Concatenator: sequence data matrices handling made easy

Concatenator is a simple and user-friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice-versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.info:eu-repo/semantics/publishedVersio

NCBI Mass Sequence Downloader–Large dataset downloading made easy

info:eu-repo/semantics/publishedVersio

Phylogeography of the species Psammodromus algirus

Tese de mestrado em Biologia (Biologia Evolutiva e do Desenvolvimento), apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2007In this work phylogenetic and phylogeoraphic analyses are conducted on the species Psammodromus algirus based on samples from the Iberian Peninsula and Morocco with the goal of resolving the controversy relative to this subject that exists in the literature. Four genes were used (12s, 16s, cytochrome b and NAD4) which were analysed one by one and concatenated in different combinations. The results differed from dataset to dataset if the trees were rooted; in the case of unrooted trees, the results were relatively congruent. The phylogenetic approach was thus not enough to resolve the addressed issues and reach satisfying conclusions regarding the species present biogeographic patterns. In order to address this issue a population approach was made with a larger number of samples. With the combined results from both approaches it was possible to propose an explanation for this species past migrations which is different from the ones presented in former publications. Furthermore, software was developed in the context of this thesis, which is very useful in phylogenetic/phylogeographic analyses. The program's purpose is to make data matrix conversions (FASTA to Nexus to FASTA with several program requirements in mind) and concatenation (of up to five Nexus data files) an easy task, that anyone with minimum computer skills can easily use it. The chapter about this software is the content of a paper which is in press in at the time of writing this thesis. Finally, comments are weaved on the outcome of this thesis, and brief remarks are made on the future of the two main components of this workResumo alargado disponível em português no document

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms.info:eu-repo/semantics/publishedVersio

Projeto Jogos+Vida – Prevenção do Consumo de Substâncias Psicoativas

O JOGOS+VIDA é um projeto de prevenção do consumo de substâncias psicoativas (SPA’s) promovido pela Associação de Futebol de Viseu, sob a orientação do SICAD (Serviço de Intervenção nos Comportamentos Aditivos e nas Dependências). Pretende afastar os jovens de comportamentos de risco, através da adoção de estilos de vida saudáveis, aliando atividades desportivas ao Treino de Competências Pessoais e Sociais. Esta estratégia surge como forma de aumentar os fatores de proteção e diminuir o impacto dos fatores de risco. Integra ações dirigidas a alunos do 3º ciclo/Secundário e Profissional e a pais (questões relacionadas com SPA’s, estilos de comunicação adequados facilitadores da relação pais/filhos), de modo a proporcionar um atendimento personalizado aos jovens/famílias com fatores de risco (Gabinete de Atendimento “Checkpoint”); bem com a grupos-alvo estratégicos (formação), tais como assistentes operacionais e outros técnicos, de forma a aumentar os seus conhecimentos sobre SPA’s para que as suas intervenções futuras se revelem mais eficazes.Abstract: JOGOS+VIDA is a project to prevent the use of psychoactive substances promoted by the Viseu Football Association, under the guidance of Intervention Service in Behaviors Additives and the Dependencies. It aims to dissuade youngsters from risky behavior, through the promotion of healthy lifestyles, combining sports activities with personal and social training skills. This strategy comes up to increase the protective factors and reduce the impact of risk factors. The activities are aimed to young people in Middle/High School/ Vocational Courses and Institutionalized Youngsters (themes: psychoactive substances issues, sexuality and risk behaviors); Parents (questions about psychoactive substances, appropriate communication skills); Strategic target groups (Training), such as custodian and other technicians, so that they can intervene more effectively in their work context. The project has an office "Checkpoint”, as a support for the activities, which intends to provide personalized service to young people and families with risk factors

Organizational and Methodological Influence of Risk Management in Projects

Project risk management is essential to managers’ decision making and business success, because it allows the manager to identify, analyse  and  decide  on the most appropriate way to respond to different adversities that may arise during the development of new products, services, processes, projects, continuous improvement, etc. This requires a mind-set that risks have a major influence on the bottom line and use analytical methods or risk management software. It is essential to integrate the entire organizational structure into risk mitigation intervention. The purpose of this paper is to address some of the important topics to consider for well implemented and successful risk management. An approach is taken at both organizational and methodological levels. Keywords: Risk management, PMBOK, Stakeholders, Methods, New product developmen

Repeated evolution of blanched coloration in a lizard across independent white-sand habitats

The White Sands lizards of New Mexico are a rare and classic example of convergent evolution where three species have evolved blanched coloration on the white gypsum dunes. Until now, no geological replicate of the pattern had been described. However, one of the White Sands species, the lesser earless lizard (Holbrookia maculata), has been discovered to also inhabit the Salt Basin Dunes of Texas, where it has also evolved a blanched morph. We here present a first phenotypic and genetic description of the Salt Basin Dunes population of H. maculata. Phylogenetic inference based on a housekeeping gene (ND4) and a classic candidate gene in the melanin-synthesis pathway (Melanocortin 1 Receptor; Mc1r) shows the newly discovered population as an independent lineage, with no evidence of genetic parallelism in the coding region of Mc1r. Initial morphological data suggest that while this population displays convergent evolution in blanched coloration, there are divergent patterns in limb length and habitat use behavior between the gypsum environments. Our findings present the White Sands/Salt Basin Dunes as an exceptionally promising comparative model for studies of adaptation and convergent evolution

Excessive and asymmetrical removal of heterozygous sites by maxSH biases downstream population genetic inference: Implications for hybridization between two primroses

Techniques of reduced-representation sequencing (RRS) have revolutionized ecological and evolutionary genomics studies. Precise establishment of orthologs is a critical challenge for RRS, especially when a reference genome is absent. The proportion of shared heterozygous sites across samples is an alternative criterion for filtering paralogs. In the prevailing pipeline for variant calling of RRS data – PYRAD/IPYRAD, maxSH is an often overlooked parameter with implications to detecting and filtering paralogs according to shared heterozygosity. Using empirical genotyping by sequencing data of two primroses (Primula alpicola Stapf and Primula florindae Ward) and their putative hybrids, and extra data sets of Californian golden cup oaks, we explore the impact of maxSH on filtering paralogs and further downstream analyses. Our study sheds light on the simultaneous validity and risk of filtering paralogs using maxSH, and its significant effects on downstream analyses of outlier detection, population assignment, and demographic modeling, emphasizing the importance of attention to detail during bioinformatic processes. The mutual confirmation between results of population assignment and demographic modeling in this study suggested maxSH = 0.10 has a potentially excessive and asymmetrical effect on the removal of truly shared heterozygous sites as paralogs. These results indicate that hybridization origin hypotheses of putative hybrids represented by results with maxSH = 0.25 and 0.50 are more credible. In conclusion, we revealed the critical hazard of paralogs filtration according to sharing heterozygosity at first, so that we propose to use specific protocols, rather than maxSH, to filter potential paralogs for closely related lineages.info:eu-repo/semantics/acceptedVersio

Production of pellets by pharmaceutical extrusion and spheronisation, part I: evaluation of Technological and formulation variables

O processo de peletização consiste na aglomeração por via úmida de pós de uma substância ativa e excipientes sob a forma de unidades esféricas. Estas unidades esféricas, denominadas pela expressão anglo-saxônica pellets, diferem de grânulos obtidos pelo processo clássico de granulação no que respeita às características físicas conseguidas. Um dos processos de peletização usualmente empregado para a produção de pellets consiste em duas operações unitárias fundamentais: a extrusão e a esferonização. O presente trabalho pretende apresentar uma revisão da técnica de extrusão e esferonização para produção de pellets farmacêuticos abordando as implicações dos aspectos tecnológicos e de formulação que envolvem este processo.The pelletisation process consists of the agglomeration of fine powders of a drug substance and excipients into spherical units. These units are referred as pellets and differ from those obtained from the granulation process in terms of their physical characteristics. One of the pelletisation processes usually applied for production of pellets comprising an active drug is based on two fundamental unit operations: extrusion and spheronisation. The present work intends to describe and revise the literature of the so-called extrusion and spheronisation process regarding the implication of the technological and formulation parameters in the production of pellets

Population structure in Quercus suber L. revealed by nuclear microsatellite markers

Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressureinfo:eu-repo/semantics/publishedVersio