Abundance and distribution of juvenile pink shrimps Farfantepenaeus spp. in a mangrove estuary and adjacent bay on the northern shore of São Paulo State, southeastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Sediment toxicity assessment of Guanabara Bay, Rio de Janeiro, Brazil.

Guanabara Bay (GB) comprises of estuarine and marine environments of high ecological and socio-economic relevance, together with port, industrial and urban areas. The anthropogenic activities produce environmental impacts, including the aquatic pollution. The sediment quality assessment is important to evaluate the effects of contamination, once sediments are a repository for most of the contaminants. In this Study, the quality of sediments from GB was evaluated, in rainy and dry periods, throughout the employment of acute toxicity tests with the amphipod Tiburonella viscana, and chronic bioassays with embryos of the sea-urchin Lytechinus variegatus. In the dry period, acute toxicity was found in the sediments from stations 1, 2 3 (NW) and 7 (near Guapimirim Environmental Protection Area). The bioassays with liquid phases showed effects, but were strongly influenced by the unionized ammonia levels, which were high in this period. In the rainy period, acute toxicity was found in sediments samples from stations 1, 2, 3, 6, 8, 10, 11, 12 and 15. Chronic toxicity could be clearly detected, as ammonia concentrations tended to be low in the most part of the samples. The results showed that the sediment toxicity is influenced by precipitation rates, which increase the input of contaminants to the Bay, and also allowed subdividing GB in three main zones: northwest (stations 1, 2, 3, 5), northeast (stations 6, 7, 8, 9) and centre-south (stations 10, 11, 12, 13, 14, 15). Results also showed that the quality of GB sediments is poor, and that toxicity tests could determine the combined effects of pollutants.

Acute and chronic toxicity of sediment samples from Guanabara Bay (RJ) during the rainy period

A Baía de Guanabara é um ambiente marinho-estuarino de grande relevância ecológica e sócio-econômica, e sujeita a uma ampla gama de impactos ambientais. O sedimento é o principal destino para a maioria das substâncias introduzidas nos corpos d'água, podendo fornecer uma medida integrada da qualidade ambiental, a qual pode ser avaliada por várias abordagens. Neste projeto, a qualidade de sedimentos da Baía de Guanabara foi por uma abordagem ecotoxicológica, por meio de testes de toxicidade aguda de sedimento integral, utilizando Tiburonella viscana, e testes de toxicidade crônica de água intersticial, elutriato e interface sedimento-água, utilizando embriões de Lytechinus variegatus. Os sedimentos foram coletados em 14 estações de amostragem. Nos testes crônicos houve efeitos significativos na maioria das amostras, enquanto os sedimentos coletados nas estações 1, 2, 3, 6, 8, 10, 11, 12 e 15 apresentaram também toxicidade aguda. Houve grande concordância entre os resultados dos diferentes testes, e sua integração mostrou que os sedimentos analisados encontram-se inadequados à vida aquática, indicando degradação ambiental na baía da Guanabara. Nesse contexto, o controle das fontes poluidoras e o gerenciamento dos múltiplos usos da baía devem ser implementados, no sentido da melhora da qualidade ambiental.

Relative abundance and population biology of the non-indigenous crab Charybdis hellerii (Crustacea: Brachyura: Portunidae) in a southwestern Atlantic estuary-bay complex

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ecological distribution of the shrimp Litopenaeus schmitti (Burkenroad, 1936) (Decapoda, Penaeoidea) in Ubatuba Bay, São Paulo, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Feeding habits of the spider crab Libinia spinosa H. Milne Edwards, 1834 (Decapoda, Brachyura) in Ubatuba Bay, São Paulo, Brazil

The main goal of this study was the identification of the items of the diet of the L. spinosa, based on the stomach contents analysis. The crabs were obtained from Ubatuba region north-eastern shore of São Paulo State. In the laboratory, all the individuals were dissected, the stomach was retreated and fixed in 10% formaline. The alimentary items were identified under stereomicroscope and analysed by the method of Frequency of Occurrence. A total of 194 stomachs was analysed and nine alimentary items were obtained. Unindentified material was found in 98% of analysed stomach and poriferan were present in less then 1% of stomachs. These results pointed a diversified diet explored by this crab, as well as the employment of some different methods for food intake. This suggested that these crabs could occupy different position in the trophic chain.

A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

Background: The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules elicits phenotypic effects, requires experimental approaches that are time-consuming and laborious. Thus, a computational approach which could accurately predict such genes on a genome-wide scale would be invaluable for accelerating the pace of discovery of causal relationships between genes and diseases as well as the determination of druggability of gene products.Results: In this paper we propose a machine learning-based computational approach to predict morbid and druggable genes on a genome-wide scale. For this purpose, we constructed a decision tree-based meta-classifier and trained it on datasets containing, for each morbid and druggable gene, network topological features, tissue expression profile and subcellular localization data as learning attributes. This meta-classifier correctly recovered 65% of known morbid genes with a precision of 66% and correctly recovered 78% of known druggable genes with a precision of 75%. It was than used to assign morbidity and druggability scores to genes not known to be morbid and druggable and we showed a good match between these scores and literature data. Finally, we generated decision trees by training the J48 algorithm on the morbidity and druggability datasets to discover cellular rules for morbidity and druggability and, among the rules, we found that the number of regulating transcription factors and plasma membrane localization are the most important factors to morbidity and druggability, respectively.Conclusions: We were able to demonstrate that network topological features along with tissue expression profile and subcellular localization can reliably predict human morbid and druggable genes on a genome-wide scale. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing morbidity and druggability.

Genome-Wide Analysis of Differentially Expressed Genes During the Early Stages of Tomato Infection by a Potyvirus

Plant responses against pathogens cause up-and downward shifts in gene expression. To identify differentially expressed genes in a plant-virus interaction, susceptible tomato plants were inoculated with the potyvirus Pepper yellow mosaic virus (PepYMV) and a subtractive library was constructed from inoculated leaves at 72 h after inoculation. Several genes were identified as upregulated, including genes involved in plant defense responses (e. g., pathogenesis-related protein 5), regulation of the cell cycle (e. g., cytokinin-repressed proteins), signal transduction (e. g., CAX-interacting protein 4, SNF1 kinase), transcriptional regulators (e. g., WRKY and SCARECROW transcription factors), stress response proteins (e. g., Hsp90, DNA-J, 20S proteasome alpha subunit B, translationally controlled tumor protein), ubiquitins (e. g., polyubiquitin, ubiquitin activating enzyme 2), among others. Downregulated genes were also identified, which likewise display identity with genes involved in several metabolic pathways. Differential expression of selected genes was validated by macroarray analysis and quantitative real-time polymerase chain reaction. The possible roles played by some of these genes in the viral infection cycle are discussed.

Taphonomy of Bouchardia rosea (Rhynchonelliformea, Brachiopoda) shells from Ubatuba Bay, Brazil: implications for the use of taphonomic signatures in (paleo)environmental analysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Differential benthic occupation by crabs in the Ubatuba bay, São Paulo, Brazil

The goal of this work was to examine the occurrence of brachyurans in soft bottom sublittoral habitats and their association with some environmental factors. The relative abundance of crabs in two depth strata (from 4.5 to 9 m and from 9 to 18 m) was quantified. Crabs were collected with an otter-trawl with 3.7 m of mouth opening and 12-mm mesh in the cod end. Monthly sampling, consisted of a single trawl in each stratum during a 1-yr period, were carried out. Fifteen brachyuran and six anomuran species were found, including Callinectes ornatus Ordway, 1863; Callinectes danae Smith, 1869; Hepatus pudibundus (Herbst, 1785); Libinia spinosa H. Milne-Edwards, 1834; Persephona punctata (Linnaeus, 1758), and P. mediterranea (Herbst, 1794), which were the most abundant and frequent in the area. The most abundant swimming crabs in both strata were C. ornatus and C, dan(re. Size differences in C. ornatus were observed between strata, suggesting a spatial separation of juveniles and adult crabs.

Brachyuran community in Ubatuba Bay, northern coast of São Paulo State, Brazil

A bruchyuran crab assemblage from eight transacts at a non-consolidated sublittoral site in Ubatuba Bay was studied on a monthly basis from September 1995 to August 1996. Data about number of individuals of 50 species found and other information such as distribution of the dominant crabs are reported. The family Majidae was represented by 13 species, followed by Xanthidae (13), Portunidae (10), Leucosiidae (5), Calaphidae (2), Dromiidae (2), Parthenopidae (2), Goneplacidae (1), Pinnotharidne (1), and Ocvpodidae (1). The brachyuran taxocoenosis was dominated by Callinectes ornatus (60.4%), Callinectes danae (18.8%), and Hepatus pudibundus (7.7%). representing together 86.9% of the total number of collected brachyurans. The Shannon-Weaver diversity index ranged from 1.10 to 2.06 between transects, and from 1.33 to 2.22 between months, depending more on equitability than on richness.

Composition and abundance of shrimp species (penaeidea and caridea) in Fortaleza Bay, Ubatuba, São Paulo, Brazil

The abundance and spatio-temporal distribution of the caridean and penaeid fauna from Fortaleza Bay, Ubatuba, São Paulo, Brazil, were analyzed. Seven transects were sampled over a one year period from November 1988 to October 1989. A total of 17047 shrimps were captured, representing 13 species belonging to 5 families. The interaction of temperature and type of sediment was fundamental in determining the presence and abundance of shrimp species in the area.

Spatial and seasonal distributions of Callinectes danae (Decapoda, Portunidae) in Ubatuba Bay, São Paulo, Brazil

The spatial and seasonal distributions of Callinectes danae Smith, 1869, in Ubatuba Bay, São Paulo, Brazil, were investigated as a part of a broad study on the general biology of portunids along the northern coast of São Paulo State, Brazil. Swimming crabs were collected during one year, from September 1995 to August 1996, along eight transects determined according to local physiographic features. Three replicate trawls were performed monthly at each transect. Depth. salinity, dissolved oxygen, temperature, organic matter content, and texture of the sediment were measured. Callinectes danae individuals were concentrated in shallow water close to the discharge of estuaries where the bottom is composed of fine and very fine sand. The species was more abundant in the warmer months. During the study period, C. danae exhibited continuous reproduction with a peak of reproductive intensity in June. Within this area, some sites are particularly favorable for C. danae establishment due to a combination of factors and prevailing local conditions.