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 percent 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.

Sex ratio and size structure of Micropogonias furnieri (Desmarest, 1823) (Perciformes, Sciaenidae) in Sepetiba Bay, Rio de Janeiro, Brazil

Sex ratio and size structure constitute basic information in assessing reproductive potential and estimating stock size in fish populations. One hundred fifty-one individuals of Micropogonias furnieri caught by experimental otter trawls, in three zones (inner, central, and outer) of Sepetiba Bay between October 1998 and September 1999 were examined. Males outnumbered females (1.3:1.0) in all zones but no significant differences were detected. Only in the outer zone (5.0:1.0) were male/female rates significantly different according to the chi-square test. No temporal differences were observed in sex ratio. Fish size ranged from 81 to 244 mm total length (TL) with significant differences in 155 to 185 mm TL size classes, where males predominated, and a slightly higher number of females were observed for the smaller size class (TL = 95-150 mm). Size distribution varied according to the zone, with juveniles predominating in the inner and adults in the outer zone. Spatial difference in size structure observed in this study indicates that the inner bay is a rearing ground during the first life-cycle period, and movement toward the sea occurs as fish increase in size.