Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes

Tese de doutoramento, Biologia e Ecologia das Alterações Globais (Biologia do Genoma e Evolução), Universidade de Lisboa, Faculdade de Ciências, 2018Current scientific literature indicates that climate change will cause an average world temperature increase between 1 and 4ºC, along with changes in precipitation patterns and extreme weather events in the next 50 years. These are likely to have a negative impact for biodiversity in general, and forest ecosystems should be particularly affected, especially those in Mediterranean areas, like the cork oak (Quercus suber L.) “montados”. In order to understand how species can respond to such alterations, it is important to know their evolutionary history and genetic architecture of adaptive traits. Advances in sequencing technologies have relatively recently brought down the cost of sequencing per base pair to a point where even small research facilities can obtain genomic information of non-model organisms. These advances made SNP markers become the most abundant type of genetic variation in eukaryotic genomes, especially with the advent of Reduced Representation libraries such as RAD-Seq and GBS. Yet, despite their widespread use, SNP data analyses still bore its own set of bioinformatics challenges. While most of these are related with the practical aspects of the process, such as being able to handle very large datasets, or discriminate between neutral and non-neutral markers, some fundamental problems, like reproducibility are also important issues affecting research in this area. In this thesis, genomic and transcriptomic data from Q. suber was used to assess the evolutionary history of the species, detect the effects of natural selection across the cork oak’s distribution range and find any associations between the obtained markers and environmental variables. The main methodological contributions of this thesis are in the form of three software suites: (1) 4Pipe4, a software for automatically mining SNP markers from NGS data when no reference genome nor strain information is present, (2) NCBI Mass Sequence Downloader, a program to automate the downloading of large datasets from the NCBI databases, and (3) Structure_threader, a software to automate and parallelize analyses using several popular clustering analyses programs. All of these programs were developed with the intent to improve the automation and reproducibility value of the analysis processes they are meant to be part of. The main findings of this thesis are that (1) the evolutionary history and population structure of Q. suber is not as neatly structured as chloroplastidial markers indicate, (2) local adaptation plays and important role in the distribution of the species’ genetic variability, and (3) the cork oak may be better equipped, from a genetic point of view, to adapt to climate change than what previous studies based solely on ecological modelling indicated

Strateško pozicioniranje zdravstvenoga i wellness turizma u razvoju regije Duoro uvrštene na UNESCO-ov popis svjetske baštine

In a wine producing region like the Douro Valley (NE Portugal), embedded in the schist-greywacke complex of the Douro-Beira district and the source of high-quality mineral and spring waters, what is the strategic positioning of health and wellness tourism? What is the importance of thermal baths in the revitalisation of rural areas, and who are the main agents behind these dynamics? These are the main questions we will address in this article. Relatively overlooked until recently, health and wellness tourism has been growing in relevance in Europe and Portugal in the 21st century and is now considered a strategic product. Thermal baths were traditionally restricted to therapeutical treatments, but well-being has become a core concern today. Thermal bathhouses and resorts can be found throughout Portugal, four of which are located in the Douro region. Furthermore, their revitalisation bolsters sustainable development of Portugal’s inland regions, “reclaiming” an activity with a centuries-long history under a new paradigm. To achieve the study’s goals, we have combined documentation research with fieldwork, including semi-structured interviews conducted with the main actors involved in these dynamics.Kakvo je strateško pozicioniranje zdravstvenoga i wellness turizma u vinorodnoj regiji poput doline Douro (na sjeveroistoku Portugala), koja se nalazi na području regije Douro-Beira, građene od škriljavca i grauvake, s bogatim izvorima visokokvalitetne mineralne i izvorske vode? Kolika je važnost toplica u revitalizaciji ruralnih područja i tko su glavni nositelji toga procesa? To su glavna pitanja kojima se bavimo u ovom članku. Donedavno relativno zanemaren, zdravstveni i wellness turizam postaje sve važniji u Europi i Portugalu u 21. stoljeću i sve se više smatra strateškim turističkim proizvodom. Toplice su u prošlosti bile ograničene na liječenje, ali danas se u žarište ovoga oblika turizma sve više stavlja blagostanje. Toplica ima po cijelom Portugalu, a četiri su na području regije Douro. Štoviše, njihova revitalizacija koristi se kao poticaj za razvoj područja u unutrašnjosti Portugala na način da se oživljava djelatnost s višestoljetnom tradicijom u okviru novoga koncepta. Ciljevi rada ostvareni su kombinacijom istraživanja sekundarnih izvora i terenskoga istraživanja, koje je uključilo polustrukturirane intervjue s glavnim sudionicima ovoga procesa

The strategic position of health and wellness tourism in the development of the Douro Demarcated Region World Heritage Site

In a wine producing region like the Douro Valley (NE Portugal), embedded in the schist-greywacke complex of the Douro-Beira district and the source of high-quality mineral and spring waters, what is the strategic positioning of health and wellness tourism? What is the importance of thermal baths in the revitalisation of rural areas, and who are the main agents behind these dynamics? These are the main questions we will address in this article. Relatively overlooked until recently, health and wellness tourism has been growing in relevance in Europe and Portugal in the 21st century and is now considered a strategic product. Thermal baths were traditionally restricted to therapeutical treatments, but well-being has become a core concern today. Thermal bathhouses and resorts can be found throughout Portugal, four of which are located in the Douro region. Furthermore, their revitalisation bolsters sustainable development of Portugal's inland regions, "reclaiming" an activity with a centuries-long history under a new paradigm. To achieve the study's goals, we have combined documentation research with fieldwork, including semi-structured interviews conducted with the main actors involved in these dynamic

Eficácia da própolis na estomatite protética em idosos : ensaio clínico multicêntrico randomizado

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Ceilândia, Programa de Pós-Graduação em Ciências e Tecnologias em Saúde, 2016.Introdução: Estomatite Protética é um quadro associado à infecção fúngica de etiologia multifatorial, comum em usuários de prótese total. O desenvolvimento de produtos à base de própolis para seu tratamento tem atraído interesse especial devido a sua efetividade e segurança, tornando-se uma excelente alternativa para o uso em idosos. O objetivo desse estudo foi avaliar a eficácia de uma formulação muco-adesiva à base de gel contendo extrato padronizado de própolis (EPP-AF®) para tratamento de estomatite protética por Candida spp. Métodos: Um total de 40 pacientes idosos foi alocado em dois grupos, aleatoriamente, em um ensaio clínico de não inferioridade (NCT02818803). O grupo controle (MIC) foi tratado com gel de miconazol 20 mg/g e o grupo de estudo (PROP) foi tratado com a formulação contento extrato padronizado de própolis a 2% (20 mg/g) (EPP-AF®) durante 14 dias. Os pacientes foram examinados por um cirurgião-dentista nos dias T0, T7 e T14. A classificação de Newton foi usada para classificar a estomatite protética. As unidades formadoras de colônia (UFC/mL) foram quantificadas e identificadas (CHROMagar Candida®) para comparação antes e depois do tratamento (dias T0 e T14). Resultados: Idade, gênero, tempo de uso da prótese, características basais da classificação de Newton e contagem inicial de UFC/mL não diferiram nos dois grupos. Ambos os tratamentos reduziram os valores na escala de Newton (P<0.0001), indicando melhora clínica dos sinais da candidíase com taxa de cura clínica de 70%. A cura microbiológica com redução significativa da carga fúngica no dia T14 foi de 70% no grupo miconazol e de 25% no grupo EPP-AF®. Nenhum efeito adverso foi registrado nos grupos. Conclusão: O EPP-AF® parece ser não-inferior ao miconazol considerando a taxa de cura clínica e pode ser recomendado como tratamento adjuvante para estomatite protética em pessoas idosas.Background: Oral candidiasis is a common infection in complete denture wearers such as in older adults. Oral candidiasis, also known as denture stomatitis has multifactorial etiology. The development of propolis-based products for its treatment has attracted special interest because of their effectiveness and safety, which make them optimal for use in older adults. The aim of this study was to evaluate the efficacy of a standard formulation of Brazilian propolis extract gel (EPP-AF®) for the treatment of denture stomatitis due to Candida spp in this population. Methods: A total of 40 older patients were randomly allocated in a non-inferiority clinical trial (NCT02818803) into two groups. The control group (MIC) received 20 mg/g miconazole oral gel and the study group (PROP) received mucoadhesive formulation containing standardized extract of 2% (20 mg/g) propolis (EPP-AF®) during 14 days. Patients were examined by a dentist on days 1, 7 and 14. The Newton’s score was used to classify the lesion levels of denture stomatitis. The colony forming unities were quantified (CFU/mL) and their species were identified (CHROMagar Candida®) before and after the treatment. Baseline characteristics did not differ between groups. Both treatments reduced Newton's score (P <0.0001), indicating clinical improvement of the symptoms of candidiasis with clinical cure rate of 70%. The microbiological cure with significant reduction in fungal burden on T14 was 70% in the miconazole group and 25% in the EPP-AF® group. The EPP -AF® appears to be non-inferior to miconazole considering the clinical cure rate and could be recommended as an alternative treatment in older patients

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

A Study on Superconducting Coils for Superconducting Magnetic Energy Storage (SMES) Applications

Part 15: Energy TransformationInternational audienceSuperconducting coils (SC) are the core elements of Superconducting Magnetic Energy Storage (SMES) systems. It is thus fundamental to model and implement SC elements in a way that they assure the proper operation of the system, while complying with design specifications. As a part of a larger model, a coil design model is here presented and verified with tests made in a laboratory prototype. The limitations of the superconducting tape used, namely the negative effect of magnetic field components on its critical current value, are also verified and a possible solution to avoid that effect is studied