FC - Teses de Doutoramento
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- Dominance pheromones in male and female cichlid fishPublication . Ashoori, Samyar; Canário, Adelino Vicente Mendonça; Hubbard, Peter C.; Fonseca, Paulo Jorge Quintais Cancela daDominance hierarchies are formed within groups of fish in response to social competition for limited resources such as food, mates and space. In a dominance hierarchy, a fish displays dominant behaviours toward individuals lower in rank and submissive behaviours toward those higher in rank. Dominant fish exhibit agonistic behaviours, such as chasing and biting while defending a nest, and sexual behaviours, such as more frequent courtship. During and after formation of dominance hierarchies, a variety of physiological (e.g., endocrine), morphological (e.g., coloration), and behavioural (e.g., courtship) changes can occur. In Mozambique tilapia (Oreochromis mossambicus), dominant males release urine containing pheromones when interacting with other males or pre-ovulatory females. Male urine has been shown to contain two molecules, 20α- and 20β-pregnanetriol-3-glucuronates (P3Gs), which act as sex pheromones and stimulate ovulation in females. Males also appear to be able to discriminate the sexual state of females using olfactory cues present in urine and faeces. Furthermore, behavioural experiments, such as those using the mirror assay, have shown that urine from dominant males can reduce aggression in focal males, but P3Gs alone do not affect aggression. The identity of dominance signals present in urine is largely unknown. However, there is evidence that the signal in the urine of dominant males that controls aggression may be a multicomponent pheromone. In the laboratory, during the mouthbrooding period, females have occasionally been observed to display dominant behaviours and create territories for themselves, suggesting that females may compete with each other. We hypothesized that these behaviours might be mediated by chemical signals. This thesis aimed to identify the urinary dominance pheromones released by dominant males and pre-ovulatory females of Mozambique tilapia, using analytical chemistry, electrophysiology and behavioural analysis. The basic methodology consisted of collecting urine and faeces samples from dominant and subordinate males and pre-ovulatory and post-spawning females and using solid phase extraction (SPE) and high-performance liquid chromatography (HPLC) to fractionate the odorants involved. Electrophysiological methods tested the olfactory potency of the fractions, and those with the highest bioactivity were isolated to identify their chemical structure using liquid chromatography associated with mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR). The effect of putative pheromones on modulating aggression was tested using the mirror assay. Furthermore, it was tested whether mature males use chemical signals to discern the ovulation status of females and for mate choice through a preference assay. The results showed that dominant males release amino acids through urine, but high-performance liquid chromatography (HPLC) fractions containing amino acids did not affect male aggression. Similarly, a mixture of amino acids did not induce a significant preference response in focal males. Tilapias had olfactory sensitivity to extracts obtained from different solid phase media, including C18 eluate, C18 filtrate, mixed-mode cation exchange (MCX) bases, and mixed-mode anion exchange (MAX) acids—but none of the extracts separately affected male aggression, supporting previous suggestions of a multicomponent dominance pheromone. Mass spectrometry identified higher concentrations of cholic acid and taurocholic acids in the faeces of pre-ovulatory females than in post-spawning females. To assess the possible involvement of faeces in modulating aggressive behaviours in Mozambique tilapia, mirror assays were conducted; however, HPLC fractions containing bile acids (used as stimuli) did not affect aggression in focal males. However, male tilapia showed a preference for pre-ovulatory conditioned water, as well as their faeces (and bile acids within), compared to post-spawning females. However, males preferred equally pre-ovulatory female-conditioned water and water containing 17β-estradiol 3-glucuronate (released by pre-ovulatory females), suggesting this compound could be part of a pheromone bouquet to synchronise reproductive activity between males and females or as a token of female quality. Taken together, the findings of this thesis significantly enhance our understanding of the nature of chemical compounds involved in chemical communication in Mozambique tilapia. Moreover, it offers valuable information for future strategies in identifying dominant pheromones, from designing the behavioural experiments and monitoring the experimental fish to isolation and fractionation of samples for structural analysis.
- Tackling fungal resistance with new ketoconazole derivatives targeting plasma membrane sphingolipidsPublication . Bento-Oliveira, Andreia; Almeida, Rodrigo Freire Martins deThe search for new antifungal drugs is a relevant and timely subject due to fungal resistance to antimicrobial agents which is an emerging public health threat. Recently developed diphenylphosphane derivatives of ketoconazole exhibited potential as antifungal therapeutic agents. The mode of action of these compounds is not yet fully uncovered, although evidence suggests that they might interact with sphingolipids in the fungal membrane, which are major component of sphingolipid-enriched gel domains (SLEDs). Moreover, it was shown that the antifungal polyene nystatin has pore-forming activity in highly ordered gel membranes that do not contain sterols, contradicting the classical ergosterol-dependent mode of action. Hence, SLEDs which are not found in animal membranes are promising targets for antifungal drugs and are possibly involved in certain antifungal drug action and resistance mechanisms. The objectives of this thesis were 1) to explore the biophysical properties of the plasma membrane of the budding yeast Saccharomyces cerevisiae focusing on SLEDs, and 2) to uncover the preferential interaction of ketoconazole and diphenylphosphane derivatives, and nystatin with membranes containing specific fungal lipids and distinct biophysical properties as compared to mammalian ones, correlating this interaction with the drugs activity. Fluorescence spectroscopy was used together with an array of membrane systems, from intact cells in suspension to simpler systems such as isolated plasma membrane and liposomes prepared from S. cerevisiae lipid extracts or synthetic lipids. For ketoconazole derivatives, this work also allowed to unravel how structural differences influence their interaction (partition and relative distribution) with membranes and how that could correlate with their biological activity through direct interference on the permeability of the plasma membrane. Overall, the results presented herein point to SLEDs as promising targets for antifungal agents, with potential to uncover new approaches to fight antifungal drug resistance.
- Assessment reliability and treatment of depressionPublication . Zelenina, Maria; Prata, Diana; Averbeck, BrunoDepression is a global problem, which causes significant distress, heavy economic burden, and is potentially lethal. The amount of research articles that try to understand causes of depression and investigate potential cures, have been growing over the last few decades. To ensure the validity of depression research, it is important to use valid measurements of depression. In this work, we examine two measures of depression - the Child Behavior Checklist (CBCL) and a depression-related subset of scales of the Hierarchical Taxonomy of Psychopathology (HiTOP). We find both scales to be valid in their corresponding samples. Finally, we look into oxytocin, a neuropeptide that has shown potential as a treatment of depression in combination with antidepressants and/or cognitive behavior therapy. We look at the longevity of the effect of oxytocin on human brain, as measured by electroencephalography (EEG), and the nature of this effect. Our findings can inform the design of future experiments that use oxytocin in human research.
- Proteome profiling in obstructive sleep apnea severity and treatment response towards early diagnosis and prognosis predictionPublication . Valentim-Coelho, Cristina; Penque, Deborah; Dias, Deodália; Antunes, Marília Cristina de SousaObstructive Sleep Apnea (OSA) is characterized by recurrent episodes of apneas/hypopneas during sleep, leading to intermittent hypoxia and sleep fragmentation that can result in cardiometabolic diseases. A Proteomic approach was applied to investigate RBC homeostasis regulation in the context of OSA, before (t0) and after six months (t6) of PAP treatment. This work aims the discovery of candidate blood biomarkers for the diagnosis/prognosis of OSA and/or the monitoring/effectiveness of therapy. RBC samples were analysed through 2D-DIGE and the differentially expressed protein spots identified by MALDI-TOF/TOF MS. Three GAPDH-proteoforms were detected as decreased in OSA RBCs when compared to control ones that after PAP increased. An acidic PRDX2-proteoform, reported as hyperoxidized, showed changes between groups. By Western-Blot the results indicated that the redox-oligomeric state of GAPDH and PRDX2 may be compromising the homeostasis of OSA RBCs. The GAPDH monomer combined with BMI and the PRDX2 S-S dimer combined with the HOMA-IR showed to be promising biomarkers for predicting OSA and the severity of OSA, respectively. A Shotgun LC-MS/MS study was also performed on RBCs from patients with Mild and Severe OSA, before and after six months of PAP, using Snorers as controls. Dysregulation in Glycolysis and Pentose Phosphate pathways was observed in Severe OSA RBCs. Mild OSA showed a decrease in the Rapoport-Luebering shunt, which is associated with increased affinity for Hb-O2. Proteins of the immunoproteasome were upregulated in Severe OSA RBCs maybe to respond to severe oxidative stress. In Mild OSA RBCs, proteins related to the ubiquitination/neddylation-(Ub/Ned)-dependent proteasome system were up-regulated. After PAP, proteins of Glycolysis and Ub/Ned-dependent proteasome system showed reactivated in Severe OSA RBC. In Mild-OSA RBC, PAP induced upregulation of immunoproteasome proteins, suggesting that this treatment may increase oxidative stress in these patients. Once validated these proteins maybe candidate biomarkers for OSA.
- The calcium-binding protein S100B as a novel chaperone preventing Tau aggregation in Alzheimer’s diseasePublication . Moreira, Guilherme G.; Gomes, Cláudio Emanuel MoreiraAlzheimer's disease (AD), the foremost cause of dementia, is characterized by persistent neuroinflammation and amyloid- and tau protein aggregation. Notably, S100 proteins are upregulated in neurodegenerative conditions, including AD, where they localize in proximity to amyloid plaques and neurons with tau-containing neurofibrillary tangles (NFTs). This dissertation examines the role of S100B in modulating tau aggregation during the early stages of AD. Our findings reveal that S100B colocalizes with microtubule-bound tau and interacts dynamically with tau in a calcium-dependent manner, specifically targeting aggregation-prone segments within the repeat region. As a holdase-type chaperone, S100B inhibits tau aggregation at substoichiometric concentrations by suppressing secondary nucleation pathways, as confirmed through seeding assays and direct observation of S100B's interaction with tau oligomers and fibrils. Furthermore, S100B, consistent with its extracellular chaperone function, effectively inhibits proteopathic tau seeding. In exploring tau liquid-liquid phase separation (LLPS), identified as an early event in tau aggregation, we demonstrate that S100B inhibits tau condensation in a calcium-dependent manner, shifting the phase boundary to higher PEG concentrations. S100B integrates into tau droplets, stabilizing tau and reducing the formation of toxic aggregates, preserving the liquid-like properties of tau droplets. Additionally, S100B’s capacity to buffer Zn²⁺, mitigates Zn²⁺-induced tau LLPS. In subsequent investigations, we assessed the inhibitory effects of various S100 proteins on K18 aggregation. S100B and S100A1 were identified as the most potent inhibitors, while other S100 proteins demonstrated varying inhibition levels. Kinetic analyses revealed distinct preferences: S100B and S100A1 predominantly inhibited secondary aggregation pathways, while S100A9 targeted primary pathways. NMR studies mapped tau-binding regions for S100A1 across tau’s repeat domain, whereas S100A9 interacted with the PHF6 segment and the C-terminal region. S100A1 reduced the seeding activity of pre-formed K18 fibrils in tau-RD biosensor cells, whereas S100A9 was ineffective. These findings underscore the neuroprotective role of S100 proteins, particularly S100B, in tauopathies.
- Sediment dynamics in the shorefacePublication . Romão, Soraia; Taborda, Rui; Silva, Paulo Manuel Cruz Alves da; Baptista, Paulo Renato Enes BaganhaCoastal areas face increasing pressure from urbanization and human activities, exacerbating erosion and environmental challenges. Coastal engineering structures, such as breakwaters, groins, seawalls, and jetties, have been used to stabilize beaches, but often prove inadequate. Beach nourishment has emerged as a promising alternative; however, significant challenges remain in assessing sediment transport associated with shoreface nourishments, and in understanding their efficiency and longevity. This thesis aims to enhance the understanding of sediment dynamics in the upper shoreface of wave-dominated coastal environments, with a focus on optimizing sediment management and improving the long-term sustainability of shoreface nourishments. To achieve these objectives, this research employs a multi-faceted approach combining physical experiments, field data collection, and numerical modelling. Chapter 3 describes a physical model experiment using magnetic tracers to measure sediment transport in a controlled environment. The effectiveness of the magnetic tracers is compared to fluorescent tracers in an experiment conducted in the large wave flume (Großer Wellenkanal, GWK)in Hannover. Results showed similar dispersion patterns and net transport rates for both tracers, though the magnetic tracers exhibited lower recovery rates, indicating the need for further research. Wave streaming emerged as a key process driving sediment transport under non-breaking waves in the direction of wave propagation. In chapter 4, field measurements, including a tracer experiment, are combined with numerical modelling to assess sediment transport in the shoreface of Costa Nova, Aveiro. The Delft3D model is used to simulate the interaction of waves, currents, sediment transport, and morphology in this complex, energetic environment. Data from the tracer experiment validate the model’s performance. A Lagrangian model is also developed to estimate sediment particle pathways based on the simulated transport fields. The results reveal that onshore bed load transport dominates during calm conditions, while longshore suspended transport prevails during moderate wave energy events. These findings improve the understanding of shoreface sediment dynamics. In chapter 5, the implemented numerical model is applied to analyse the processes and dynamics of a shoreface nourishment conducted in Costa Nova in the summer of 2020. A short- and seasonal-term analysis of the nourishment’s evolution highlights the critical role of incident wave conditions, particularly during moderate to energetic events. These conditions not only protect the beach by dissipating wave energy but also nourish adjacent areas through sediment spreading. A conceptual model is presented that illustrates the short- and seasonal-term impacts of the nourishment. In the short term, the nourishment behaves as a detached breakwater, affecting hydrodynamics; at a seasonal term, sediment redistribution contributes to both the subaerial and submerged beach. The thesis develops tools to support the optimization of nourishment placement to enhance its effectiveness. Future research should focus on refining model accuracy through better sediment characterization and improved acceleration techniques. This work contributes to the understanding of shoreface nourishment and supports sustainable coastal protection strategies.
- Gravitational, erosional, sedimentary, and volcanic processes on the submarine environment of ocean volcanic islandsPublication . Innocentini, Simone; Madeira, José Eduardo de Oliveira; Quartau, Rui; Casalbore, DanieleVolcanic ocean islands are shaped by a complex interplay of volcanic, erosional, sedimentary, and marine processes. While their subaerial evolution is well-documented, their submarine portions remain underexplored, particularly shallow-water areas that hold key insights into island development. This PhD research investigates the post-volcanism evolution of insular shelves by integrating onshore and offshore datasets from two case studies: Porto Santo (Madeira Archipelago) and Corvo (Azores Archipelago). These islands, despite both being of volcanic origin, exhibit distinct geological histories, oceanographic conditions, and morphological characteristics, making them ideal for comparative analysis. A multidisciplinary approach was employed, combining high-resolution bathymetric surveys, seismic reflection profiling, sediment sampling, and geomorphological analysis. Porto Santo's southern insular shelf was studied using existing geophysical datasets and sediment samples, while Corvo's submarine environment was newly mapped through targeted oceanographic campaigns. Data processing involved acoustic imaging, stratigraphic interpretation, and sedimentological assessments to reconstruct the evolution of their submarine landscapes. The results indicate that both islands are shaped by a combination of subaerial and wave-induced erosion, sediment deposition, and gravitational mass-wasting processes at different magnitudes. Porto Santo has reached a mature stage of development, featuring an extensive bioclastic sandy beach that transitions into depositional bodies on the shelf, dominated by present-day carbonate factory. In contrast, Corvo exhibits a rugged landscape, characterized by steep cliffs and a high-energy marine environment shelf dominated by mass-wasting deposits and terrigenous depositional bodies. The comparative analysis underscores the influence of sea-level fluctuations, island age, and oceanographic dynamics in controlling shelf morphology and sedimentary architecture. These findings enhance our understanding of volcanic island evolution and provide valuable insights into coastal stability, marine resource management, and natural hazard assessment. The research results contribute to sustainable development initiatives, particularly in mitigating erosion risks, managing marine aggregates, and preserving marine ecosystems.
- Ichnology of the Quaternary eolianites from the Iberian PeninsulaPublication . Carvalho, Carlos Neto de; Cachão, Mário A. P.; Cunha, Pedro P.; Muñiz, FernandoIn the last years, 14 Pleistocene vertebrate ichnological sites in Portugal and five sites in Southwest Spain (3) and Gibraltar (2) were found and described under this thesis project. The first ichnological record of vertebrates in the Cenozoic of Portugal includes large footprints of the red deer Cervus elaphus found in Pessegueiro islet. An ichnotaxonomic review of the Quaternary sites worldwide allowed the description of five new ichnogenera and respective ichnospecies, corresponding to mammals Leporidichnites malhaoi (European rabbit), Suidichnus galani (Iberian wild boar) and Bovinichnus uripeda (aurochs), as well as birds Corvidichnus odemirensis (Western jackdaw) and Buboichnus vicentinus (Eagle owl), in addition to the first occurrence of proboscideans trackways (Palaeoloxodon antiquus) in mainland Europe. Tracks and trackways of wolf, fox, Iberian lynx, goose, seagull and other coastal birds were also described in coastal paleoenvironments dating from the Middle to Upper Pleistocene coastal paleoenvironments (MIS6, MIS5d, MISb and MIS3). Seven track-bearing levels with footprints were dated using Optically-Stimulated Luminescence (OSL) within the scope of the present work (five of them in Portugal), therefore contributing for improving the knowledge about the sequence stratigraphy of the Pleistocene successions. It is worth highlighting the description of the Matalascañas Trampled Surface (Huelva, SW Spain). This surface contains abundant and well-preserved physical and biogenic sedimentary structures, despite its almost instantaneous exposure and degradaon under wave and tidal erosion over the “El Asperillo” cliff. OSL dating of the “Trampled Surface of Matalascañas” allows atiributing their human footprints and trackways to Neanderthals. Human footprints were described from four other sites, all new, two of them in Portugal. A review of ichnological sites with hominin footprints identified 115 occurrences around the world, with footprints atributable to Neanderthals being rare. The five new Iberian sites correspond to more than half of the ichnological occurrences now known for this species. The occasionally presence of certain species in coastal environments, and the association of footprints of different species, allowed the development of interpretaons such as a seasonal (the Matalascañas seasonal lake as a maternity/nursery for the European forest elephant, or the partitioning of food resources demonstrated by the morphometric variation of aurochs footprints) and evolutionary paleoecology (the large size of Sus scrofa scrofa inferred by the tracks, translating possible predation pressure at the end of the Middle Pleistocene), as well as trophic inferences (the Neanderthal presence in interaction with megafauna known as being part of its food diet). The presence of Neanderthal trackways and footprints associated with Mode 3 and Expedited Mode 1 lithic tools, together with ichnological records of megafauna, including P.antiquus, favors the hypothesis that the Matalascañas coastal lake may have been a seasonal habitat for the Neanderthals. Neanderthals may have intentionally hunted/procuring deer and aurochs, or more accessible food targets, such as newborn elephants and females weakened during childbirth, opportunistically eliminating stillbirths and females died in unsuccessful births. The short-range provenance of the lithic materials found, as well as their expeditious nature, do not indicate setlement, but rather of a transit site for Neanderthals. A new predation/feeding structure is described, with the orientation and concentration of multiple eagle owl tracks, along with two converging shorebird tracks, defining a possible snapshot of active capture and manipulation of prey. The rarity of raptor and passerine behaviors in the fossil record gives special significance to this study with compelling evidence of their presence, along with Charadriiformes (including Laridae), shorebirds and possibly coots, which lived or raided in search of food in Pleistocene coastal habitats. Body fossils and ichnofossils of bees were found in four interdune paleosols in southwestern Portugal. Dense ichnoassociations developed on omission surfaces were formed in carbonate paleosols during the climate deterioration that occurred at the end of the Sub-Boreal interval in the Iberian Peninsula, around 2.9 ka ago. The bee cells identified as Palmiraichnus are traditionally atributed to the Andrenidae and Stenotridae families, while the present work expands the possible producers of this ichnogenus to the Eucera complex (Apidae). This is possible because, for the first time, Palmiraichnus castellanosi is described with the exceptional joint preservation of the bee that developed its life cycle until adulthood. These are the first bee ichnofossils described in the Quaternary fossil record of Europe mainland and the first worldwide record that includes the full preservation of the cocoon with its inhabitant. The Quaternary ichnological sites found in coastal areas from the Quaternary of the southwestern Iberian Peninsula have heritage value, despite their preservation in rocks that are poorly consolidated and subject to active erosion, posing a strong challenge to their “in situ” conservation. An analysis of a wide range of examples of geoheritage valorization of sites with vertebrate tracks on the various continents is presented, demonstrating that the investment made in their conservation has boosted an increasing number of tourist projects based on the valorization of this geological heritage and favors the socio-economic development of regions where they are included, especially when integrated into thematic routes and geoparks.
- Assessing and enhancing the accessibility of emerging connected tv applicationsPublication . Costa, Daniel Filipe Ribeiro da; Duarte, Carlos Alberto Pacheco dos AnjosConnected TV’s technological advances in the last years provide users with a better experience in terms of image,sound and interactive capabilities. By enabling access to the internet, connected TVs have extended the reach of multimedia content they offer. Like everyone else, people with visual disabilities want to watch and make use of the these TV platforms’ new features. The goal of this PhD thesis is to characterize and address Connected TV’s accessibility problems, with a special emphasis on visually impaired users. This dissertation describes the methodology applied to achieve this goal. The first step employed both qualitative and quantitative research methods to understand the interest of these users on this type of device, and to fully characterize their interaction difficulties and needs. A second stage aimed to explore the increasing trend of integrating mobile devices and TV platforms to propose and validate accessible solutions involving multiple modalities or adaptive interaction in order to increase the accessibility of the resulting TV platform. Results from the first stage revealed several accessibility issues with TV based applications when compared with their Desktop versions even though the automated accessibility evaluation favors the former. The survey results confirms the difficulties these users face everyday when interacting with their TV sets and underlines their willingness to welcome a new alternative that ameliorates this interaction. In the second stage, we followed an User Centered Design approach to develop our solution. The result was A4TV (Accessibility for TV),an adaptive multimodal assistive technology for TV platforms. Each iteration focused on different features and aspects that we intended to research. From every iteration resulted a list of Design Recommendations that condensed the findings from the different employed studies. We could find interesting results related with audio rendering content and contextual information from TV applications, alternative methods of input and the suggestion of adaptations to the user based on explicit and implicit knowledge.
- Mapeando o (des)conhecido:Publication . Viegas, Sofia B.; Leitão, Henrique; Castelo, Cláudia; Figueiredo, Rui Paulo NóbregaPaíses como Bélgica, França, Alemanha, Portugal e Reino Unido são detentores das mais extensas e completas coleções botânicas de África, provenientes das suas antigas colónias, numa expressão da relação entre Ciência e Império. Em Portugal, as principais coleções botânicas africanas encontram-se nos Herbários de Coimbra, Lisboa e Porto, contudo, muitos botânicos experientes desconhecem as coleções africanas deste último. Também a história institucional da Universidade do Porto parece ignorar a existência destas coleções e o seu significado. Com esta investigação quis-se perceber o contributo destas coleções para o conhecimento geral da botânica africana, e, em particular, para o conhecimento botânico das ex-colónias portuguesas durante o século XX até 1974, e as circunstâncias que levaram à sua atual invisibilidade. O cruzamento de fontes documentais e impressas com a informação das etiquetas dos espécimes das coleções, trouxe várias novidades nos planos científico e histórico, nomeadamente a existência de vários espécimes Tipo; a representação de regiões ainda hoje mal conhecidas, como o litoral norte de Moçambique; e, pela sua antiguidade, a representação de ecossistemas que poderão já não existir. Nesta tese defende-se que estas coleções terão sido aproveitadas para afirmação da importância da Universidade do Porto no panorama nacional, materializando o contributo da instituição ao desenvolvimento colonial ambicionado pelo país, para assim acautelar a sua continuidade face a diversas ameaças à sua existência, bem como tentar reverter uma situação de subfinanciamento que se verificava desde a sua criação, em 1911. Porém, foi possivelmente em consequência da ligação destas coleções ao passado colonial do país que terá resultado na sua invisibilidade atual. Numa instituição onde vários professores e funcionários foram saneados após o 25 de abril de 1974, aparentemente emergiu uma vontade de invisibilizar linhas de investigação associadas à política colonial do Estado Novo, criando-se uma imagem da Universidade do Porto desvinculada da ciência colonial.