Modeling of coastal water contamination in Fortaleza (Northeastern Brazil)

An important tool in environmental management projects and studies due to the complexity of environmental systems, environmental modeling makes it possible to integrate many variables and processes, thereby providing a dynamic view of systems. In this study the bacteriological quality of the coastal waters of Fortaleza (Brazil) was modeled considering multiple contamination sources. Using the software SisBaHiA, the dispersion of thermotolerant coliforms and Escherichia coli from three sources of contamination (rivers, storm drains and submarine outfall) was analyzed. The models took into account variations in bacterial decay due to solar radiation and other environmental factors. Fecal pollution discharged from rivers and storm drains is transported westward by coastal currents, contaminating strips of beach water to the left of each storm drain or river. Exception to this condition only occurs on beaches protected by the breakwater of the harbor, where counterclockwise vortexes reverse this behavior. The results of the models were consistent with field measurements taken during the dry and the rainy season. Our results show that the submarine outfall plume was over 2 km from the nearest beach. The storm drains and the Maceió stream are the main factors responsible for the poor water quality on the waterfront of Fortaleza

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

Background: Coffee is one of the world’s most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results: Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion: We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/ coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance

Genetic structure of sigmodontine rodents (Cricetidae) along an altitudinal gradient of the Atlantic Rain Forest in southern Brazil

The population genetic structure of two sympatric species of sigmodontine rodents (Oligoryzomys nigripes and Euryoryzomys russatus) was examined for mitochondrial DNA (mtDNA) sequence haplotypes of the control region. Samples were taken from three localities in the Atlantic Rain Forest in southern Brazil, along an altitudinal gradient with different types of habitat. In both species there was no genetic structure throughout their distribution, although levels of genetic variability and gene flow were high

25 Years of Self-organized Criticality: Concepts and Controversies

Introduced by the late Per Bak and his colleagues, self-organized criticality (SOC) has been one of the most stimulating concepts to come out of statistical mechanics and condensed matter theory in the last few decades, and has played a significant role in the development of complexity science. SOC, and more generally fractals and power laws, have attracted much comment, ranging from the very positive to the polemical. The other papers (Aschwanden et al. in Space Sci. Rev., 2014, this issue; McAteer et al. in Space Sci. Rev., 2015, this issue; Sharma et al. in Space Sci. Rev. 2015, in preparation) in this special issue showcase the considerable body of observations in solar, magnetospheric and fusion plasma inspired by the SOC idea, and expose the fertile role the new paradigm has played in approaches to modeling and understanding multiscale plasma instabilities. This very broad impact, and the necessary process of adapting a scientific hypothesis to the conditions of a given physical system, has meant that SOC as studied in these fields has sometimes differed significantly from the definition originally given by its creators. In Bak’s own field of theoretical physics there are significant observational and theoretical open questions, even 25 years on (Pruessner 2012). One aim of the present review is to address the dichotomy between the great reception SOC has received in some areas, and its shortcomings, as they became manifest in the controversies it triggered. Our article tries to clear up what we think are misunderstandings of SOC in fields more remote from its origins in statistical mechanics, condensed matter and dynamical systems by revisiting Bak, Tang and Wiesenfeld’s original papers