Morphological and ecological studies on the phylum Cycliophora

Cycliophora é um filo animal descrito recentemente que acomoda, apenas, duas espécies: Symbion pandora Funch e Kristensen, 1995 e S. americanus Obst, Funch e Kristensen, 2006. Este filo é caracterizado por um ciclo de vida assaz complexo, cuja posição filogenética tem sido debatida desde a sua descoberta. Esta dissertação visa aprofundar o conhecimento geral existente acerca destes enigmáticos e pouco explorados metazoários. Assim, vários aspectos da morfologia e ecologia de ciclióforos foram estudados através de observações in vivo, técnicas de microscopia e reconstrução tridimensional. A mioanatomia de várias fases do ciclo de vida é descrita para S. pandora e S. americanus. Os nossos resultados revelam uma similaridade contundente entre a musculatura das duas espécies. A mioanatomia geral de Symbion é, ainda, comparada à de outros metazoários. A expressão de algumas substâncias imunorreactivas, como são exemplo a serotonina e as sinapsinas, é investigada em várias formas do ciclo de vida. Quando comparados com outros representantes de Spiralia, conclui-se que a neuroanatomia geral dos ciclióforos se assemelha mais às formas larvares do que aos adultos. Apesar de possuírem um plano corporal sofisticado, com extensas áreas ciliadas e uma mioanatomia complexa, descobrimos que o macho de ambas as espécies Symbion é composto por apenas algumas dezenas de células. Baseando-nos nestas observações, inferimos que a complexidade dos metazoários não se relaciona com o tamanho corporal nem com o número de células de um organismo. Estudos sobre a ultra-estrutura da fêmea revelaram, entre outras estruturas, um putativo poro genital, extensões citoplasmáticas do oócito e glândulas posteriores. Morfologia e implicações funcionais destas estruturas são aqui discutidas. A anatomia do protonefrídeo da larva cordóide é descrita. A arquitectura deste órgão diverge daquela presente noutros representantes de Nephrozoa, particularmente ao nível da área de filtração da célula terminal. As nossas observações são discutidas em termos filogenéticos. A maturação sexual em ciclióforos é investigada. Os nossos resultados sugerem que a transição de reprodução assexual a sexual se relacione com a idade da forma séssil, a “feeding stage”. A presença da larva Prometeus assente no tronco desta também poderá influenciar o processo, embora mais estudos sejam desejáveis para o comprovar. Os nossos resultados são discutidos integrativa e comparativamente com o conhecimento prévio sobre Cycliophora. A cumulação deste conhecimento será essencial para a compreensão da evolução e filogenia deste enigmático filo.

Contribution of biomass combustion to air pollutant emissions

In Portugal, it was estimated that around 1.95 Mton/year of wood is used in residential wood burning for heating and cooking. Additionally, in the last decades, burnt forest area has also been increasing. These combustions result in high levels of toxic air pollutants and a large perturbation of atmospheric chemistry, interfere with climate and have adverse effects on health. Accurate quantification of the amounts of trace gases and particulate matter emitted from residential wood burning, agriculture and garden waste burning and forest fires on a regional and global basis is essential for various purposes, including: the investigation of several atmospheric processes, the reporting of greenhouse gas emissions, and quantification of the air pollution sources that affect human health at regional scales. In Southern Europe, data on detailed emission factors from biomass burning are rather inexistent. Emission inventories and source apportionment, photochemical and climate change models use default values obtained for US and Northern Europe biofuels. Thus, it is desirable to use more specific locally available data. The objective of this study is to characterise and quantify the contribution of biomass combustion sources to atmospheric trace gases and aerosol concentrations more representative of the national reality. Laboratory (residential wood combustion) and field (agriculture/garden waste burning and experimental wildland fires) sampling experiments were carried out. In the laboratory, after the selection of the most representative wood species and combustion equipment in Portugal, a sampling program to determine gaseous and particulate matter emission rates was set up, including organic and inorganic aerosol composition. In the field, the smoke plumes from agriculture/garden waste and experimental wildland fires were sampled. The results of this study show that the combustion equipment and biofuel type used have an important role in the emission levels and composition. Significant differences between the use of traditional combustion equipment versus modern equipments were also observed. These differences are due to higher combustion efficiency of modern equipment, reflecting the smallest amount of particulate matter, organic carbon and carbon monoxide released. With regard to experimental wildland fires in shrub dominated areas, it was observed that the largest organic fraction in the samples studied was mainly composed by vegetation pyrolysis products. The major organic components in the smoke samples were pyrolysates of vegetation cuticles, mainly comprising steradienes and sterol derivatives, carbohydrates from the breakdown of cellulose, aliphatic lipids from vegetation waxes and methoxyphenols from the lignin thermal degradation. Despite being a banned practice in our country, agriculture/garden waste burning is actually quite common. To assess the particulate matter composition, the smoke from three different agriculture/garden residues have been sampled into 3 different size fractions (PM2.5, PM2.5-10 and PM>10). Despite distribution patterns of organic compounds in particulate matter varied among residues, the amounts of phenolics (polyphenol and guaiacyl derivatives) and organic acids were always predominant over other organic compounds in the organosoluble fraction of smoke. Among biomarkers, levoglucosan, β-sitosterol and phytol were detected in appreciable amounts in the smoke of all agriculture/garden residues. In addition, inositol may be considered as an eventual tracer for the smoke from potato haulm burning. It was shown that the prevailing ambient conditions (such as high humidity in the atmosphere) likely contributed to atmospheric processes (e.g. coagulation and hygroscopic growth), which influenced the particle size characteristics of the smoke tracers, shifting their distribution to larger diameters. An assessment of household biomass consumption was also made through a national scale survey. The information obtained with the survey combined with the databases on emission factors from the laboratory and field tests allowed us to estimate the pollutant amounts emitted in each Portuguese district. In addition to a likely contribution to the improvement of emission inventories, emission factors obtained for tracer compounds in this study can be applied in receptor models to assess the contribution of biomass burning to the levels of atmospheric aerosols and their constituents obtained in monitoring campaigns in Mediterranean Europe.

Pregnancy and newborns disorders followed by urine metabolomics

Chapter 1 introduces the scope of the work by identifying the clinically relevant prenatal disorders and presently available diagnostic methods. The methodology followed in this work is presented, along with a brief account of the principles of the analytical and statistical tools employed. A thorough description of the state of the art of metabolomics in prenatal research concludes the chapter, highlighting the merit of this novel strategy to identify robust disease biomarkers. The scarce use of maternal and newborn urine in previous reports enlightens the relevance of this work. Chapter 2 presents a description of all the experimental details involved in the work performed, comprising sampling, sample collection and preparation issues, data acquisition protocols and data analysis procedures. The proton Nuclear Magnetic Resonance (NMR) characterization of maternal urine composition in healthy pregnancies is presented in Chapter 3. The urinary metabolic profile characteristic of each pregnancy trimester was defined and a 21-metabolite signature found descriptive of the metabolic adaptations occurring throughout pregnancy. 8 metabolites were found, for the first time to our knowledge, to vary in connection to pregnancy, while known metabolic effects were confirmed. This chapter includes a study of the effects of non-fasting (used in this work) as a possible confounder. Chapter 4 describes the metabolomic study of 2nd trimester maternal urine for the diagnosis of fetal disorders and prediction of later-developing complications. This was achieved by applying a novel variable selection method developed in the context of this work. It was found that fetal malformations (FM) (and, specifically those of the central nervous system, CNS) and chromosomal disorders (CD) (and, specifically, trisomy 21, T21) are accompanied by changes in energy, amino acids, lipids and nucleotides metabolic pathways, with CD causing a further deregulation in sugars metabolism, urea cycle and/or creatinine biosynthesis. Multivariate analysis models´ validation revealed classification rates (CR) of 84% for FM (87%, CNS) and 85% for CD (94%, T21). For later-diagnosed preterm delivery (PTD), preeclampsia (PE) and intrauterine growth restriction (IUGR), it is found that urinary NMR profiles have early predictive value, with CRs ranging from 84% for PTD (11-20 gestational weeks, g.w., prior to diagnosis), 94% for PE (18-24 g.w. pre-diagnosis) and 94% for IUGR (2-22 g.w. pre-diagnosis). This chapter includes results obtained for an ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) study of pre-PTD samples and correlation with NMR data. One possible marker was detected, although its identification was not possible. Chapter 5 relates to the NMR metabolomic study of gestational diabetes mellitus (GDM), establishing a potentially predictive urinary metabolic profile for GDM, 2-21 g.w. prior to diagnosis (CR 83%). Furthermore, the NMR spectrum was shown to carry information on individual phenotypes, able to predict future insulin treatment requirement (CR 94%). Chapter 6 describes results that demonstrate the impact of delivery mode (CR 88%) and gender (CR 76%) on newborn urinary profile. It was also found that newborn prematurity, respiratory depression, large for gestational age growth and malformations induce relevant metabolic perturbations (CR 82-92%), as well as maternal conditions, namely GDM (CR 82%) and maternal psychiatric disorders (CR 91%). Finally, the main conclusions of this thesis are presented in Chapter 7, highlighting the value of maternal or newborn urine metabolomics for pregnancy monitoring and disease prediction, towards the development of new early and non-invasive diagnostic methods.

Degradação do perfil bioquímico de um concentrado de Nannochloropsis sp. durante o seu período de validade

As algas do género Nannochloropsis são microalgas marinhas que apresentam um perfil bioquímico único, principalmente no que é respeitante a lípidos, e uma vasta gama de compostos bioativos que possibilitam a sua aplicabilidade comercial em várias áreas biotecnológicas, destacando-se a alimentação e nutrição humana, indústria cosmética e farmacêutica, produção de biocombustíveis e a sua utilização em aquacultura. Em aquacultura, são usadas maioritariamente microalgas vivas, cuja produção representa elevados custos. Tem havido assim uma pesquisa de dietas alternativas, entre as quais os concentrados de microalgas se apresentam promissores. Os desafios atuais das empresas produtoras de concentrados de microalgas prendem-se com a conservação e armazenamento destes concentrados. Assim, neste trabalho foi proposto o estudo da influência da refrigeração, congelação e adição de conservantes a PhytoBloom Green Formula®, concentrado de Nannochloropsis sp. comercializado pela empresa Necton S.A., com o objetivo de averiguar a variação de parâmetros bioquímicos e organoléticos com a exposição do concentrado aos diferentes métodos de conservação. Pretendia-se assim observar se estes processos podem ser usados para aumentar o tempo de prateleira do concentrado em estudo. Para tal, foram avaliadas amostras recolhidas em três pontos temporais e analisados os seguintes parâmetros: perfil de ácidos gordos, quantificação de hidroperóxidos lipídicos, quantificação espectrofotométrica de clorofila a e carotenóides, bem como parâmetros organoléticos. Inicialmente, foi efetuada uma avaliação de diferentes parâmetros organoléticos, não se observando variações relevantes entre amostras das diferentes condições. Assim, foi posteriormente realizada a avaliação bioquímica. Primeiramente, foi efetuada a quantificação de ácidos gordos por GC-FID das diferentes amostras, nas quais não se observou diferenças significativas entre as condições experimentais. Foi também efetuado um ensaio de FOX II, que permitiu avaliar o grau de peroxidação lipídica de cada amostra por quantificação de hidroperóxidos lipídicos formados. As amostras nas quais houve adição de conservantes apresentaram um teor menor de hidropéroxidos lipídicos, permitindo inferir que a ação dos conservantes com propriedades antioxidantes permitiu uma melhor conservação da amostra. Quando se determinou a concentração de clorofila a e de carotenóides verificou-se que, em ambos os casos, a congelação conduziu a uma estabilização da concentração destes pigmentos. No entanto, os melhores resultados foram obtidos usando a combinação de congelação com adição de conservantes. Estes resultados, embora promissores, carecem de uma confirmação por um novo estudo, completando com análises com maior rigor e sensibilidade associados, no sentido de se verificar qual o método mais vantajoso para a extensão do tempo de prateleira de PhytoBloom Green Formula®.

Degradação do perfil bioquímico de um concentrado de Nannochloropsis sp. durante o seu período de validade

As algas do género Nannochloropsis são microalgas marinhas que apresentam um perfil bioquímico único, principalmente no que é respeitante a lípidos, e uma vasta gama de compostos bioativos que possibilitam a sua aplicabilidade comercial em várias áreas biotecnológicas, destacando-se a alimentação e nutrição humana, indústria cosmética e farmacêutica, produção de biocombustíveis e a sua utilização em aquacultura. Em aquacultura, são usadas maioritariamente microalgas vivas, cuja produção representa elevados custos. Tem havido assim uma pesquisa de dietas alternativas, entre as quais os concentrados de microalgas se apresentam promissores. Os desafios atuais das empresas produtoras de concentrados de microalgas prendem-se com a conservação e armazenamento destes concentrados. Assim, neste trabalho foi proposto o estudo da influência da refrigeração, congelação e adição de conservantes a PhytoBloom Green Formula®, concentrado de Nannochloropsis sp. comercializado pela empresa Necton S.A., com o objetivo de averiguar a variação de parâmetros bioquímicos e organoléticos com a exposição do concentrado aos diferentes métodos de conservação. Pretendia-se assim observar se estes processos podem ser usados para aumentar o tempo de prateleira do concentrado em estudo. Para tal, foram avaliadas amostras recolhidas em três pontos temporais e analisados os seguintes parâmetros: perfil de ácidos gordos, quantificação de hidroperóxidos lipídicos, quantificação espectrofotométrica de clorofila a e carotenóides, bem como parâmetros organoléticos. Inicialmente, foi efetuada uma avaliação de diferentes parâmetros organoléticos, não se observando variações relevantes entre amostras das diferentes condições. Assim, foi posteriormente realizada a avaliação bioquímica. Primeiramente, foi efetuada a quantificação de ácidos gordos por GC-FID das diferentes amostras, nas quais não se observou diferenças significativas entre as condições experimentais. Foi também efetuado um ensaio de FOX II, que permitiu avaliar o grau de peroxidação lipídica de cada amostra por quantificação de hidroperóxidos lipídicos formados. As amostras nas quais houve adição de conservantes apresentaram um teor menor de hidropéroxidos lipídicos, permitindo inferir que a ação dos conservantes com propriedades antioxidantes permitiu uma melhor conservação da amostra. Quando se determinou a concentração de clorofila a e de carotenóides verificou-se que, em ambos os casos, a congelação conduziu a uma estabilização da concentração destes pigmentos. No entanto, os melhores resultados foram obtidos usando a combinação de congelação com adição de conservantes. Estes resultados, embora promissores, carecem de uma confirmação por um novo estudo, completando com análises com maior rigor e sensibilidade associados, no sentido de se verificar qual o método mais vantajoso para a extensão do tempo de prateleira de PhytoBloom Green Formula®.

Lipidomic analysis of mesenchymal cells candidates for cell therapy

Mesenchymal stromal cells are adult stem cells found mostly in the bone marrow. They have immunosuppressive properties and they have been successfully applied as biological therapy in several clinical trials regarding autoimmune diseases. Despite the great number of clinical trials, MSCs’ action is not fully understand and there are no identified markers that correlate themselves with the immunomodulatory power. A lipidomic approach can solve some of these problems once lipids are one of the major cells’ components. Therefore, in this study cells’ lipidome was analysed and its deviations were evaluated according to the medium of culture and to the presence of pro-inflammatory stimuli, mimicking physiological conditions in which these cells are used. This was the first study ever made that aimed to analyse the differences in the phospholipid profile between mesenchymal stromal cells non-stimulated and stimulated with proinflammatory stimulus. This analysis was conducted in both cells cultured in medium supplemented with animal serum and in cells cultured in a synthetic medium. In cells cultured in the standard medium the levels of phosphatidylcholine (PC) species with shorter fatty acids (FAs) acyl chains decreased under pro-inflammatory stimuli. The level of PC(40:6) also decreased, which may be correlated with enhanced levels of lysoPC (LPC)(18:0) - an anti-inflammatory LPC - observed in cells subjected to TNF-α and IFN-γ. Simultaneously, the relative amounts of PC(36:1) and PC(38:4) increased. TNF-α and IFN- γ also enhanced the levels of phosphatidylethanolamine PE(40:6) and decreased the levels of PE(38:6). Higher expression of phosphatidylserine PS(36:1) and sphingomyelin SM(34:0) along with a decrease in PS(38:6) levels were observed. However, in cells cultured in a synthetic medium, TNF-α and IFN-γ only enhanced the levels of PS(36:1). These results indicate that lipid metabolism and signaling is modulated during mesenchymal stromal cells action.

Development of infrared spectroscopy for assessing bacterial quality in foods

Rapid and specific detection of foodborne bacteria that can cause food spoilage or illness associated to its consumption is an increasingly important task in food industry. Bacterial detection, identification, and classification are generally performed using traditional methods based on biochemical or serological tests and the molecular methods based on DNA or RNA fingerprints. However, these methodologies are expensive, time consuming and laborious. Infrared spectroscopy is a reliable, rapid, and economic technique which could be explored as a tool for bacterial analysis in the food industry. In this thesis it was evaluated the potential of IR spectroscopy to study the bacterial quality of foods. In Chapter 2, it was developed a calibration model that successfully allowed to predict the bacterial concentration of naturally contaminated cooked ham samples kept at refrigeration temperature during 8 days. In this part, it was developed the methodology that allowed the best reproducibility of spectra from bacteria colonies with minimal sample preparation, which was used in the subsequent work. Several attempts trying different resolutions and number of scans in the IR were made. A spectral resolution of 4 cm-1, with 32 scans were the settings that allowed the best results. Subsequently, in Chapter 3, it was made an attempt to identify 22 different foodborne bacterial genera/species using IR spectroscopy coupled with multivariate analysis. The principal component analysis, used as an exploratory technique, allowed to form distinct groups, each one corresponding to a different genus, in most of the cases. Then, a hierarchical cluster analysis was performed to further analyse the group formation and the possibility of distinction between species of the same bacterial genus. It was observed that IR spectroscopy not only is suitable to the distinction of the different genera, but also to differentiate species of the same genus, with the simultaneous use of principal component analysis and cluster analysis techniques. The utilization of IR spectroscopy and multivariate statistical analysis were also investigated in Chapter 4, in order to confirm the presence of Listeria monocytogenes and Salmonella spp. isolated from contaminated foods, after growth in selective medium. This would allow to substitute the traditional biochemical and serological methods that are used to confirm these pathogens and that delay the obtainment of the results up to 2 days. The obtained results allowed the distinction of 3 different Listeria species and the distinction of Salmonella spp. from other bacteria that can be mistaken with them. Finally, in chapter 5, high pressure processing, an emerging methodology that permits to produce microbiologically safe foods and extend their shelf-life, was applied to 12 foodborne bacteria to determine their resistance and the effects of pressure in cells. A treatment of 300 MPa, during 15 minutes at room temperature was applied. Gram-negative bacteria were inactivated to undetectable levels and Gram-positive showed different resistances. Bacillus cereus and Staphylococcus aureus decreased only 2 logs and Listeria innocua decreased about 5 logs. IR spectroscopy was performed in bacterial colonies before and after HPP in order to investigate the alterations of the cellular compounds. It was found that high pressure alters bands assigned to some cellular components as proteins, lipids, oligopolysaccharides, phosphate groups from the cell wall and nucleic acids, suggesting disruption of the cell envelopes. In this work, bacterial quantification and classification, as well as assessment of cellular compounds modification with high pressure processing were successfully performed. Taking this into account, it was showed that IR spectroscopy is a very promising technique to analyse bacteria in a simple and inexpensive manner.

Efeito de um concentrado de microalgas liofilizadas na larvicultura de dourada, Sparus aurata

Dissesrtação de Mestrado, Biologia Marinha, Especialização em Pescas e Aquacultura, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2009

Evaluation of the in vitro biological activities of extracts from carob tree and mediterranean oaks

Dissertação mest., Engenharia Biológica, Universidade do Algarve, 2009

Effect of polyunsaturated fatty acids (PUFAs) on the proliferation and extracellular matrix mineralization and gene expression of gilthead seabream skeletal cell lines

The aquaculture industry aims at replacing significant amounts of marine fish oil by vegetable oils in fish diet. Dietary lipids have been shown to alter the fatty acid composition of bone compartments, which would impact the local production of factors controlling bone formation. Knowledge on the mechanisms underlying the nutritional regulation of bone metabolism is however scarce in fish. Two in vitro bone-derived cell systems developed from seabream (an important species for aquaculture in the Mediterranean region) vertebra, capable of in vitro mineralization and exhibiting prechondrocyte (VSa13) and pre-osteoblast (VSa16) phenotype, were used to assess the effect of certain polyunsaturated fatty acids (PUFAs; arachidonic (AA), eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids) on cell proliferation, extracellular matrix (ECM) mineralization and gene expression. While all PUFAs promoted morphological changes in both cell lines, VSa16 cell proliferation appeared to be stimulated by PUFAs in a dose dependent manner until 100M, whereas proliferation of VSa13 cells was impaired at concentrations above 10M. AA, EPA and DHA inhibited VSa13 ECM mineralization, alone and in combination, while VSa16 ECM mineralization was only inhibited by AA and EPA. DHA had the opposite effect, increasing mineralization almost by 2 fold. When EFAs were combined, DHA apparently compensated for the inhibitory effect of AA and EPA. Expression of marker genes for bone and lipid metabolisms has been investigated by qPCR and shown to be regulated in pre-osteoblasts exposed to individual PUFAs. Our results show that PUFAs are effectors of fish bone cell lines, altering cell morphology, proliferation and mineralization when added to culture medium. This work also demonstrates the suitability of our in vitro cell systems to get insights into mineralization-related effects of PUFAs in vivo and to evaluate the replacement of fish oils by vegetable oil sources in fish feeds.

Biological membranes : biophysical properties and aquaporin function

Tese de doutoramento, Farmácia (Bioquímica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Iron homeostasis in immune mononuclear cells : a potential role in a atherogenesis

Tese de doutoramento, Biologia (Biologia-Molecular), Universidade de Lisboa, Faculdade de Ciências, 2015

Pharmacogenetics and nutrigenetics in crohn’s disease

Tese de doutoramento, Biologia (Genética), Universidade de Lisboa, Faculdade de Ciências, 2015

Tropical paleoclimate reconstructions from stable isotopes of mangrove lipid biomarkers

Thesis (Ph.D.)--University of Washington, 2014

Micromorphology of the labellum and structure of the osmophore in a group of closely related species of the sexually deceptive Orchid genus Ophrys (orchidaceae)

Tese de doutoramento, Biologia (Biologia Celular), Universidade de Lisboa, Faculdade de Ciências, 2016