Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems

YesComputational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems.EPSR

A cladistic phylogeny of the family Patellidae (Mollusca: Gastropoda)

A phylogenetic hypothesis for the patellid limpets is reconstructed by cladistic analysis of morphological characters from 37 species, representing all but one of the living members of the family. Characters included in the analysis are derived from shell shape and microstructure, headfoot and pallial complex, radula and sperm. The species fall into four clades, providing the basis for a new phylogenetic classification into four monophyletic genera: Helcion (four species; southern Africa), Cymbula (eight species; southern Africa, eastern Atlantic, southern Indian Ocean), Scutellastra (17 species; southern and southwestern Africa, Australia, Indo-West Pacific, Eastern Pacific) and Patella (nine species; northeastern Atlantic and Mediterranean). The analysis suggests sister-group relationships between Helcion and Cymbula, and between Scutellastra and Patella. In combination with present-day patterns of geographical distribution, this phylogenetic hypothesis is used to discuss the historical biogeography of the Patellidae. Scutellastra may have originated in southern Africa and dispersed across the Pacific, or alternatively may be a primitively Tethyan group. Both Helcion and Cymbula appear to have originated in southern Africa, but three Cymbula species have dispersed respectively to northwest Africa, St Helena and the southern Indian Ocean. The patellids of the northeastern Atlantic form a single clade, Patella (including P. pellucida), which may have arrived by northward dispersal of an ancestor from southern Africa, or possibly by vicariance of a widespread ancestral Tethyan distribution. The known fossil record of patellids is too fragmentary to permit choice between these alternatives

Estrutura populacional de Petrolisthes armatus (Gibbes) (Decapoda, Anomura, Porcellanidae) da Ilha do Farol, Matinhos, Paraná, Brasil Population structure of Petrolisthes armatus (Gibbes) (Decapoda, Anomura, Porcellanidae) from Farol Isle, Matinhos, Paraná, Brazil

<abstract language="eng">Population structure of the porcelain crab Petrolisthes armatus (Gibbes, 1850) from the rocky shore of the Farol isle (25º51'S, 48º32'W) was carried out in the following aspects: annual fluctuation of the density, distribution of the developmental stages and sexes over year round, size composition and recruiting period of juveniles into the population. Monthly collections were made in the three sites of the midlittoral, from November/89 to April/91, with the aid of a trap. The air temperature ranged from 13ºC to 28ºC, that of the surface water from 16ºC lo 29ºC and the salinity of the surface water from 06.7‰ to 31.5‰. A total of 5.585 individuals of Petrolisthes armatus was collected, among which, 116 were in the megalopa stage, 1,579 juveniles, 830 immature males, 729 immature females, 1,161 mature males, 744 mature females and 426 ovigerous females. The population density ranged from 15.3 to 305.0 ind.m-2, with a peak in January. This density is the highest among the porcelain crab populations known from the literature. The species has continuous reproduction, but, there were two main cohorts in the year: summer one that was longer and more abundant and the winter one that was shorter and the less numerous