Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish

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

Mitochondrial genome sequence of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae): Mitochondrial genes utility to investigate the evolutionary history of Coleoptera and its bioluminescence

The Coleoptera order is the richest group among Metazoa, but its phylogenetics remains incompletely understood. Among Coleoptera, bioluminescence is found within the Elateroidea, but the evolution of this character remains a mystery. Mitochondrial DNA has been used extensively to reconstruct phylogenetic relationships, however, the evolution of a single gene does not always correspond to the species evolutionary history and the molecular marker choice is a key step in this type of analysis. To create a solid basis to better understand the evolutionary history of Coleoptera and its bioluminescence, we sequenced and comparatively analyzed the mitochondrial genome of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae). © 2007 Elsevier B.V. All rights reserved.

Building the sugarcane genome for biotechnology and identifying evolutionary trends

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

Evolutionary transition to freshwater by ancestral marine palaemonids: evidence from osmoregulation in a tide pool shrimp

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

Genomics-based design of defined growth media for the plant pathogen Xylella fastidiosa

Based on the genetic analysis of the phytopathogen Xylella fastidiosa genome, five media with defined composition were developed and the growth abilities of this fastidious prokaryote were evaluated in liquid media and on solid plates. All media had a common salt composition and included the same amounts of glucose and vitamins but differed in their amino acid content. XDM1 medium contained amino acids threonine, serine, glycine, alanine, aspartic acid and glutamic acid, for which complete degradation pathways occur in X fastidiosa; XDM2 included serine and methionine, amino acids for which biosynthetic enzymes are absent, plus asparagine and glutamine, which are abundant in the xylem sap; XDM3 had the same composition as XDM2 but with asparagine replaced by aspartic acid due to the presence of complete degradation pathway for aspartic acid; XDM4 was a minimal medium with glutamine as a sole nitrogen source; XDM5 had the same composition as XDM4, plus methionine. The liquid and solidified XDM2 and XDM3 media were the most effective for the growth of X. fastidiosa. This work opens the opportunity for the in silico design of bacterial defined media once their genome is sequenced. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier B.V. B.V. All rights reserved.

The surprising evolutionary history of South American deer

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

New Insights on Nontechnical Losses Characterization Through Evolutionary-Based Feature Selection

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

Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach

Background: The tectum is a structure localized in the roof of the midbrain in vertebrates, and is taken to be highly conserved in evolution. The present article assessed three hypotheses concerning the evolution of lamination and citoarchitecture of the tectum of nontetrapod animals: 1) There is a significant degree of phylogenetic inertia in both traits studied (number of cellular layers and number of cell classes in tectum); 2) Both traits are positively correlated accross evolution after correction for phylogeny; and 3) Different developmental pathways should generate different patterns of lamination and cytoarchitecture.Methodology/Principal Findings: The hypotheses were tested using analytical-computational tools for phylogenetic hypothesis testing. Both traits presented a considerably large phylogenetic signal and were positively associated. However, no difference was found between two clades classified as per the general developmental pathways of their brains.Conclusions/Significance: The evidence amassed points to more variation in the tectum than would be expected by phylogeny in three species from the taxa analysed; this variation is not better explained by differences in the main course of development, as would be predicted by the developmental clade hypothesis. Those findings shed new light on the evolution of an functionally important structure in nontetrapods, the most basal radiations of vertebrates.

Hybrid evolutionary algorithm for the Capacitated Centered Clustering Problem

The Capacitated Centered Clustering Problem (CCCP) consists of defining a set of p groups with minimum dissimilarity on a network with n points. Demand values are associated with each point and each group has a demand capacity. The problem is well known to be NP-hard and has many practical applications. In this paper, the hybrid method Clustering Search (CS) is implemented to solve the CCCP. This method identifies promising regions of the search space by generating solutions with a metaheuristic, such as Genetic Algorithm, and clustering them into clusters that are then explored further with local search heuristics. Computational results considering instances available in the literature are presented to demonstrate the efficacy of CS. (C) 2010 Elsevier Ltd. All rights reserved.

Multi-objective evolutionary particle swarm optimization in the assessment of the impact of distributed generation

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

Multi Objective Evolutionary Algorithm Applied to the Optimal Power Flow Problem

This work presents the application of a multiobjective evolutionary algorithm (MOEA) for optimal power flow (OPF) solution. The OPF is modeled as a constrained nonlinear optimization problem, non-convex of large-scale, with continuous and discrete variables. The violated inequality constraints are treated as objective function of the problem. This strategy allows attending the physical and operational restrictions without compromise the quality of the found solutions. The developed MOEA is based on the theory of Pareto and employs a diversity-preserving mechanism to overcome the premature convergence of algorithm and local optimal solutions. Fuzzy set theory is employed to extract the best compromises of the Pareto set. Results for the IEEE-30, RTS-96 and IEEE-354 test systems are presents to validate the efficiency of proposed model and solution technique.

Comparative genomics analyses of citrus-associated bacteria

Xylella fastidiosa 9a5c (XF-9a5c) and Xanthomonas axonopodis pv. citri (XAC) are bacteria that infect citrus plants. Sequencing of the genomes of these strains is complete and comparative analyses are now under way with the genomes of other bacteria of the same genera. In this review, we present an overview of this comparative genomic work. We also present a detailed genomic comparison between XF-9a5a and XAC. Based on this analysis, genes and operons were identified that might be relevant for adaptation to citrus. XAC has two copies of a type II secretion system, a large number of cell wall-degrading enzymes and sugar transporters, a complete energy metabolism, a whole set of avirulence genes associated with a type III secretion system, and a complete flagellar and chemotatic system. By contrast, XF-9a5c possesses more genes involved with type IV pili biosynthesis than does XAC, contains genes encoding for production of colicins, and has 4 copies of Type I restriction/modification system while XAC has only one.

Contributions and perspectives of chicken genomics in Brazil: from biological model to export commodity

Chicken is one of the most important sources of animal protein for human consumption, and breeding programmes have been responsible for constant improvements in production efficiency and product quality. Furthermore, chicken has largely contributed to fundamental discoveries in biology for the last 100 years. In this article we review recent developments in poultry genomics and their contribution to adding functional information to the already existing structural genomics, including the availability of the complete genome sequence, a comprehensive collection of mRNA sequences ( ESTs), microarray platforms, and their use to complement QTL mapping strategies in the identification of genes that underlie complex traits. Efforts of the Brazilian Poultry Genomics Programme in this area resulted in generation of a resource population, which was used for identification of Quantitative Trait Loci ( QTL) regions, generation of ESTs and candidate gene studies that contributed to furthering our understanding of the complex biological processes involved in growth and muscular development in chicken.

Thermal relationships and exercise physiology in anuran amphibians: Integration and evolutionary implications

Thermal and water balance are coupled in anurans, and species with particularly permeable skin avoid overheating more effectively than minimizing variance of body temperature. In turn, temperature affects muscle performance in several ways, so documenting the mean and variance of body temperature of active frogs can help explain variation in behavioral performance. The two types of activities studied in most detail, jumping and calling, differ markedly in duration and intensity, and there are distinct differences in the metabolic profile and fiber type of the supporting muscles. Characteristics of jumping and calling also vary significantly among species, and these differences have a number of implications that we discuss in some detail throughout this paper. One question that emerges from this topic is whether anuran species exhibit activity temperatures that match the temperature range over which they perform best. Although this seems the case, thermal preferences are variable and may not necessarily reflect typical activity temperatures. The performance versus temperature curves and the thermal limits for anuran activity reflect the thermal ecology of species more than their systematic position. Anuran thermal physiology, therefore, seems to be phenotypically plastic and susceptible to adaptive evolution. Although generalizations regarding the mechanistic basis of such adjustments are not yet possible, recent attempts have been made to reveal the mechanistic basis of acclimation and acclimatization. (C) 2007 Elsevier B.V. All rights reserved.

Physical mapping of the Nile tilapia (Oreochromis niloticus) genome by fluorescent in situ hybridization of repetitive DNAs to metaphase chromosomes - a review

The Nile tilapia (Oreochromis niloticus) has received increasing scientific interest over the past few decades for two reasons: first, tilapia is an enormously important species in aquaculture worldwide, especially in regions where there is a chronic shortage of animal protein; and second, this teleost fish belongs to the fascinating group of cichlid fishes that have undergone a rapid and extensive radiation of much interest to evolutionary biologists. Currently, studies based on physical and genetic mapping of the Nile tilapia genome offer the best opportunities for applying genomics to such diverse questions and issues as phylogeography, isolation of quantitative trait loci involved in behaviour, morphology, and disease, and overall improvement of aquacultural stocks. In this review, we have integrated molecular cytogenetic data for the Nile tilapia describing the chromosomal location of the repetitive DNA sequences, satellite DNAs, telomeres, 45S and 5S rDNAs, and the short and long interspersed nucleotide elements [short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs)], and provide the beginnings of a physical genome map for this important teleost fish. (C) 2004 Elsevier B.V. All rights reserved.