Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

Diversity, composition and phenology of araneid orb-weavers (Araneae, Araneidae) associated with riparian forests in southern Brazil

The Araneidae is a speciose family including web-spinning spiders that are very abundant in various terrestrial ecosystems. Several studies demonstrate that changes in vegetation surrounding rivers, streams and brooks affect the associated araneofauna. The aim of this research was to compare differences found in diversity (abundance and richness), composition and phenology of Araneidae spiders sampled in different habitats in four riparian forest catchments in southern Brazil. Samples were taken from riparian forests in four rivers of Rio Grande do Sul State: Piratini, Camaquã, Sinos and Maquiné rivers, each in a different hydrographic basin. Samples were taken twice seasonally on each basin during two years, sampling the araneofauna of the tree-shrub strata with beating tray. Six transects were employed on each basin, two per habitat: edge with grassland, forest interior and river edge. Araneids totalled 20 genera and 65 species. Comparing riparian forests significant differences are found. Spider abundance differed among riparian forests as well as species richness. Overall, Piratini river riparian forest had the higher abundance and richness for Araneidae; the lower values were in Sinos river forest. The stronger degradation and fragmentation of the riparian forests of Sinos river probably influenced the results, with human disturbance gradients associated negatively to web building. We present data on the diversity of these spiders, which were very abundant in the riparian forest interior and very rich in species in the grassland/riparian forest edge. Species composition also differs among the studied habitats (the above plus river/riparian forest edge). For the most abundant species the phenological pattern across the seasons was also analysed.