Shannon entropy analysis of the genome code

This paper studies the chromosome information of twenty five species, namely, mammals, fishes, birds, insects, nematodes, fungus, and one plant. A quantifying scheme inspired in the state space representation of dynamical systems is formulated. Based on this algorithm, the information of each chromosome is converted into a bidimensional distribution. The plots are then analyzed and characterized by means of Shannon entropy. The large volume of information is integrated by averaging the lengths and entropy quantities of each species. The results can be easily visualized revealing quantitative global genomic information.

Rapid Evolution of the Sequences and Gene Repertoires

Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.

Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Integration of the project team in the classic maintenance cycle

A manutenção é uma área extremamente importante, principalmente na indústria. Devidamente organizada, permitirá um fluxo produtivo devidamente planeado e executado, que permitirá a qualquer empresa manter o nível de facturação desejado e o prazo de entrega acordado com os clientes. De outra forma, poderá originar o caos. No entanto, os desafios de gestão da produção mais correntes, nomeadamente através do Lean Manufacturing, passam a exigir um pouco mais do que uma simples manutenção. Torna-se obrigatório fazer análises económicas que permitam averiguar quando cada equipamento passa a exigir custos de manutenção excessivos, os quais poderão obrigar a um recondicionamento mais acentuado do equipamento, o qual pode passar inclusivamente por uma melhoria da sua performance. Nestes casos, terá que existir uma “cumplicidade” entre a Direcção de Produção e a Manutenção, no sentido de averiguar o melhor momento para proceder a uma melhoria do equipamento, numa perspectiva de funcionamento global em linha de produção, adaptando-o à performance que será exigida ao conjunto. Neste domínio, o Projecto passa a prestar um serviço valiosíssimo à empresa, integrando-se no conjunto Produção + Manutenção, criando valor na intervenção, através do desenvolvimento de um trabalho que permite não só repor o estado natural da produção, mas sim promover uma melhoria sustentada da mesma. Este trabalho pretende reflectir e avaliar a relevância do Projecto neste tipo de operações, contribuindo de uma forma sistemática e sustentada para a melhoria contínua dos processos de fabrico. É apresentado um caso de estudo que pretende validar todo o desenvolvimento anteriormente realizado na matéria.