Species distributions within the plot were found to be non-random: there was greater floristic similarity within than between habitats, and >40% of the more abundant species were positively or negatively associated with at least one habitat. Patterns of habitat association were not independent of phylogenetic relatedness: the community was overdispersed with respect to space and habitat type. Closely related species tended to occur in different habitats, while neighboring trees tended to belong to more distantly related species. We conclude that habitat specialization is important for the coexistence of species in restinga forests and that habitat heterogeneity is therefore an essential factor in explaining the maintenance of diversity of this unique but fragile and threatened type of forest. © 2014 The Author

plantR: An R package and workflow for managing species records from biological collections

Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting and standardisation of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections. To help collection curators and final users perform those tasks, we introduce plantR, an open-source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage this type of data in taxonomy, ecology and biodiversity conservation. It is implemented in R and designed to handle relatively large datasets as fast as possible. Initially designed to handle plant species records, many of the plantR features also apply to other groups of organisms, given that the data structure is similar. The plantR workflow includes tools to (a) download records from different data repositories, (b) standardise typical fields associated with species records, (c) validate the locality, geographical coordinates, taxonomic nomenclature and species identifications, including the retrieval of duplicates across collections, and (d) summarise and export records, including the construction of species lists with vouchers. Other R packages provide tools to tackle some of the workflow steps described above. But in addition to the new tools and resources related to data standardisation and validation, the greatest strength of plantR is to provide a comprehensive and user-friendly workflow in one single environment, performing all tasks from data retrieval to export. Thus, plantR can help researchers better assess data quality and avoid data leakage in a wide variety of studies using species records

The erosion of biodiversity and biomass in the Atlantic Forest biodiversity hotspot

Tropical forests are being deforested worldwide, and the remaining fragments are suffering from biomass and biodiversity erosion. Quantifying this erosion is challenging because ground data on tropical biodiversity and biomass are often sparse. Here, we use an unprecedented dataset of 1819 field surveys covering the entire Atlantic Forest biodiversity hotspot. We show that 83−85% of the surveys presented losses in forest biomass and tree species richness, functional traits, and conservation value. On average, forest fragments have 25−32% less biomass, 23−31% fewer species, and 33, 36, and 42% fewer individuals of late-successional, large-seeded, and endemic species, respectively. Biodiversity and biomass erosion are lower inside strictly protected conservation units, particularly in large ones. We estimate that biomass erosion across the Atlantic Forest remnants is equivalent to the loss of 55−70 thousand km2 of forests or US$2.3−2.6 billion in carbon credits. These figures have direct implications on mechanisms of climate change mitigation

Estimating interaction credit for trophic rewilding in tropical forests

Trophic rewilding has been suggested as a restoration tool to restore ecological interactions and reverse defaunation and its cascading effects on ecosystem functioning. One of the ecological processes that has been jeopardized by defaunation is animal-mediated seed dispersal. Here, we propose an approach that combines joint species distribution models with occurrence data and species interaction records to quantify the potential to restore seed-dispersal interactions through rewilding and apply it to the Atlantic Forest, a global biodiversity hotspot. Using this approach, we identify areas that should benefit the most from trophic rewilding and candidate species that could contribute to cash the credit of seed-dispersal interactions in a given site. We found that sites within large fragments bearing a great diversity of trees may have about 20 times as many interactions to be cashed through rewilding as small fragments in regions where deforestation has been pervasive. We also ranked mammal and bird species according to their potential to restore seed-dispersal interactions if reintroduced while considering the biome as a whole and at finer scales. The suggested approach can aid future conservation efforts in rewilding projects in defaunated tropical rainforests

Supplemental information, code, and data for the MS: Defaunation impacts carbon storage in tropical forests.

<p># MS_Carbon<br> Supplemental information, code, and data for the MS: <br> Carolina Bello, Mauro Galetti, Marco A. Pizo, Luiz Fernando S. Magnago, Mariana Ferreira Rocha, Renato A. F. Lima, Carlos A. Peres, Otso Ovaskainen, and Pedro Jordano (2015). Defaunation impacts carbon storage in tropical forests.</p> <p> </p> <p>*Summary*:<br> Carbon storage is widely acknowledged as one of the most valuable forest ecosystem services. Deforestation, logging, fragmentation and climate change have significant impacts on tropical carbon stocks, however an elusive and yet undetected decrease in carbon storage may be due to defaunation of large seed dispersers. Many large tropical trees with sizeable contributions to carbon stock rely on large vertebrates for seed dispersal and regeneration, yet many of these frugivores are threatened by hunting, illegal trade and habitat loss. We used a large dataset on tree species composition and abundance, seed, fruit and carbon related traits, and plant-animal interactions to estimate the loss of carbon storage capacity of tropical forests in defaunated scenarios. By simulating the local extinction of trees that depend on large frugivores at 31 Atlantic Forest communities, we found that defaunation has the potential to significantly erode carbon storage even when only a small proportion (10%) of large-seeded trees are extirpated.</p> <p> </p

Impact of Brazilian expanded criteria for liver transplantation in patients with hepatocellular carcinoma: a multicenter study

Introduction and objectives: Hepatocellular carcinoma (HCC) is one of the main indications for orthotopic liver transplantation (OLT). In Brazil, selection criteria for HCC is an expanded version of the Milan Criteria (MC), the so-called ''Brazilian Milan Criteria'' (BMC). Our aims were to evaluate post-OLT outcomes in patients with HCC and analyze the BMC performance. Materials and Methods: We conducted a multicenter, retrospective cohort study, analyzing medical records of 1,059 liver transplant recipients with HCC. Tumor was staged according to MC and BMC and correlated with overall survival (OS) and disease-free survival (DFS). We compared the ability of MC and BMC to predict OS and DFS using Delta C-statistic. Results: Post-OLT OS were 63% in five years and HCC recurrence was observed in 8% of patients. At diagnosis, 85% of patients were within MC. Patients within MC at diagnosis and in the explant showed a higher OS and DFS than patients outside MC and within BMC and patients outside both criteria (p < 0.001). Patients outside MC in the explant had an increased risk of tumor recurrence (HR: 3.78; p < 0.001) and poor survival (HR:1.77; p = 0.003). The BMC presented a lower performance than MC in properly classifying patients regarding recurrence risk. Conclusions: In a large Brazilian cohort of HCC patients submitted to liver transplantation, we observed satisfactory overall survival and recurrence rates. However, patients transplanted within the Brazilian expanded criteria had lower OS and DFS when compared to patients within MC, which may generate future discussions regarding the criteria currently used