Patterns of genetic variation in populations of infectious agents

<p>Abstract</p> <p>Background</p> <p>The analysis of genetic variation in populations of infectious agents may help us understand their epidemiology and evolution. Here we study a model for assessing the levels and patterns of genetic diversity in populations of infectious agents. The population is structured into many small subpopulations, which correspond to their hosts, that are connected according to a specific type of contact network. We considered different types of networks, including fully connected networks and scale free networks, which have been considered as a model that captures some properties of real contact networks. Infectious agents transmit between hosts, through migration, where they grow and mutate until elimination by the host immune system.</p> <p>Results</p> <p>We show how our model is closely related to the classical SIS model in epidemiology and find that: depending on the relation between the rate at which infectious agents are eliminated by the immune system and the within host effective population size, genetic diversity increases with <it>R</it>₀or peaks at intermediate <it>R</it>₀levels; patterns of genetic diversity in this model are in general similar to those expected under the standard neutral model, but in a scale free network and for low values of <it>R</it>₀a distortion in the neutral mutation frequency spectrum can be observed; highly connected hosts (hubs in the network) show patterns of diversity different from poorly connected individuals, namely higher levels of genetic variation, lower levels of genetic differentiation and larger values of Tajima's D.</p> <p>Conclusion</p> <p>We have found that levels of genetic variability in the population of infectious agents can be predicted by simple analytical approximations, and exhibit two distinct scenarios which are met according to the relation between the rate of drift and the rate at which infectious agents are eliminated. In one scenario the diversity is an increasing function of the level of transmission and in a second scenario it is peaked around intermediate levels of transmission. This is independent of the type of host contact structure. Furthermore for low values of <it>R</it>₀, very heterogeneous host contact structures lead to lower levels of diversity.</p

Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance

The deposited review is a post-print version and has been submitted to peer review.This publication hasn't any creative commons license associated.This deposit is composed by the review, and it hasn't any supplementary materials associated.The publication deposited was in a state of Epub Ahead of Print, at the time when the upload was made.Antibiotics target essential cellular functions but bacteria can become resistant by acquiring either exogenous resistance genes or chromosomal mutations. Resistance mutations typically occur in genes encoding essential functions; these mutations are therefore generally detrimental in the absence of drugs. However, bacteria can reduce this handicap by acquiring additional mutations, known as compensatory mutations. Genetic interactions (epistasis) either with the background or between resistances (in multiresistant bacteria) dramatically affect the fitness cost of antibiotic resistance and its compensation, therefore shaping dissemination of antibiotic resistance mutations. This Review summarizes current knowledge on the evolutionary mechanisms influencing maintenance of resistance mediated by chromosomal mutations, focusing on their fitness cost, compensatory evolution, epistasis, and the effect of the environment on these processes.PD and RB were supported by Fundação para a Ciência e Tecnologia (FCT), fellowships SFRH/BPD/118474/2016 and SFRH/BPD/109517/2015, respectively. Current research is supported by project JPIAMR/0001/2016-ERA NET and ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI – ‘Fundos Europeus Estruturais e de Investimento’ from ‘Programa Operacional Regional Lisboa 2020’, and by national funds from FCT – ‘Fundação para a Ciência e a Tecnologia’.info:eu-repo/semantics/acceptedVersio

Contributos para uma definição de funções, necessidades e modalidades de recrutamento

Este trabalho teve por objectivo definir funções que poderão ser desempenhadas pelo Pessoal Civil do Exército, nomeadamente os Grupos Administrativo, Auxiliar e Operário, bem como determinar as necessidades de recrutamento que daí resultam, para uma optimização dos efectivos militares em funções operacionais. Constituiu preocupação central da nossa análise, a substituição de militares por civis sem descaracterizar o Exército como Instituição Militar. Este assunto, reveste-se de cabal importância pelas implicações que a passagem para um Exército Profissional terá nos efectivos de praças e no normal funcionamento da Instituição em tempo de paz. Como enquadramento conceptual, procurámos teorias de planeamento de recursos humanos, com interesse para o tema. Efectuámos uma análise aos principais diplomas legislativos do Regime Geral da Função Pública e caracterizámos os Grupos de Pessoal a estudar. Após a recolha das tarefas, desempenhadas pelas principais carreiras dos grupos, construímos um modelo que nos orientou na identificação das funções e que constituiu o nosso principal instrumento de medida. Escolhemos um Regimento, um Estabelecimento e um Órgão para efectuar o levantamento das funções, possíveis de substituição por civis, e com base nas especialidades militares que as desempenham, extrapolamos para todas as especialidades dos praças. Encontrámos um conjunto de funções que poderão ser desempenhadas pelos civis dos Grupos estudados, resultando daqui um aumento percentual de necessidades para 2004. A melhor forma de recrutamento será a abertura de concursos internos em que os praças, em regime de contrato, poderão concorrer, fruto dos incentivos que a Lei do Serviço Militar lhes confere

Multiple Resistance at No Cost: Rifampicin and Streptomycin a Dangerous Liaison in the Spread of Antibiotic Resistance

Evidence is mounting that epistasis is widespread among mutations. The cost of carrying two deleterious mutations, or the advantage of acquiring two beneficial alleles, is typically lower that the sum of their individual effects. Much less is known on epistasis between beneficial and deleterious mutations, even though this is key to the amount of genetic hitchhiking that may occur during evolution. This is particularly important in the context of antibiotic resistance: Most resistances are deleterious, but some can be beneficial and remarkably rifampicin resistance can emerge de novo in populations evolving without antibiotics. Here we show pervasive positive pairwise epistasis on Escherichia coli fitness between beneficial mutations, which confer resistance to rifampicin, and deleterious mutations, which confer resistance to streptomycin. We find that 65% of double resistant strains outcompete sensitive bacteria in an environment devoid of antibiotics. Weak beneficial mutations may therefore overcome strong deleterious mutations and can even render double mutants strong competitors.LAO/ITQB, FCT

Fractional order color image processing

Many image processing algorithms make use of derivatives. In such cases, fractional derivatives allow an extra degree of freedom, which can be used to obtain better results in applications such as edge detection. Published literature concentrates on grey-scale images; in this paper, algorithms of six fractional detectors for colour images are implemented, and their performance is illustrated. The algorithms are: Canny, Sobel, Roberts, Laplacian of Gaussian, CRONE, and fractional derivative

Implementation of a cryogenic facility for space debris analysis

This paper has resulted from a continued study of spacecraft material degradation and space debris formation. The design and implementation of a thermal vacuum cycling cryogenic facility for the evaluation of space debris generation at a low Earth orbit (LEO) is presented. The facility used for spacecraft external material evaluation is described, and some of the obtained results are presented. The infrastructure was developed in the framework of a study for the European Space Agency (ESA). The main purpose of the cryogenic facility is to simulate the LEO spacecraft environment, namely thermal cycling and vacuum ultraviolet (VUV) irradiation to simulate the spacecraft material degradation and the generation of space debris. In a previous work, some results under LEO test conditions showed the effectiveness of the cryogenic facility for material evaluation, namely: the degradation of satellite paints with a change in their thermo-optical properties, leading to the emission of cover flakes; the degradation of the pressure-sensitive adhesive (PSA) used to glue Velcro’s to the spacecraft, and to glue multilayer insulation (MLI) to the spacecraft’s. The paint flakes generated are space debris. Hence, in a scenario of space missions where a spacecraft has lost the thermal shielding capability, the failure of PSA tape and the loss of Velcro properties may contribute to the release of the full MLI blanket, contributing to the generation of space debris that presents a growing threat to space missions in the main Earth orbits

System for space materials evaluation in LEO environment

This paper describes the conception and experimental setup of a new concept for a Vacuum Ultraviolet with extreme Thermal Vacuum Cycle system and the evaluation of LEO satellites materials with the equipment. The system was developed in the framework of a study of spacecraft debris generation due to satellites materials degradation, when exposed to space environment. The study was developed in the framework of an ESA project. Its main purpose was to evaluate the characteristics and the quantity of debris resulting from surface of satellites due spacecraft materials degradation and provide input to space debris models. The experimental setup developed partially simulates the space environment, on an accelerated mode, as endured by a spaceship in Low Earth Orbit, allows the testing of materials to a Vacuum, Ultraviolet and thermal cycles. This thermal cycling provided to the sample holder was implemented using an innovative mechanical thermal switching architecture. This architecture allows temperature cycling of +200 ºC to -200 ºC without the use of LN2. The experimental setup design, manufacture and final characterization is presented

Multidrug-resistant bacteria compensate for the epistasis between resistances

Mutations conferring resistance to antibiotics are typically costly in the absence of the drug, but bacteria can reduce this cost by acquiring compensatory mutations. Thus, the rate of acquisition of compensatory mutations and their effects are key for the maintenance and dissemination of antibiotic resistances. While compensation for single resistances has been extensively studied, compensatory evolution of multiresistant bacteria remains unexplored. Importantly, since resistance mutations often interact epistatically, compensation of multiresistant bacteria may significantly differ from that of single-resistant strains. We used experimental evolution, next-generation sequencing, in silico simulations, and genome editing to compare the compensatory process of a streptomycin and rifampicin double-resistant Escherichia coli with those of single-resistant clones. We demonstrate that low-fitness double-resistant bacteria compensate faster than single-resistant strains due to the acquisition of compensatory mutations with larger effects. Strikingly, we identified mutations that only compensate for double resistance, being neutral or deleterious in sensitive or single-resistant backgrounds. Moreover, we show that their beneficial effects strongly decrease or disappear in conditions where the epistatic interaction between resistance alleles is absent, demonstrating that these mutations compensate for the epistasis. In summary, our data indicate that epistatic interactions between antibiotic resistances, leading to large fitness costs, possibly open alternative paths for rapid compensatory evolution, thereby potentially stabilizing costly multiple resistances in bacterial populations.Fundação para a Ciência e a Tecnologia, European Research Council.info:eu-repo/semantics/publishedVersio

Space debris generation in GEO: Space materials testing and evaluation

The aim of this work is to evaluate what happens to the spacecraft materials beyond the spacecraft End of Life. A review of spacecraft external materials and effects of space environment is presented. This paper results from a continued study on spacecraft material degradation, and space debris formation in geostationary orbit (GEO). In this paper a 20-year GEO dose profile that combines simultaneous UV, particles irradiation and thermal cycling was applied to a set of external spacecraft materials. These materials comprised MLI assemblies, Velcros fixation and spacecraft painting. The evaluation of these external spacecraft materials, exposed to simulated space environment have confirmed the criticality of degradation of MLI, Velcros fixation and painting, with delamination mechanisms and particulate contamination. The synergy of space radiation (particles, UV) and thermal cycling ages the material and induces mechanical stress, causing creation of brittle surfaces, cracks and delamination. These phenomena cause serious damage to exposed surfaces, changing the surfaces thermo-optical properties, and may induce the generation of space debris. In particular, experimental results show the delamination of internal MLI layers and the severe degradation of the Velcros