Satellyptus: analysis and database of microsatellites from ESTs of Eucalyptus

The main goal of our research was to search for SSRs in the Eucalyptus EST FORESTs database (using a software for mining SSR-motifs). With this objective, we created a database for cataloging Eucalyptus EST-derived SSRs, and developed a bioinformatics tool, named Satellyptus, for finding and analyzing microsatellites in the Eucalyptus EST database. The search for microsatellites in the FORESTs database containing 71,115 Eucalyptus EST sequences (52.09 Mb) revealed 20,530 SSRs in 15,621 ESTs. The SSR abundance detected on the Eucalyptus ESTs database (29% or one microsatellite every four sequences) is considered very high for plants. Amongst the categories of SSR motifs, the dimeric (37%) and trimeric ones (33%) predominated. The AG/CT motif was the most frequent (35.15%) followed by the trimeric CCG/CGG (12.81%). From a random sample of 1,217 sequences, 343 microsatellites in 265 SSR-containing sequences were identified. Approximately 48% of these ESTs containing microsatellites were homologous to proteins with known biological function. Most of the microsatellites detected in Eucalyptus ESTs were positioned at either the 5 or 3 end. Our next priority involves the design of flanking primers for codominant SSR loci, which could lead to the development of a set of microsatellite-based markers suitable for marker-assisted Eucalyptus breeding programs.

Isolamento e caracterização de promotores órgão-específicos a partir de informações do Banco FORESTs (Eucalyptus Genome Sequencing Project Consortium)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Boron transport in Eucalyptus. 2. Identification in silico of a putative boron transporter for xylem loading in eucalypt

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

The post-transcriptional gene silencing pathway in Eucalyptus

Post-transcriptional gene silencing (PTGS) is a conserved surveillance mechanism that identifies and cleaves double-stranded RNA molecules and their cellular cognate transcripts. The RNA silencing response is actually used as a powerful technique (named RNA interference) for potent and specific inhibition of gene expression in several organisms. To identify gene products in Eucalyptus sharing similarities with enzymes involved in the PTGS pathway, we queried the expressed sequence tag database of the Brazilian Eucalyptus Genome Sequence Project Consortium (FORESTs) with the amino acid sequences of known PTGS-related proteins. Among twenty-six prospected genes, our search detected fifteen assembled sequences encoding products presenting high level of similarity (E value < 10 -40) to proteins involved in PTGS in plants and other organisms. We conclude that most of the genes known to be involved in the PTGS pathway are represented in the FORESTs database. Copyright by the Brazilian Society of Genetics.

Eucalyptus ESTs associated with resistance to herbicide inhibitors of aromatic and branched-chain amino acid synthesis

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

Eucalyptus ESTs involved in the production of 9-cis epoxycarotenoid dioxygenase, a regulatory enzyme of abscisic acid production

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

Biomass burning fuel consumption rates: a field measurement database

Landscape fires show large variability in the amount of biomass or fuel consumed per unit area burned. Fuel consumption (FC) depends on the biomass available to burn and the fraction of the biomass that is actually combusted, and can be combined with estimates of area burned to assess emissions. While burned area can be detected from space and estimates are becoming more reliable due to improved algorithms and sensors, FC is usually modeled or taken selectively from the literature. We compiled the peerreviewed literature on FC for various biomes and fuel categories to understand FC and its variability better, and to provide a database that can be used to constrain biogeochemical models with fire modules. We compiled in total 77 studies covering 11 biomes including savanna (15 studies, average FC of 4.6 t DM (dry matter) ha 1 with a standard deviation of 2.2), tropical forest (n = 19, FC = 126 +/- 77), temperate forest (n = 12, FC = 58 +/- 72), boreal forest (n = 16, FC = 35 +/- 24), pasture (n = 4, FC = 28 +/- 9.3), shifting cultivation (n = 2, FC = 23, with a range of 4.0-43), crop residue (n = 4, FC = 6.5 +/- 9.0), chaparral (n = 3, FC = 27 +/- 19), tropical peatland (n = 4, FC = 314 +/- 196), boreal peatland (n = 2, FC = 42 [42-43]), and tundra (n = 1, FC = 40). Within biomes the regional variability in the number of measurements was sometimes large, with e. g. only three measurement locations in boreal Russia and 35 sites in North America. Substantial regional differences in FC were found within the defined biomes: for example, FC of temperate pine forests in the USA was 37% lower than Australian forests dominated by eucalypt trees. Besides showing the differences between biomes, FC estimates were also grouped into different fuel classes. Our results highlight the large variability in FC, not only between biomes but also within biomes and fuel classes. This implies that substantial uncertainties are associated with using biome-averaged values to represent FC for whole biomes. Comparing the compiled FC values with co-located Global Fire Emissions Database version 3 (GFED3) FC indicates that modeling studies that aim to represent variability in FC also within biomes, still require improvements as they have difficulty in representing the dynamics governing FC.

Evolução do uso da terra entre 1996 e 1999 no município de Botucatu-SP

Este trabalho teve o objetivo de avaliar a evolução do uso da terra no município de Botucatu - SP, no período de três anos, considerando-se seis tipos de cobertura vegetal (cana-de-açúcar, reflorestamento, floresta nativa, pastagem, cítrus e outros), tendo como base as imagens de satélite Landsat 5, bandas 3; 4 e 5, órbita 220, ponto 76, quadrante A, passagem de 8 de junho de 1999. O Sistema de Informações Geográficas - IDRISI for Windows 3.2, foi utilizado para as análises. Os resultados mostraram que esse programa foi eficiente para auxiliar na identificação e mapeamento das áreas com uso da terra, facilitando o processamento dos dados. As imagens de satélite TM/LANDSAT 5 forneceram um excelente banco de dados para a classificação supervisionada. O município não vem sendo preservado ambientalmente, pois apresenta-se coberto com menos de 20% de florestas nativas, mínimo exigido por lei. As áreas de pastagem, principal componente da paisagem do município, confirmam a vocação da região para a pecuária.

Sensoriamento remoto e geoprocessamento aplicados ao uso da terra em microbacias hidrográficas, Botucatu - SP

O presente trabalho teve como objetivo identificar e quantificar o uso da terra em dez microbacias ocorrentes na bacia do Rio Capivara, município de Botucatu - SP, a partir da estruturação de um banco de dados utilizando o Sistema de Informações Geográficas (SIG) - IDRISI. Os resultados mostram que as classes de uso da terra, uso agrícola e pastagem, foram as mais significativas, pois ocuparam mais da metade da área das microbacias. O alto índice de uso da terra por pastagens, capoeiras, reflorestamento e matas reflete a predominância de solos arenosos com baixa fertilidade. As imagens obtidas do satélite LANDSAT 5 permitiram o mapeamento do uso da terra de maneira rápida, além de fornecer um excelente banco de dados para futuro planejamento e gerenciamento das atividades agropecuárias regionais. O SIG-IDRISI permitiu identificar, por meio de seus diferentes módulos para georreferenciamento, classificação digital e modelo matemático, as classes de uso da terra com rapidez.

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

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

Natural history of the coral snake Micrurus Pyrrhocryptus Cope 1862 (Elapidae) from semideciduous forests of western Brazil.

Coral snakes in the genus Micrurus are widely distributed in the Neotropics, with more than 50 species already described in this region. They are primarily ground or leaf litter dwellers, feed on snakes or other elongate vertebrates, and tend to reproduce during the rainy season. We present data on the biology of Micrurus pyrrhocryptus from two semideciduous forests of Mato Grosso do Sul state, western Brazil. Two snake species were consumed: the dipsadid Sibynomorphus lavillai and the typhlopid Typhlops brongersmianus. Sexual dimorphism is marked in M. pyrrhocryptus. with males attaining larger sizes and having longer tails. Activity was concentrated in the wet season, when reproduction occurs. The defensive behavior in this species is similar to that displayed by other Micron's, although less pronounced.

Population and reproductive biology of the crab Uca burgersi (Crustacea : Ocypodidae) in three subtropical mangrove forests

Population and reproductive biology were studied in three populations of the crab Uca burgersi Holthuis, 1967, in the Indaia, Cavalo and Ubatumirim mangrove forests (Ubatuba, São Paulo State, Brazil). Crabs were collected during low tide (August 2001 through July 2002), by digging the sediment, with a standard capture effort (two persons for 30 min.). Carapace width was measured, and gonad developmental stage was recorded from all specimens. U. burgersi was most abundant in the Cavalo mangrove, where the largest mate was found. Juvenile crabs were found year-round at all three sites. However, the ratio of ovigerous females was very low, even null in the Cavalo mangrove. The gonad development rate indicated that U. burgersi was reproducing continuously, but more intensively during spring and summer, with recruitment occurring in winter. The synchrony between the populational and reproductive biology in the three areas showed that local features were not the limiting factors. It is suggested that this species is a habitat generalist.

Floristic relationships among inland swamp forests of Southeastern and Central-Western Brazil

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

The role of riverine forests for food supply for the omnivorous fish Brycon opalinus Cuvier, 1819 (Characidae) in the Serra do Mar, Southeast Brazil

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