CodABC:A computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.This work was supported by the Spanish Government with the “Juan de la Cierva” fellowship JCI-2011-10452 to M.A., the European Research Council (ERC Grant Agreement No. 617457) to D.P., and Fundac¸~ao para a Ci^encia e a Tecnologia (FCT) (grant EXCL/BIA-ANM/0549/2012) to J.S.L.Peer reviewe

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called CodABC, to jointly estimate recombination, substitution and synonymous and non-synonymous rates from coding data. CodABC uses approximate Bayesian computation (ABC) with and without regression adjustment and implements a variety of codon models, intracodon recombination and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-touse examples, and can run in parallel on multicore machines.Ministerio de Ciencia e Innovación | Ref. JCI-2011-10452Fundação para a Ciência e a Tecnologia | Ref. EXCL/BIA-ANM/0549/201

Combined use of a new SNP-based assay and multilocus SSR markers to assess genetic diversity of Xylella fastidiosa subsp. pauca infecting citrus and coffee plants

Two haplotypes of Xylella fastidiosa subsp. pauca (Xfp) that correlated with their host of origin were identified in a collection of 90 isolates infecting citrus and coffee plants in Brazil, based on a single-nucleotide polymorphism in the gyrB sequence. A new single-nucleotide primer extension (SNuPE) protocol was designed for rapid identification of Xfp according to the host source. The protocol proved to be robust for the prediction of the Xfp host source in blind tests using DNA from cultures of the bacterium, infected plants, and insect vectors allowed to feed on Xfp-infected citrus plants. AMOVA and STRUCTURE analyses of microsatellite data separated most Xfp populations on the basis of their host source, indicating that they were genetically distinct. The combined use of the SNaPshot protocol and three previously developed multilocus SSR markers showed that two haplotypes and distinct isolates of Xfp infect citrus and coffee in Brazil and that multiple, genetically different isolates can be present in a single orchard or infect a single tree. This combined approach will be very useful in studies of the epidemiology of Xfp-induced diseases, host specificity of bacterial genotypes, the occurrence of Xfp host jumping, vector feeding habits, etc., in economically important cultivated plants or weed host reservoirs of Xfp in Brazil and elsewhere [Int Microbiol 2015; 18(1):13-24]Keywords: Citrus variegated chlorosis · coffee leaf scorch · vector transmission· xylem-limited bacteria · haplotype characterization · host-plant associatio

Fighting assessment triggers rapid changes in activity of the brain social Decision-Making network of cichlid fish

Social living animals have to adjust their behavior to rapid changes in the social environment. It has been hypothesized that the expression of social behavior is better explained by the activity pattern of a diffuse social decision-making network (SDMN) in the brain than by the activity of a single brain region. In this study, we tested the hypothesis that it is the assessment that individuals make of the outcome of the fights, rather than the expression of aggressive behavior per se, that triggers changes in the pattern of activation of the SDMN which are reflected in socially driven behavioral profiles (e.g., dominant vs. subordinate specific behaviors). For this purpose, we manipulated the perception of the outcome of an agonistic interaction in an African cichlid fish (Oreochromis mossambicus) and assessed if either the perception of outcome or fighting by itself was sufficient to trigger rapid changes in the activity of the SDMN. We have used the expression of immediate early genes (c-fos and egr-1) as a proxy to measure the neuronal activity in the brain. Fish fought their own image on a mirror for 15 min after which they were allocated to one of three conditions for the two last minutes of the trial: (1) they remained fighting the mirror image (no outcome treatment); (2) the mirror was lifted and a dominant male that had just won a fight was presented behind a transparent partition (perception of defeat treatment); and (3) the mirror was lifted and a subordinate male that had just lost a fight was presented behind a transparent partition (perception of victory treatment). Results show that these short-term social interactions elicit distinct patterns in the SDMN and that the perception of the outcome was not a necessary condition to trigger a SDMN response as evidenced in the second treatment (perception of defeat treatment). We suggest that the mutual assessment of relative fighting behavior drives these acute changes in the state of the SDMN.Fundação para a Ciência e Tecnologia-FCTinfo:eu-repo/semantics/publishedVersio

Multi-agent system for dynamic scheduling

This paper proposes a flexible manufacturing system based on intelligent computational agents. A Multi-Agent System composed of 4 types of reactive agents was designed to control the operation of a real implementation in the Intelligent Automation Lab at Instituto Superior Tecnico. This implementation was ´ based and constructed analogously to a known benchmark, AIPPRIMECA. The agents were modelled using Petri nets and agent communications were defined through the combination of FIPA Interaction Protocols. The system was tested under the conditions of static and dynamic scenarios, having its performance validated whenever possible by comparison with results from a Potential Fields Approach in the same benchmark. Overall, the performance exhibited by the proposed MAS was slightly better and it is worth highlighting the simple behaviour of each agent and ability to respond in real-time to all the dynamic scenarios tested

Extensão Protocolar para Comunicação Fiável em Ambientes IoT

The current developments in the Information Technology area, and particularly in Computer Networks related fields, have sustained a considerable scientific and technological progress of the area usually denominated as the Internet of Things (IoT). In this context, this article focuses on the design, implementation and test of a communication protocol extension oriented to IoT environments. The proposed solution is designed to provide reliable multi-hop communication capabilities for commonly used and open platform IoT devices (e.g. Arduino). The implemented API provides a modular set of service primitives that will allow the successful development of IoT applications with differentiated reliability and coverage requirements.Acompanhando o desenvolvimento atual na área das Tecnologias de Informação, e sobretudo a nível das Redes de Computadores, é notório o avanço científico e tecnológico da área designada por Internet of Things (IoT). Neste contexto, este artigo centra-se na proposta e desenvolvimento de uma extensão protocolar de comunicação vocacionada para ambientes IoT. A solução proposta foi desenhada para proporcionar capacidade de comunicação multi-hop fiável para dispositivos IoT de uso generalizado e plataforma aberta (e.g.,Arduino). A API implementada fornece um conjunto modular de primitivas de serviço que permitirá suportar o desenvolvimento de aplicações IoT com requisitos diferenciados de fiabilidade e abrangência.Este trabalho foi apoiado pelos projecto COMPETE: POCI-01-0145-FEDER-007043 e pela Fundação para a Ciência e Tecnologia no âmbito do projecto UID/CEC/00319/2013

Unveiling time in dose-response models to infer host susceptibility to pathogens

The biological effects of interventions to control infectious diseases typically depend on the intensity of pathogen challenge. As much as the levels of natural pathogen circulation vary over time and geographical location, the development of invariant efficacy measures is of major importance, even if only indirectly inferrable. Here a method is introduced to assess host susceptibility to pathogens, and applied to a detailed dataset generated by challenging groups of insect hosts (Drosophila melanogaster) with a range of pathogen (Drosophila C Virus) doses and recording survival over time. The experiment was replicated for flies carrying the Wolbachia symbiont, which is known to reduce host susceptibility to viral infections. The entire dataset is fitted by a novel quantitative framework that significantly extends classical methods for microbial risk assessment and provides accurate distributions of symbiont-induced protection. More generally, our data-driven modeling procedure provides novel insights for study design and analyses to assess interventions