Estudo da variação da abundância e diversidade de procariotas em sedimentos subsuperficiais marinhos

Os sedimentos marinhos subsuperficiais profundos são, atualmente, um ambiente ainda pouco conhecido do ponto de vista microbiológico, nomeadamente quanto aos processos metabólicos que nele têm lugar e quanto à sua possível influência nos ciclos biogeoquímicos. O acesso a amostras colhidas em sedimentos profundos, particularmente no âmbito dos programas IODP (International Ocean Discovery Program) e ECORD (European Consortium for Ocean Research Drilling) tem permitido recolher informação sobre a estrutura das comunidades de procariotas bem como sobre alguns dos fatores que regulam a sua distribuição e atividade. Este estudo teve como objetivo caracterizar a distribuição e a diversidade estrutural das comunidades de procariotas em sedimentos subsuperficiais profundos colhidos no Arco Izu-Bonin-Mariana, no mar das Filipinas, com recurso a métodos independentes de cultivo (PCR-DGGE) e à contagem de células por microscopia de epifluorescência. Os resultados apontam para a existência de comunidades de Bacteria e Archaea diversas. Os valores do índice de diversidade de Shannon-Weaver (H’) calculados com base nos perfis de DGGE (Bacteria) foram significativamente mais elevados (3,035 – 1,971) nas camadas superficiais (< 140 mafm) do que nos sedimentos (2,519 - 1,049) correspondentes a profundidades superiores entre 163 e 879 mafm. A abundância máxima (8,66 x 106 células.gps-1) foi registada à profundidade de 67 mafm e valor mínimo (2,26 x 106 células.gps-1) foi observado em amostras colhidas a 879 mafm de profundidade. Abundância e diversidade apresentaram correlação negativa com a profundidade e com o teor de sulfato. Os resultados indicam que ao longo da coluna de sedimento se estabelecem comunidades de procariotas estruturalmente diferentes e adaptadas ao ambiente geoquímico prevalecente, nomeadamente em termos dos aceitadores de eletrões disponíveis. O estudo do microbioma destas amostras representativas do ambiente sedimentar subsuperficial profundo será continuado e detalhado, com recurso a técnicas de sequenciação avançada.

Physiology and metabolic profile of Moringa olifera and Eucalyptus globulus plants subjected to climate changes

As alterações climáticas emergentes têm um grande impacto no crescimento e desenvolvimento de espécies florestais, nomeadamente em espécies de valor industrial e medicinal, como é o caso do eucalipto (Eucalyptus globulus) e da moringa (Moringa oleifera). Assim, é urgente conhecer as respostas fisiológicas e entender as variações que ocorrem nos perfis metabólicos de espécies vegetais. Neste trabalho, plantas jovens de Eucalyptus globulus foram expostas a radiação UVB (12kJ/m2) e foram avaliadas as respostas fisiológicas e o perfil metabólico, um e onze dias após a aplicação da radiação. A dose de UVB usada não afetou as reações fotoquímicas nem as trocas gasosas, contudo ao nível do metabolismo do carbono (AST e amido) e do conteúdo de pigmentos verificaram-se pequenas alterações (AST e pigmentos). Através da análise do perfil metabólico de E. globulus foram encontrados compostos voláteis e semi-voláteis pertencentes às famílias dos terpenos, sesquiterpenos e aldeídos. Em geral, os sesquiterpenos e os álcoois monoterpénicos apresentaram uma tendência para manter e, em alguns casos, diminuir com o stress, enquanto que o grupos dos aldeídos aumentou e os monoterpenos apresentaram um comportamento mais heterogéneo. O E. globulus mostrou ser uma espécie tolerante à aplicação da dose de UVB usada neste trabalho. Por outro lado, plantas jovens de M. oleifera foram expostas a défice hídrico (DH). Um grupo de plantas foi recolhido um dia após o final da exposição e o outro grupo após onze dias do final da exposição. Foi avaliado o perfil metabólico desta espécie através de GC/MS. Os dados cromatográficos indicaram que em condições de stress (DH(1) e DH(11)), as quantidades de compostos associados a vias primárias e secundárias de defesa (como os alcanos, álcoois, ácidos carboxílicos, esteróis, aminoácidos e açucares) sofreram algumas alterações. As plantas analisadas 11 dias após a remoção do stress mostraram maiores variações do perfil de metabolitos. No entanto, tanto um como onze dias após a remoção do stress, as plantas apresentaram a formação de novos rebentos. Apesar do perfil de metabolitos ter sofrido algumas alterações, por não se registarem casos de morte, conclui-se que as plantas de moringa mostraram ser tolerantes aos tratamentos aplicados.

Community response in disasters: an ecological learning framework

Natural disasters are frequently exacerbated by anthropogenic mechanisms and have social and political consequences for communities. The role of community learning in disasters is seen to be increasingly important. However, the ways in which such learning unfolds in a disaster can differ substantially from case to case. This article uses a comparative case study methodology to examine catastrophes and major disasters from five countries (Japan, New Zealand, UK, US and Germany) to consider how community learning and adaptation occurs. An ecological model of learning is considered, where community learning is of small loop (adaptive, incremental, experimental) type or large loop (paradigm changing) type. Using this model we consider that there are three types of community learning that occur in disasters (navigation, organisation, reframing). The type of community learning that actually develops in a disaster depends upon a range of social factors such as stress and trauma, civic innovation and coercion.

Water framework directive implementation: intercalibration exercise for biological quality elements: a case study for the south coast of Portugal

This work summarises the Intercalibration Exercise (IE) required for the Common Implementation Strategy of the Water Framework Directive (WFD; 2000/60/EC) that was carried out in Portugal, and applied to a coastal region. The WFD aims to achieve good ec ological status for all waters in the European Community by 2015. The Ecological Status of a water body is determined us ing a range of Hydromorphological and Physico-Chemical Quality Elements as well Biological Quality Elements (BQE ). In coastal waters, the Biological Elements include Phytoplankton, Other Aquatic Flora and Benthic Inverteb rate Fauna. Good cooperation with the other Member States allowed the IE to proceed without a complete da ta set, and Portugal was ab le to intercalibrate and harmonise methods within the North Ea st Atlantic Geographica l Intercalibration Group for most of the BQE. The appropriate metrics and corre sponding methods were agreed under the framework of the RECITAL (Reference Conditions and Intercalibra tion) project, funded by the Port uguese Water Institu te, INAG. Some preliminary sampling was undertaken, but not su fficient to establish the Reference Conditions. The study area was a coastal lagoon in the southern part of Portugal. The focus was on the Phytoplankton Quality Element, but other BQE were also taken into account. Two sampli ng stations in Ria Formosa coastal lagoon were considered in this exercise: Ramalhete a nd Ponte. The metrics adopted by the Intercalibration Exercise groups were applied enabli ng the classification for the two sta tions of Good/High Status for the majority of the BQE parameters.

Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.

A proteomic study of the effects of nutrient restriction in utero on postnatal metabolism

It is widely recognized that protein restriction in utero may cause metabolic and endocrine adaptations, which may be of benefit to the neonate on a short-term basis but may cause adverse long-term conditions such as obesity, Type 2 diabetes, metabolic syndrome, hypertension and cardiovascular diseases. Adequate foetal and early post natal nutrient and energy supply is therefore essential for adult animal health, performance and life span. In this project it was investigated the progressive adaptations of the hepatic proteome in male mink offspring exposed to either a low protein (FL) or an adequate protein (FA) diet in utero fed either on a low protein (LP) or on an adequate (AP) diet from weaning until sexual maturity. Specifically, the aim was to determine the metabolic adaptations at selected phases of the animal’s first annual cycle and establish the metabolic priorities occurring during those phases. The three different morphological stages studied during the first year of development included, end of bone growth at 4 months of age, maximal fat accretion at 6 months of age and sexual maturity at 12 months of age. A reference proteome of mink liver coming from these different animal groups were generated using 2D electrophoresis coupled to MALDI-TOF analysis and the way in which dietary treatment affect their proteome was established. Approximately 330 proteins were detected in the mink liver proteome. A total of 27 comparisons were carried out between all different animal groups which resulted in 20 differentially expressed proteins. An extensive survey was conducted towards the characterization of these proteins including their subcellular localization, the biological processes in which they are involved and their molecular functions. This characterization allowed the identification of proteins in various processes including the glycolysis and fatty acid metabolism. The detailed analysis of the different dietary treatment animal groups was indicative of differences in metabolism and also to changes associated with development in mink.

Contamination of farmed gilthead sea bream (Sparus aurata, Linnaeus, 1758) by the parasite Amyloodinium ocellatum: a proteomic approach

Dissertação de mestrado, Aquacultura e Pescas, Faculdade de Ciências e Tecnologia, Uniersidade do Algarve, 2015

How historical and present climat conditions affected the distribution of the mediterranean whter shrew?:a phylogeographical and ecological approach

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2014

Libraries and Canon-Formation: the Case of English in the Collections of the Library of the Faculty of Humanities, Lisbon University

Abstract: The project for researching the role played by libraries in canon-formation (namely through their policies regarding the creation, organization, preservation, and utilization of the collections) will be presented and discussed. We selected the Library of the Faculty of Humanities, Lisbon University, a modern academic library, created in 1859, by royal decree of D. Pedro V, following his canonical choice. Actually, the two contemporary rulers of new Britannia— Prince Albert, his cousin, and Queen Victoria—held this king in high consideration for his outstanding contribution to Portuguese modernisation. Representing various fields of study, the collections were decisive to canon-formation in the Faculty of Humanities. Thus, we have been trying to answer the following questions: who has been creating, organizing, preserving, and utilizing the collections, from the mid-nineteenth century onwards? When, where and how? Presently, we are studying the collections in English, namely the works belonging or referring to the long nineteenth century. Richard Garnett’s “The International Library of Famous Literature” (London, 1899) is our first case-study. The anthology determined the Western literary, cultural and visual canon at the turning of the century, as evidenced by comparing it to the Portuguese and Spanish editions, published at the beginning of the twentieth century.

Regulatory interactions between the metabolic sensors SIRT1 and AMPK in modulating PPARα linked functions, in obesity-dependent type 2 diabetes mellitus

Tese de doutoramento, Ciências Biomédicas (Ciências Funcionais), Universidade de Lisboa, Faculdade de Medicina, 2014

Topical bacteriophage therapy of the infected diabetic foot

Tese de doutoramento, Medicina (Medicina Interna), Universidade de Lisboa, Faculdade de Medicina, 2014

Identification of bacteria associated with Dinoflagellates (Dinophyceae) Alexandrium spp. using tyramide signal amplification fluorescent in situ hybridization and confocal microscopy

In the marine environment, phytoplankton and bacterioplankton can be physically associated. Such association has recently been hypothesized to be involved in the toxicity of the dinoflagellate genus Alexandrium. However, the methods, which have been used so far to identify, localize, and quantify bacteria associated with phytoplankton, are either destructive, time consuming, or lack precision. In the present study we combined tyramide signal amplification–fluorescent in situ hybridization (TSA-FISH) with confocal microscopy to determine the physical association of dinoflagellate cells with bacteria. Dinoflagellate attached microflora was successfully identified with TSA-FISH, whereas FISH using monolabeled probes failed to detect bacteria, because of the dinoflagellate autofluorescence. Bacteria attached to entire dinoflagellates were further localized and distinguished from those attached to empty theca, by using calcofluor and DAPI, two fluorochromes that stain dinoflagellate theca and DNA, respectively. The contribution of specific bacterial taxa of attached microflora was assessed by double hybridization. Endocytoplasmic and endonuclear bacteria were successfully identified in the nonthecate dinoflagellate Gyrodinium instriatum. In contrast, intracellular bacteria were not observed in either toxic or nontoxic strains of Alexandrium spp. Finally, the method was successfully tested on natural phytoplankton assemblages, suggesting that this combination of techniques could prove a useful tool for the simultaneous identification, localization, and quantification of bacteria physically associated with dinoflagellates and more generally with phytoplankton.

In vitro study of the effect of wound dressings on planktonic and biofilms from diabetic foot isolates

The management of wound bioburden has previously been evaluated using various antimicrobial wound dressings on bacterial pathogens isolated from various wounds. In this present study, the antimicrobial effect of silver-impregnated dressings (Acticoat and Silvercel) and honey-impregnated dressing (Medihoney™ Apinate) on both planktonic bacteria and quasi-biofilms by Staphylococcus aureus and Proteus mirabilis were assessed using a 6-well plate and standard agar technique. In the 6-well plate assay, a bacterial suspension of 108 colony forming unit (CFU)/mL was inoculated on each dressing in excess Luria-Bertani broth and incubated at 35 – 37°C for 30 and 60 minutes and 24 hours. After each incubation time, bacteria were recovered in sodium thioglycolate solution (STS) and the CFU/mL determined on LB agar. Dressings were cut into circular shapes (2cm diameter and placed on Mueller Hinton agar plates pre-inoculated with bacterial suspensions to determine their zones of inhibition (ZOI) after 24 hours incubation. None of the dressings was effective to significantly inhibit bacterial growth or biofilm formation at all the times tested. Acticoat and Medihoney™ Apinate produced ZOIs between 1.5 – 15 mm against both Staphylococcus aureus and Proteus mirabilis. It is possible that, dressings augmented with antibiotics can significantly reduce quasi-biofilms on standard agar.

Reduction of trimethylamine N-oxide to trimethylamine by the human gut microbiota: supporting evidence for ‘metabolic retroversion’

Dietary sources of methylamines such as choline, trimethylamine (TMA), trimethylamine N-oxide (TMAO), phosphatidylcholine (PC) and carnitine are present in a number of foodstuffs, including meat, fish, nuts and eggs. It is recognized that the gut microbiota is able to convert choline to TMA in a fermentation-like process. Similarly, PC and carnitine are converted to TMA by the gut microbiota. It has been suggested that TMAO is subject to ‘metabolic retroversion’ in the gut (i.e. it is reduced to TMA by the gut microbiota, with this TMA being oxidized to produce TMAO in the liver). Sixty-six strains of human faecal and caecal bacteria were screened on solid and liquid media for their ability to utilize trimethylamine N-oxide (TMAO), with metabolites in spent media profiled by Proton Nuclear Magnetic Resonance (1H NMR) spectroscopy. Enterobacteriaceae produced mostly TMA from TMAO, with caecal/small intestinal isolates of Escherichia coli producing more TMA than their faecal counterparts. Lactic acid bacteria (enterococci, streptococci, bifidobacteria) produced increased amounts of lactate when grown in the presence of TMAO, but did not produce large amounts of TMA from TMAO. The presence of TMAO in media increased the growth rate of Enterobacteriaceae; while it did not affect the growth rate of lactic acid bacteria, TMAO increased the biomass of these bacteria. The positive influence of TMAO on Enterobacteriaceae was confirmed in anaerobic, stirred, pH-controlled batch culture fermentation systems inoculated with human faeces, where this was the only bacterial population whose growth was significantly stimulated by the presence of TMAO in the medium. We hypothesize that dietary TMAO is used as an alternative electron acceptor by the gut microbiota in the small intestine/proximal colon, and contributes to microbial population dynamics upon its utilization and retroversion to TMA, prior to absorption and secondary conversion to TMAO by hepatic flavin-containing monooxygenases. Our findings support the idea that oral TMAO supplementation is a physiologically-stable microbiota-mediated strategy to deliver TMA at the gut barrier.

Environmental exposure to toxicants mixtures from a multi-purpose estuary: perspectives for a biomonitoring study in Portugal

This work was focused on a multi-purpose estuarine environment (river Sado estuary, SW Portugal) around which a number of activities (e.g., fishing, farming, heavy industry, tourism and recreational activities) coexist with urban centres with a total of about 200 000 inhabitants. Based on previous knowledge of the hazardous chemicals within the ecosystem and their potential toxicity to benthic species, this project intended to evaluate the impact of estuarine contaminants on the human and ecosystem health. An integrative methodology based on epidemiological, analytical and biological data and comprising several lines of evidence, namely, human contamination pathways, human health effects, consumption of local produce, estuarine sediments, wells and soils contamination, effects on commercial benthic organisms, and genotoxic potential of sediments, was used. The epidemiological survey confirmed the occurrence of direct and indirect (through food chain) exposure of the local population to estuarine contaminants. Furthermore, the complex mixture of contaminants (e.g., metals, pesticides, polycyclic aromatic hydrocarbons) trapped in the estuary sediments was toxic to human liver cells exposed in vitro, causing cell death, oxidative stress and genotoxic effects that might constitute a risk factor for the development of chronic-degenerative diseases, on the long term. Finally, the integration of data from several endpoints indicated that the estuary is moderately impacted by toxicants that affect also the aquatic biota. Nevertheless, the human health risk can only be correctly assessed through a biomonitoring study including the quantification of contaminants (or metabolites) in biological fluids as well as biomarkers of early biological effects (e.g., biochemical, genetic and omics-based endpoints) and genetic susceptibility in the target population. Data should be supported by a detailed survey to assess the impact of the contaminated seafood and local farm products consumption on human health and, particularly, on metabolic diseases or cancer development.