Repositório RCAAP

In recent years, several Earth-sized exoplanets have been detected in short-period orbits of a few Earth days, around low-mass stars. Despite their small size compared to gas giants, their close-in orbits, combined with the small radius of the host star compared to our Sun’s, make these worlds the best targets for atmospheric characterisation among rocky exoplanets. These worlds have stellar irradiation levels that can be several times that of the Earth, suggesting that a Venus-like climate is more likely. In this work, I use a Global Circulation Model (GCM), the Generic-GCM, to model a possible Venuslike atmosphere on TRAPPIST-1 c as a benchmark of highly-irradiated rocky exoplanets orbiting Mdwarf stars. The model has been developed at the Laboratoire de Météorologie Dynamique (LMD) for exoplanet and paleoclimate studies. It includes a 3D dynamical core common to all terrestrial planets and a planet-specific physical part. In addition, the Generic-GCM has a generalised radiative transfer routine for variable atmospheric compositions. The overarching goal is twofold: (1) to study the largescale atmospheric circulation of highly-irradiated rocky exoplanets; and (2) to address the observational prospects of this kind of planet by producing phase curves (reflection and emission) and transmission spectra to support future space missions (e.g., James Webb Space Telescope, JWST). I assumed that TRAPPIST-1 c is a synchronous rotator with zero eccentricity and obliquity. It has a Venus-like atmosphere, a 92 bar surface atmospheric pressure, and a radiatively active sulphuric acid prescribed global cloud cover. I run a test to assess the Generic-GCM representation of the large-scale atmospheric circulation on Venus, comparing the results with a Venus specific GCM: the IPSL-VGCM. First, the Generic-GCM reproduces the superrotation pressure range and high-latitudes jets observed in the IPSLVGCM. Second, the Generic-GCM responds well to decreasing insolation by reducing the zonal wind speeds. Third, superrotation is a robust dynamical feature present in the range of insolation explored. The results for TRAPPIST-1 c indicate a warmer atmosphere than that of Venus, possibly a consequence of carbon dioxide absorption of stellar radiation, which is strongest in the near-infrared. The day-night heat redistribution in the planet is done through eastward superrotation jets (equatorial and two high-latitudes) and meridional circulation. The latter comprises two large cells, one per hemisphere (northern and southern), crossing the pole. Heat transport is mainly explained by its mean meridional circulation component, with a minor poleward contribution of the stationary waves in the mid-latitudes. The cloud top temperature field shows a distinctive chevron-like pattern and an eastward shift of the peak thermal emission from the substellar point, suggesting an advection of warm air masses by the equatorial zonal superrotation jet. There is evidence for an equatorial wave (c¯ ∼ 130 m s−1 , Tw = 17.5 hours). The TRAPPIST-1 c reflection phase curves reach a maximum planet-to-star contrast on the order of 10−6 , confirming that high albedo sulphuric acid aerosols of Venus-like cloudy exoplanets may favour their detection by JWST and other future instruments. This work also shows that thermal phase curves can sound different atmospheric levels, depending on the spectral band: carbon dioxide absorption bands will sound mesospheric levels, while continuum bands will sound the cloud top. The simulated transmission spectrum of TRAPPIST-1 c is flattened by clouds, screening almost all but the strongest carbon dioxide absorption bands (e.g., 4.3 µm, 15 µm). Detection of weaker CO2 spectral lines might be possible, suggesting a higher abundance, Venus-like carbon dioxide atmosphere. In particular, the work shows that detecting the 4.8 µm CO2 spectral band might be possible, indicating a high-pressure atmosphere. The removal of Venus-like aerosols from simulations leads to a warmer deep atmosphere, including the development of polar warming. The parametric study reveals that larger exoplanets will have more intense zonal equatorial jets but a smaller eastward shift of the hotspot and larger planet-to-star contrast in the phase curves. The higher-order spin-orbit resonances will modulate the amplitude and peak emission of the thermal phase curve, suggesting that this observable can be used to constrain the rotation state.

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Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a chronic infection affecting ruminants worldwide. In wildlife, MAP was first detected in the European rabbit and has since then been reported in a very broad host range. Information on the ecological factors that increase infection risk, as well as evidence for the transmission paths linking livestock, wildlife, and the environment, remain scarce. Thus, the objectives of this thesis included estimating MAP prevalence in the mammal community of a Mediterranean agro-forestry farmstead, the Companhia das Lezírias, through field and wet lab approaches, assessing MAP’s spatial distribution, determining which factors modulate exposure of wildlife to MAP, and predicting MAP risk within the study area. Using molecular detection of IS900 as a proxy, MAP was detected in ten wild mammal species, with emphasis on wild rabbit (19% overall prevalence), in cattle (54% individual prevalence and 100% herd prevalence) and in soil (44% prevalence). Wildlife diversity showed a positive influence on MAP presence in mammal feces, while wildlife abundance showed a negative influence. Land use variables showed distinct degrees of influence on MAP presence in feces of specific groups of mammals: mixed forest showed positive influence in carnivores, and shrubland showed positive influence in wild rabbit. The spatial prediction of MAP occurrence risk in wildlife generated two hotspots; however, model accuracy was low. In conclusion, the variables considered were insufficient to accurately predict MAP occurrence risk in mammals in our study area, showing the need for further studies. Increasing the number of samples and sampled species, as well as considering new variables, could improve prediction accuracy. Despite these limitations, this study represents a significant step forward in the knowledge of MAP occurrence at the livestock-wildlife interface in a Mediterranean agroecosystem.

Services of general interest (SGI) contribute to the European Union’s objectives, being fundamental to territorial cohesion and convergence, with a preeminent role in rural and peripheral territories. Hence, disparities in access to these services lead to critical regional disparities, impairing cohesion. It is in economic harsh times that SGI are preponderant, especially in more rural or peripheral regions and health services are one of the most impactful SGI, being an iconic representative of the Welfare State. Therefore, an assessment of regional health services must be developed in relation to Welfare State Regimes performance. This study is developed within this framework, with the objectives of understanding: how national and local expenditures in health are related to Welfare State Regimes; and how their expenses impact territorial cohesion through differentiated regional health service provision and population health status. The work was developed in two phases: one centred on the assessment of total and health expenditures made by national and local governments, discussed in the framework of distinct Welfare Regimes; another, that analyses regional health service provision and population health status, in their relationship with regional socio-economic characteristics and the framework of Welfare Regimes. Indicators regarding health expenditures countries' efforts, health status, and services at a regional scale were retrieved from Eurostat. Results confirm that the provision of services and health status differ among Welfare Regimes and territorial typologies. Urban regions showed better results than rural ones, with the Welfare Regime precluding this reality. We conclude that regional health disparities are a concerning factor that harms territorial cohesion.

Acute Respiratory Distress Syndrome (ARDS) is an inflammatory condition developed from parenchyma damage that ultimately leads to loss of aerated tissue. In the lung, the gas exchange occurs in the alveoli comprised by alveolar type (AT) 2 cells and AT1 cells. AT2 are known to be the alveolar stem cells as they can transdifferentiate into AT1 cells or dedifferentiate trough TGF-β driven epithelial-mesenchymal transition (EMT). In abnormal conditions, such as ARDS, the alveolar repair is impaired and both processes lead to a compromised parenchymal structure and gas exchange. For this reason, the mechanisms underlying the repair and differentiation should be further understood. Recent data suggest that epithelial CCR10 expression is not only associated with evolution towards fibrosis, but also with epithelial mobility. For this reason, we aimed to investigate the impact of different cytokines on CCR10 expression in alveolar epithelial cells in a wound healing assay. We used 7-day 2D cultures of the human A549 cell line, which are lung adenocarcinoma epithelial cells that resemble AT2 cells in vitro. After manual wound making, cells were exposed to IFNγ (type I), IL13 (type II), IL22 (type III), IL1β+IL6 (pro-inflammatory), TGFβ (EMT), GM-CSF and CCL28 (expressed by AT2 cells in demanding conditions). We found that CCL28, a CCR10 ligand, and IL13 increased the mean CCR10 expression by A549 cells. The levels of this chemokine receptor and frequency of KI-67+ cells were negatively correlated with percentage of wound closure, suggesting that like cell proliferation, CCR10 expression impacts wound repair. Interestingly, we observed that CCR10 highest mean expression was in cells in intermediate state, as we characterized in flow cytometry as Podoplanin+CD63+ . Using this same technique, we assessed A549 cell differentiation and observed that this process occurred in all conditions except for TGFβ and IFNγ, which were associated with an increase in Vimentin and decrease in E-cadherin levels, both characteristics of the EMT process. Despite the bigger frequency of AT2-like cells, neither TGFβ nor IFNγ had an effect on the production of pro-SFTPC, a marker of AT2 cell function, opposing CCL28 and GM-CSF that upregulated it. These results lead us to conclude that the CCL28/CCR10 axis may play a role in epithelial repair as CCL28 is a chemokine released by epithelial cells in pro-inflammatory/hypoxemic conditions as observed in ARDS. We propose that further studies should be done to assess the true function of this receptor in alveolar epithelial cells and intrinsic pathways that regulate CCR10 expression in a context of ARDS.

Bioinformatics aims to analyze and store complex biological datasets, which, due to the multidisciplinarity of the field, can be essential for finding meaning in biological systems, contributing to the modern life sciences knowledge. Transcriptomics is currently one of the areas if bioinformatics in greater expansion, namely through RNA sequencing (RNA-seq), which is an efficient transcriptome profiling approach. Its main application is the analysis of differentially expressed genes (DEGs), to assign biological meaning to specific tissues, environmental conditions, and other aspects. Reproductive strategies, resistance and stress responses can be evaluated through this technique, leading to a better understanding of the species fitness and survival. This thesis intended to detect and functionally annotate DEGs through the application of RNA seq pipelines. Moreover, since there’s still no gold standard for its best practices, this work mostly aimed to find the best suited tools and methods for each data type, such as length, depth and replicates, according to the research goals. Furthermore, it established a better understanding of the different expression profiles of species from three different genera, namely Casuarina, Coffea and Limonium. In general, the RNA-seq workflow was performed as follows: quality analysis, assembly (for non-model species), alignment, quantification, differential expression, and functional annotation. Since this project was developed as four separated analyses, each step and respective tools were evaluated according to each dataset features. The results of these analyses break the path for further studies and integration with other omics, which can help unravel relevant mechanism and pathways of the studied species. During the work of this thesis, a large set of scripts were developed to speed up and automatize the analysis, using Python and R languages, which have been made publicly available and can be applied by other users that work on similar studies.

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