Molecular reconstruction of a genetic code alteration

The genetic code establishes the rules that govern gene translation into proteins. It was established more than 3.5 billion years ago and it is one of the most conserved features of life. Despite this, several alterations to the standard genetic code have been discovered in both prokaryotes and eukaryotes, namely in the fungal CTG clade where a unique seryl transfer RNA (tRNACAG Ser) decodes leucine CUG codons as serine. This tRNACAG Ser appeared 272±25 million years ago through insertion of an adenosine in the middle position of the anticodon of a tRNACGA Ser gene, which changed its anticodon from 5´-CGA-3´ to 5´-CAG-3´. This most dramatic genetic event restructured the proteome of the CTG clade species, but it is not yet clear how and why such deleterious genetic event was selected and became fixed in those fungal genomes. In this study we have attempted to shed new light on the evolution of this fungal genetic code alteration by reconstructing its evolutionary pathway in vivo in the yeast Saccharomyces cerevisiae. For this, we have expressed wild type and mutant versions of the C. albicans tRNACGA Ser gene into S. cerevisiae and evaluated the impact of the mutant tRNACGA Ser on fitness, tRNA stability, translation efficiency and aminoacylation kinetics. Our data demonstrate that these mutants are expressed and misincorporate Ser at CUGs, but their expression is repressed through an unknown molecular mechanism. We further demonstrate, using in vivo forced evolution methodologies, that the tRNACAG Ser can be easily inactivated through natural mutations that prevent its recognition by the seryl-tRNA synthetase. The overall data show that repression of expression of the mistranslating tRNACAG Ser played a critical role on the evolution of CUG reassignment from Leu to Ser. In order to better understand the evolution of natural genetic code alterations, we have also engineered partial reassignment of various codons in yeast. The data confirmed that genetic code ambiguity affects fitness, induces protein aggregation, interferes with the cell cycle and results in nuclear and morphologic alterations, genome instability and gene expression deregulation. Interestingly, it also generates phenotypic variability and phenotypes that confer growth advantages in certain environmental conditions. This study provides strong evidence for direct and critical roles of the environment on the evolution of genetic code alterations.

Molecular genomics of a genetic code alteration

The genetic code is not universal. Alterations to its standard form have been discovered in both prokaryotes and eukaryotes and demolished the dogma of an immutable code. For instance, several Candida species translate the standard leucine CUG codon as serine. In the case of the human pathogen Candida albicans, a serine tRNA (tRNACAGSer) incorporates in vivo 97% of serine and 3% of leucine in proteins at CUG sites. Such ambiguity is flexible and the level of leucine incorporation increases significantly in response to environmental stress. To elucidate the function of such ambiguity and clarify whether the identity of the CUG codon could be reverted from serine back to leucine, we have developed a forced evolution strategy to increase leucine incorporation at CUGs and a fluorescent reporter system to monitor such incorporation in vivo. Leucine misincorporation increased from 3% up to nearly 100%, reverting CUG identity from serine back to leucine. Growth assays showed that increasing leucine incorporation produced impressive arrays of phenotypes of high adaptive potential. In particular, strains with high levels of leucine misincorporation exhibited novel phenotypes and high level of tolerance to antifungals. Whole genome re-sequencing revealed that increasing levels of leucine incorporation were associated with accumulation of single nucleotide polymorphisms (SNPs) and loss of heterozygozity (LOH) in the higher misincorporating strains. SNPs accumulated preferentially in genes involved in cell adhesion, filamentous growth and biofilm formation, indicating that C. albicans uses its natural CUG ambiguity to increase genetic diversity in pathogenesis and drug resistance related processes. The overall data provided evidence for unantecipated flexibility of the C. albicans genetic code and highlighted new roles of codon ambiguity on the evolution of genetic and phenotypic diversity.

Wind energy resource modelling in Portugal and its future large-scale alteration due to anthropogenic induced climate changes

The high dependence of Portugal from foreign energy sources (mainly fossil fuels), together with the international commitments assumed by Portugal and the national strategy in terms of energy policy, as well as resources sustainability and climate change issues, inevitably force Portugal to invest in its energetic self-sufficiency. The 20/20/20 Strategy defined by the European Union defines that in 2020 60% of the total electricity consumption must come from renewable energy sources. Wind energy is currently a major source of electricity generation in Portugal, producing about 23% of the national total electricity consumption in 2013. The National Energy Strategy 2020 (ENE2020), which aims to ensure the national compliance of the European Strategy 20/20/20, states that about half of this 60% target will be provided by wind energy. This work aims to implement and optimise a numerical weather prediction model in the simulation and modelling of the wind energy resource in Portugal, both in offshore and onshore areas. The numerical model optimisation consisted in the determination of which initial and boundary conditions and planetary boundary layer physical parameterizations options provide wind power flux (or energy density), wind speed and direction simulations closest to in situ measured wind data. Specifically for offshore areas, it is also intended to evaluate if the numerical model, once optimised, is able to produce power flux, wind speed and direction simulations more consistent with in situ measured data than wind measurements collected by satellites. This work also aims to study and analyse possible impacts that anthropogenic climate changes may have on the future wind energetic resource in Europe. The results show that the ECMWF reanalysis ERA-Interim are those that, among all the forcing databases currently available to drive numerical weather prediction models, allow wind power flux, wind speed and direction simulations more consistent with in situ wind measurements. It was also found that the Pleim-Xiu and ACM2 planetary boundary layer parameterizations are the ones that showed the best performance in terms of wind power flux, wind speed and direction simulations. This model optimisation allowed a significant reduction of the wind power flux, wind speed and direction simulations errors and, specifically for offshore areas, wind power flux, wind speed and direction simulations more consistent with in situ wind measurements than data obtained from satellites, which is a very valuable and interesting achievement. This work also revealed that future anthropogenic climate changes can negatively impact future European wind energy resource, due to tendencies towards a reduction in future wind speeds especially by the end of the current century and under stronger radiative forcing conditions.

Macroinvertebrate traits as biomonitoring tools in agricultural scenarios

Os ecossistemas de água doce – responsáveis por funções ambientais importantes e pelo fornecimento de bens e serviços insubstituíveis – têm vindo a ser severamente afectados por perturbações antropogénicas. A conversão de floresta em terreno agrícola afecta os sistemas aquáticos através de uma série de mecanismos: sedimentação; excesso de nutrientes; contaminação; alterações hidrológicas; e remoção de vegetação ripícola. As comunidades de macroinvertebrados de água doce – devido à sua diversidade, ubiquidade e sensibilidade às perturbações ambientais – revelam-se como particularmente adequadas para estudos de avaliação da integridade ecológica destes sistemas expostos simultaneamente a múltiplos factores de impacto. O uso sistemático de respostas biológicas para avaliação de mudanças ambientais – ou biomonitorização – pode ser levado a cabo através de diversas metodologias, que, de uma forma geral, não consideram aspectos funcionais das comunidades biológicas e têm aplicabilidade geograficamente restrita. A biomonitorização através de atributos biológicos (características que reflectem a adaptação das espécies ao seu meio ambiente) revela-se como uma ferramenta promissora na resolução dos problemas referidos, apresentando vantagens adicionais: relações causa-efeito directas; melhoria na diferenciação de impactos; e integração da variabilidade natural. O presente estudo apresenta uma revisão critica do estado-da-arte actual na área do uso de atributos biológicos em biomonitorização. Até à data de publicação, não estava disponível nenhum outro trabalho com a base conceptual do uso de atributos de macroinvertebrados enquanto descritores de comunidades e para efeitos de biomonitorização e gestão de sistemas de água doce. Descrevem-se as teorias ecológicas de suporte destas metodologias (conceitos de habitat-molde e de filtros paisagísticos) e os estudos que aplicaram estas teorias em cenários reais, tendo-se chamado a atenção para questões técnicas e possíveis soluções. As necessidades futuras nesta área englobam: o desenvolvimento de uma só ferramenta de biomonitorização de aplicação alargada; uma maior compreensão da variabilidade natural nas comunidades biológicas; diminuição dos efeitos de soluções de compromisso biológico e sindromas; realização de estudos autoecológicos adicionais; e detecção de impactos específicos em cenários de impacto complexos. Um dos objectivos deste estudo foi contribuir para a melhoria das técnicas de biomonitorização através de atributos, focalizando em comunidades de macroinvertebrados ribeirinhas em diferentes regiões biogeográficas (as bacias hidrográficas dos rios: Little e Salmon em New Brunswick, Canadá; Anllóns na Galiza, Espanha; Reventazón em Cartago, Costa Rica). Em cada região, foram estudados gradientes de uso agrícola de solo, incluindo desde bacias hidrográficas quase exclusivamente cobertas por floresta até bacias sob a influência maioritária de actividades agrícolas intensivas. Em cada gradiente de uso de solo, a caracterização da comunidade biológica (por amostragem de macroinvertebrados em troços de rápidos) foi acompanhada pela caracterização do habitat circundante (incluindo propriedades da bacia hidrográfica, análise química das águas e outras propriedades à escala local). A comunidade de macroinvertebrados foi caracterizada através de informação taxonómica, métricas estruturais, índices de diversidade, métricas de tolerância, índices bióticos e através da compilação de atributos biológicos e fisiológicos gerais, de história de vida e de resistência a perturbações. Análises estatísticas univariadas e multivariadas foram usadas para evidenciar os gradientes biológicos e físico-químicos, confirmar a sua co-variação, testar a significância da discriminação de níveis de impacto e estabelecer comparações inter-regionais. A estrutura de comunidades revelou os complexos gradientes de impacto, que por sua vez co-variaram significativamente com os gradientes de uso de solo. Os gradientes de impacto relacionaram-se sobretudo com entrada de nutrientes e sedimentação. Os gradientes biológicos definidos pelas medidas estruturais seleccionadas co-variaram com os gradientes de impacto estudados, muito embora apenas algumas variáveis estruturais tenham individualmente discriminado as categorias de uso de solo definidas a priori. Não foi detectada consistência nas respostas das medidas estruturais entre regiões biogeográficas, tendo-se confirmadado que as interpretações puramente taxonómicas de impactos são difíceis de extrapolar entre regiões. Os gradientes biológicos definidos através dos atributos seleccionados também co-variaram com os gradientes de perturbação, tendo sido possível obter uma melhor discriminação de categorias de uso de solo. Nas diferentes regiões, a discriminação de locais mais impactados foi feita com base num conjunto similar de atributos, que inclui tamanho, voltinismo, técnicas reproductivas, microhabitat, preferências de corrente e substrato, hábitos alimentares e formas de resistência. Este conjunto poderá vir a ser usado para avaliar de forma predictiva os efeitos das modificações severas de uso de solo impostas pela actividade agrícola. Quando analisadas simultaneamente através dos atributos, as comunidades das três regiões permitiram uma moderada mas significativa discriminação de níveis de impacto. Estas análises corroboram as evidências de que as mudanças nas comunidades de macroinvertebrados aquáticos em locais sob a influência de agricultura intensiva podem seguir uma trajectória convergente no espaço multidimensional, independentemente de factores geográficos. Foram fornecidas pistas para a identificação de parâmetros específicos que deverão ser tidos em conta no planeamento de novos programas de biomonitorização com comunidades de macroinvertebrados bentónicos, para aplicação numa gestão fluvial verdadeiramente ecológica, nestas e noutras regiões. Foram ainda sugeridas possíveis linhas futuras de investigação.

Characterisation of gas and particle emissions from wildfires

Os incêndios florestais são uma importante fonte de emissão de compostos gasosos e de aerossóis. Em Portugal, onde a maioria dos incêndios ocorre no norte e centro do país, os incêndios destroem todos os anos milhares de hectares, com importantes perdas em termos económicos, de vidas humanas e qualidade ambiental. As emissões podem alterar consideravelmente a química da atmosfera, degradar a qualidade do ar e alterar o clima. Contudo, a informação sobre as caraterísticas das emissões dos incêndios florestais nos países do Mediterrâneo é limitada. Tanto a nível nacional como internacional, existe um interesse crescente na elaboração de inventários de emissões e de regulamentos sobre as emissões de carbono para a atmosfera. Do ponto de vista atmosférico da monitorização atmosférica, os incêndios são considerados um desafio, dada a sua variabilidade temporal e espacial, sendo de esperar um aumento da sua frequência, dimensão e severidade, e também porque as estimativas de emissões dependem das caraterísticas dos biocombustíveis e da fase de combustão. O objetivo deste estudo foi quantificar e caraterizar as emissões de gases e aerossóis de alguns dos mais representativos incêndios florestais que ocorreram no centro de Portugal nos verões de 2009 e de 2010. Efetuou-se a colheita de amostras de gases e de duas frações de partículas (PM2.5 e PM2.5-10) nas plumas de fumo em sacos Tedlar e em filtros de quartzo acoplados a um amostrador de elevado volume, respetivamente. Os hidrocarbonetos totais (THC) e óxidos de carbono (CO e CO2) nas amostras gasosas foram analisados em instrumentos automáticos de ionização de chama e detetores não dispersivos de infravermelhos, respetivamente. Para algumas amostras, foram também quantificados alguns compostos de carbonilo após reamostragem do gás dos sacos Tedlar em cartuchos de sílica gel revestidos com 2,4-dinitrofenilhidrazina (DNPH), seguida de análise por cromatografia líquida de alta resolução. Nas partículas, analisou-se o carbono orgânico e elementar (técnica termo-óptica), iões solúveis em água (cromatografia iónica) e elementos (espectrometria de massa com plasma acoplado por indução ou análise instrumental por ativação com neutrões). A especiação orgânica foi obtida por cromatografia gasosa acoplada a espectrometria de massa após extração com recurso a vários solventes e separação dos extratos orgânicos em diversas classes de diferentes polaridades através do fracionamento com sílica gel. Os fatores de emissão do CO e do CO2 situaram-se nas gamas 52-482 e 822-1690 g kg-1 (base seca), mostrando, respetivamente, correlação negativa e positiva com a eficiência de combustão. Os fatores de emissão dos THC apresentaram valores mais elevados durante a fase de combustão latente sem chama, oscilando entre 0.33 e 334 g kg-1 (base seca). O composto orgânico volátil oxigenado mais abundante foi o acetaldeído com fatores de emissão que variaram desde 1.0 até 3.2 g kg-1 (base seca), seguido pelo formaldeído e o propionaldeído. Observou-se que as emissões destes compostos são promovidas durante a fase de combustão latente sem chama. Os fatores de emissão de PM2.5 e PM10 registaram valores entre 0.50-68 e 0.86-72 g kg-1 (base seca), respetivamente. A emissão de partículas finas e grosseiras é também promovida em condições de combustão lenta. As PM2.5 representaram cerca de 90% da massa de partículas PM10. A fração carbonosa das partículas amostradas em qualquer dos incêndios foi claramente dominada pelo carbono orgânico. Foi obtida uma ampla gama de rácios entre o carbono orgânico e o carbono elementar, dependendo das condições de combustão. Contudo, todos os rácios refletiram uma maior proporção de carbono orgânico em relação ao carbono elementar, típica das emissões de queima de biomassa. Os iões solúveis em água obtidos nas partículas da pluma de fumo contribuíram com valores até 3.9% da massa de partículas PM2.5 e 2.8% da massa de partículas de PM2.5-10. O potássio contribuiu com valores até 15 g mg-1 PM2.5 e 22 g mg-1 PM2.5-10, embora em massa absoluta estivesse maioritariamente presente nas partículas finas. Os rácios entre potássio e carbono elementar e entre potássio e carbono orgânico obtidos nas partículas da pluma de fumo enquadram-se na gama de valores relatados na literatura para emissões de queima de biomassa. Os elementos detetados nas amostras representaram, em média, valores até 1.2% e 12% da massa de PM2.5 e PM2.5-10, respetivamente. Partículas resultantes de uma combustão mais completa (valores elevados de CO2 e baixos de CO) foram caraterizadas por um elevado teor de constituintes inorgânicos e um menor conteúdo de matéria orgânica. Observou-se que a matéria orgânica particulada é composta principalmente por componentes fenólicos e produtos derivados, séries de compostos homólogos (alcanos, alcenos, ácidos alcanóicos e alcanóis), açúcares, biomarcadores esteróides e terpenóides, e hidrocarbonetos aromáticos policíclicos. O reteno, um biomarcador das emissões da queima de coníferas, foi o hidrocarboneto aromático dominante nas amostras das plumas de fumo amostradas durante a campanha que decorreu em 2009, devido ao predomínio de amostras colhidas em incêndios em florestas de pinheiros. O principal açúcar anidro, e sempre um dos compostos mais abundantes, foi o levoglucosano. O rácio levoglucosano/OC obtido nas partículas das plumas de fumo, em média, registaram valores desde 5.8 a 23 mg g-1 OC. Os rácios levoglucosano/manosano e levoglucosano/(manosano+galactosano) revelaram o predomínio de amostras provenientes da queima de coníferas. Tendo em conta que a estimativa das emissões dos incêndios florestais requer um conhecimento de fatores de emissão apropriados para cada biocombustível, a base de dados abrangente obtida neste estudo é potencialmente útil para atualizar os inventários de emissões. Tem vindo a ser observado que a fase de combustão latente sem chama, a qual pode ocorrer simultaneamente com a fase de chama e durar várias horas ou dias, pode contribuir para uma quantidade considerável de poluentes atmosféricos, pelo que os fatores de emissão correspondentes devem ser considerados no cálculo das emissões globais de incêndios florestais. Devido à falta de informação detalhada sobre perfis químicos de emissão, a base de dados obtida neste estudo pode também ser útil para a aplicação de modelos no recetor no sul da Europa.

Numerical Modelling of Hydrodynamic Changes Induced by a Jetty Extension: the Case of Ria de Aveiro (Portugal)

Tidally induced currents in estuarine flows are usually modulated by the tidal regime and respond differently to changes imposed to its natural propagation due to geomorphologic alterations. Some of these changes are due to the implementation of heavy engineering works, most of the times imposed by navigation needs associated with harbours growth. The main purpose of this study is to evaluate the hydrodynamic response of Ria de Aveiro to an alteration on the present geometry of its inlet, which was artificially delimited in 1808 through the construction of two jetties. In order to provide access to deeper draft vessels to the Aveiro harbour, its Administration intends to create better conditions for navigation through the extension by 200 m of the north jetty. A bidimensional hydrodynamic model SIMSYS2D was used in this study to simulate two distinct situations: the actual Ria de Aveiro configuration (2009), which is used as reference, and other including the future inlet configuration with the jetty extension. Several simulations were performed, using both bathymetries and considering extreme tidal conditions as forcing on the model oceanic open boundary. The tidal prism at the lagoon mouth and at the main lagoon channels was determined. Values of sea surface elevation and horizontal current velocity were comparatively analyzed as well as harmonic analysis results. The results for the projected inlet increase comparatively to those for the present configuration, although the differences found are not significant for most of the cases analyzed. More studies should be performed in order to clarify the long term impact of these works on the lagoon hydrodynamics.

Integration of geochemical and biological modifications in mining areas: waters, sediments and diatoms

The development of mining activities over thousands of years in the region of Aljustrel is nowadays visible as a vast area of ore tailings, slag and host rocks of sulphides mineralization. The generation of acidic waters by the alteration of pyritic minerals - Acid Mine Drainage (AMD) - causes a significant impact on the river system both in the south of the village (Rib ª. Água Forte) and in the north of it (Rib ª. Água Azeda and Barranco do Farrobo), which is reflected in extremely low pH values (< 3) and high concentrations of As, Cd, Cu, Fe, Mn, Pb, Zn and sulphates. This study aimed to assess the environmental impacts extent, integrating geochemical (surface waters and stream sediments) and biological (diatoms) parameters. Three groups of sites were defined, based on sediments and water analysis, which integration with diatom data showed the same association of groups: Group 1- impacted, with acidic pH (1.9-5.1), high metal contents (0.4-1975 mg L-1) and Fe-Mg-sulphate waters, being metals more bioavailable in waters in cationic form (Me2+); mineralogically the sediments were characterized by phyllosilicates and sulphates/oxy-hydroxysulphate phases, easily solubilized, retaining a high amount of metals when precipitated; dominant taxon was Pinnularia aljustrelica (a new species); Group 2- slightly impacted, weak acid to neutral pH (5.0-6.8), metal contents not so high (0.2-25 mg L-1) and Fe-Mg-sulphate to Mg-chloride waters; dominant taxa were Brachysira neglectissima and Achnanthidium minutissimum; Group 3- unimpacted, alkaline pH (7.0-8.4), low metal contents (0-7 mg L-1) with Mg-chloride waters. In this group, metals were associated to the primary phases (e.g. sulphides), not so easily available; the existence of high chloride contents explained the presence of typical taxa of brackish/marine (e.g. Entomoneis paludosa) waters. Taxonomical aspects of the diatoms were studied (discovery of a new species: Pinnularia aljustrelica Luis, Almeida et Ector sp. nov.), as well as morphometric (size decrease of diatoms valves, as well as the appearance of deformed valves of Eunotia exigua in Group 1 and A. minutissimum in Group 2) and physiological (effective to assess the effects of metals/acidity in the photosynthetic efficiency through PAM Fluorometry) aspects. A study was carried out in an artificial river system (microcosm) that aimed to mimic Aljustrel’s extreme conditions in controlled laboratory conditions. The chronic effects of Fe, SO42- and acidity in field biofilms, inoculated in the artificial rivers, were evaluated as well as their contribution to the communities’ tolerance to metal toxicity, through acute tests with two metals (Cu and Zn). In general, the effects caused by low pH values and high concentrations of Fe and SO42- were reflected at the community level by the decrease in diversity, the predominance of acidophilic species, the decrease in photosynthetic efficiency and the increase of enzymatic (e.g. catalase, superoxide dismutase) and non-enzymatic activities (e.g. total glutathione and total phytochelatins). However, it was possible to verify that acidity performed a protective effect in the communities, upon Cu and Zn addition. A comparative study between Aljustrel mining area and New Brunswick mining area was carried out, both with similar mining and geological conditions, reflected in similar diatom communities in both mines, but in very different geographic and climatic areas.

Novel hardware and software combination for automotive motorsport vehicles based on direct processing of graphical functions

The main motivation for the work presented here began with previously conducted experiments with a programming concept at the time named "Macro". These experiments led to the conviction that it would be possible to build a system of engine control from scratch, which could eliminate many of the current problems of engine management systems in a direct and intrinsic way. It was also hoped that it would minimize the full range of software and hardware needed to make a final and fully functional system. Initially, this paper proposes to make a comprehensive survey of the state of the art in the specific area of software and corresponding hardware of automotive tools and automotive ECUs. Problems arising from such software will be identified, and it will be clear that practically all of these problems stem directly or indirectly from the fact that we continue to make comprehensive use of extremely long and complex "tool chains". Similarly, in the hardware, it will be argued that the problems stem from the extreme complexity and inter-dependency inside processor architectures. The conclusions are presented through an extensive list of "pitfalls" which will be thoroughly enumerated, identified and characterized. Solutions will also be proposed for the various current issues and for the implementation of these same solutions. All this final work will be part of a "proof-of-concept" system called "ECU2010". The central element of this system is the before mentioned "Macro" concept, which is an graphical block representing one of many operations required in a automotive system having arithmetic, logic, filtering, integration, multiplexing functions among others. The end result of the proposed work is a single tool, fully integrated, enabling the development and management of the entire system in one simple visual interface. Part of the presented result relies on a hardware platform fully adapted to the software, as well as enabling high flexibility and scalability in addition to using exactly the same technology for ECU, data logger and peripherals alike. Current systems rely on a mostly evolutionary path, only allowing online calibration of parameters, but never the online alteration of their own automotive functionality algorithms. By contrast, the system developed and described in this thesis had the advantage of following a "clean-slate" approach, whereby everything could be rethought globally. In the end, out of all the system characteristics, "LIVE-Prototyping" is the most relevant feature, allowing the adjustment of automotive algorithms (eg. Injection, ignition, lambda control, etc.) 100% online, keeping the engine constantly working, without ever having to stop or reboot to make such changes. This consequently eliminates any "turnaround delay" typically present in current automotive systems, thereby enhancing the efficiency and handling of such systems.

The effects of chemicals in isopods : a multi-organizational evaluation

The global aim of this thesis was to evaluate and assess the effects of a pesticide (dimethoate) and a metal (nickel), as model chemicals, within different organization levels, starting at the detoxification pathways (enzymatic biomarkers) and energy costs associated (energy content quantification, energy consumption and CEA) along with the physiological alterations at the individual and population level (mortality), leading to a metabolomic analysis (using liquid 1H-NMR) and finally a gene expression analysis (transcriptome and RT-qPCR analysis). To better understand potential variations in response to stressors, abiotic factors were also assessed in terrestrial isopods such as temperature, soil moisture and UV radiation. The evaluation performed using biochemical biomarkers and energy related parameters showed that increases in temperature might negatively affect the organisms by generating oxidative stress. It also showed that this species is acclimated to environments with low soil moisture, and that in high moisture scenarios there was a short gap between the optimal and adverse conditions that led to increased mortality. As for UV-R, doses nowadays present have shown to induce significant negative impact on these organisms. The long-term exposure to dimethoate showed that besides the neurotoxicity resulting from acetylcholinesterase inhibition, this stressor also caused oxidative stress. This effect was observed for both concentrations used (recommended field dose application and a below EC50 value) and that its combination with different temperatures (20ºC and 25ºC) showed different response patterns. It was also observed that dimethoate’s degradation rate in soils was higher in the presence of isopods. In a similar study performed with nickel, oxidative stress was also observed. But, in the case of this stressor exposure, organisms showed a strategy where the energetic costs necessary for detoxification (biomarkers) seemed to be compensated by positive alterations in the energy related parameters. In this work we presented for the first time a metabolomic profile of terrestrial isopods exposed to stressors (dimethoate and niquel), since until the moment only a previous study was performed on a metabolomic evaluation in nonexposed isopods. In the first part of the study we identify 24 new metabolites that had not been described previously. On the second part of the study a metabolomic profile variation of abstract non-exposed organism throughout the exposure was presented and finally the metabolomic profile of organisms exposed to dimethoate and nickel. The exposure to nickel suggested alteration in growth, moult, haemocyanin and glutathione synthesis, energy pathways and in osmoregulation. As for the exposure to dimethoate alterations in osmoregulation, energy pathways, moult and neurotransmission were also suggested. In this work it was also presented the first full body transcriptome of a terrestrial isopod from the species Porcellionides pruinosus, which will complement the scarce information available for this group of organisms. This transcriptome also served as base for a RNA-Seq and a RT-qPCR analysis. The results of the RNA-Seq analysis performed in organisms exposed to nickel showed that this stressor negatively impacted at the genetic and epigenetic levels, in the trafficking, storage and elimination of metals, generates oxidative stress, inducing neurotoxicity and also affecting reproduction. These results were confirmed through RT-qPCR. As for the impact of dimethoate on these organisms it was only accessed through RT-qPCR and showed oxidative stress, an impact in neurotransmission, in epigenetic markers, DNA repair and cell cycle impairment. This study allowed the design of an Adverse Outcome Pathway draft that can be used further on for legislative purposes.

Evaluation of the matabolic response of osteosarcoma cells to conventional and new anticancer drugs by NMR metabolomics

The main scope of this work was to evaluate the metabolic effects of anticancer agents (three conventional and one new) in osteosarcoma (OS) cells and osteoblasts, by measuring alterations in the metabolic profile of cells by nuclear magnetic resonance (NMR) spectroscopy metabolomics. Chapter 1 gives a theoretical framework of this work, beginning with the main metabolic characteristics that globally describe cancer as well as the families and mechanisms of action of drugs used in chemotherapy. The drugs used nowadays to treat OS are also presented, together with the Palladium(II) complex with spermine, Pd2Spm, potentially active against cancer. Then, the global strategy for cell metabolomics is explained and the state of the art of metabolomic studies that analyze the effect of anticancer agents in cells is presented. In Chapter 2, the fundamentals of the analytical techniques used in this work, namely for biological assays, NMR spectroscopy and multivariate and statistical analysis of the results are described. A detailed description of the experimental procedures adopted throughout this work is given in Chapter 3. The biological and analytical reproducibility of the metabolic profile of MG-63 cells by high resolution magic angle spinning (HRMAS) NMR is evaluated in Chapter 4. The metabolic impact of several factors (cellular integrity, spinning rate, temperature, time and acquisition parameters) on the 1H HRMAS NMR spectral profile and quality is analysed, enabling the definition of the best acquisition parameters for further experiments. The metabolic consequences of increasing number of passages in MG-63 cells as well as the duration of storage are also investigated. Chapter 5 describes the metabolic impact of drugs conventionally used in OS chemotherapy, through NMR metabolomics studies of lysed cells and aqueous extracts analysis. The results show that MG-63 cells treated with cisplatin (cDDP) undergo a strong up-regulation of lipid contents, alterations in phospholipid constituents (choline compounds) and biomarkers of DNA degradation, all associated with cell death by apoptosis. Cells exposed to doxorubicin (DOX) or methotrexate (MTX) showed much slighter metabolic changes, without any relevant alteration in lipid contents. However, metabolic changes associated with altered Krebs cycle, oxidative stress and nucleotides metabolism were detected and were tentatively interpreted at the light of the known mechanisms of action of these drugs. The metabolic impact of the exposure of MG-63 cells and osteoblasts to cDDP and the Pd2Spm complex is described in Chapter 6. Results show that, despite the ability of the two agents to bind DNA, the metabolic consequences that arise from exposure to them are distinct, namely in what concerns to variation in lipid contents (absent for Pd2Spm). Apoptosis detection assays showed that, differently from what was seen for MG-63 cells treated with cDDP, the decreased number of living cells upon exposure to Pd2Spm was not due to cell death by apoptosis or necrosis. Moreover, the latter agent induces more marked alterations in osteoblasts than in cancer cells, while the opposite seemed to occur upon cDDP exposure. Nevertheless, the results from MG-63 cells exposure to combination regimens with cDDP- or Pd2Spm-based cocktails, described in Chapter 7, revealed that, in combination, the two agents induce similar metabolic responses, arising from synergy mechanisms between the tested drugs. Finally, the main conclusions of this thesis are summarized in Chapter 8, and future perspectives in the light of this work are presented.

Codon ambiguities as a mechanism to alter the genetic code in Saccharomyces cerevisiae

Although the genetic code is generally viewed as immutable, alterations to its standard form occur in the three domains of life. A remarkable alteration to the standard genetic code occurs in many fungi of the Saccharomycotina CTG clade where the Leucine CUG codon has been reassigned to Serine by a novel transfer RNA (Ser-tRNACAG). The host laboratory made a major breakthrough by reversing this atypical genetic code alteration in the human pathogen Candida albicans using a combination of tRNA engineering, gene recombination and forced evolution. These results raised the hypothesis that synthetic codon ambiguities combined with experimental evolution may release codons from their frozen state. In this thesis we tested this hypothesis using S. cerevisiae as a model system. We generated ambiguity at specific codons in a two-step approach, involving deletion of tRNA genes followed by expression of non-cognate tRNAs that are able to compensate the deleted tRNA. Driven by the notion that rare codons are more susceptible to reassignment than those that are frequently used, we used two deletion strains where there is no cognate tRNA to decode the rare CUC-Leu codon and AGG-Arg codon. We exploited the vulnerability of the latter by engineering mutant tRNAs that misincorporate Ser at these sites. These recombinant strains were evolved over time using experimental evolution. Although there was a strong negative impact on the growth rate of strains expressing mutant tRNAs at high level, such expression at low level had little effect on cell fitness. We found that not only codon ambiguity, but also destabilization of the endogenous tRNA pool has a strong negative impact in growth rate. After evolution, strains expressing the mutant tRNA at high level recovered significantly in several growth parameters, showing that these strains adapt and exhibit higher tolerance to codon ambiguity. A fluorescent reporter system allowing the monitoring of Ser misincorporation showed that serine was indeed incorporated and possibly codon reassignment was achieved. Beside the overall negative consequences of codon ambiguity, we demonstrated that codons that tolerate the loss of their cognate tRNA can also tolerate high Ser misincorporation. This raises the hypothesis that these codons can be reassigned to standard and eventually to new amino acids for the production of proteins with novel properties, contributing to the field of synthetic biology and biotechnology.

Identification of molecules and pathways regulating mistranslation in Candida albicans

Candida albicans is the major fungal pathogen in humans, causing diseases ranging from mild skin infections to severe systemic infections in immunocompromised individuals. The pathogenic nature of this organism is mostly due to its capacity to proliferate in numerous body sites and to its ability to adapt to drastic changes in the environment. Candida albicans exhibit a unique translational system, decoding the leucine-CUG codon ambiguously as leucine (3% of codons) and serine (97%) using a hybrid serine tRNA (tRNACAGSer). This tRNACAGSer is aminoacylated by two aminoacyl tRNA synthetases (aaRSs): leucyl-tRNA synthetase (LeuRS) and seryl-tRNA synthetase (SerRS). Previous studies showed that exposure of C. albicans to macrophages, oxidative, pH stress and antifungals increases Leu misincorporation levels from 3% to 15%, suggesting that C. albicans has the ability to regulate mistranslation levels in response to host defenses, antifungals and environmental stresses. Therefore, the hypothesis tested in this work is that Leu and Ser misincorporation at CUG codons is dependent upon competition between the LeuRS and SerRS for the tRNACAGSer. To test this hypothesis, levels of the SerRS and LeuRS were indirectly quantified under different physiological conditions, using a fluorescent reporter system that measures the activity of the respective promoters. Results suggest that an increase in Leu misincorporation at CUG codons is associated with an increase in LeuRS expression, with levels of SerRS being maintained. In the second part of the work, the objective was to identify putative regulators of SerRS and LeuRS expression. To accomplish this goal, C. albicans strains from a transcription factor knock-out collection were transformed with the fluorescent reporter system and expression of both aaRSs was quantified. Alterations in the LeuRS/SerRS expression of mutant strains compared to wild type strain allowed the identification of 5 transcription factors as possible regulators of expression of LeuRS and SerRS: ASH1, HAP2, HAP3, RTG3 and STB5. Globally, this work provides the first step to elucidate the molecular mechanism of regulation of mistranslation in C. albicans.