Dissecting the function of the SpoIIIJ and YqjG membrane protein insertases during bacterial spore development

Dissertation presented to obtain the Ph.D degree in Biology, Microbial Biology

Variation in protein expression levels in cell populations

Dissertation presented to obtain the Ph.D degree in Systems Biology

DNA-Protein interaction: a response regulatory protein associated with Mo homeostasis in Desulfovibrio alaskensis G20.

Dissertation for a degree in Doctor in Sustainable Chemistry

Functional and structural studies of a mini-ferritin protein

Dissertação para obtenção do Grau de Mestre em Bioquímica

Bioinspired polyethersulfone-based hollow fiber membranes as the scaffolds in renal assist device for protein-bound toxins removal from blood

Dissertation for obtaining the Master degree in Membrane Engineering

Assessment of Notch1 ligands production - key protein targets in breast cancer

Cell-to-cell communication is required for many biological processes in development and adult life. One of the most common systems utilized by a wide range of eukaryotes is the Notch signalling pathway. Four Notch receptors and five ligands have been identified in mammals that interact via their extracellular domains leading to transcription activation. Studies have shown that the Notch ligands expression is undetectable in normal breast tissues, but moderate to high expression has been detected in breast cancer. Thus, any of the Notch1 ligands can be studied as possible therapeutic targets for breast cancer. To study Notch pathway proteins there is the need to obtain stable protein solutions. E. coli is the host of excellence for recombinant proteins for the ease of use, fast growth and high cell densities. However, the expression of mammalian proteins in such systems may overwhelm the bacterial cellular machinery, which does not possess the ability for post-translational modifications, or dedicated compartments for protein synthesis. Mammalian cells are therefore preferred, despite their technical and financial increased demands. We aim to determine the best expression and purification conditions for the different ligand protein constructs, to develop specific function-blocking antibodies using the Phage Display technology. Moreover, we propose to crystallize the Notch1 ligands alone and in complex with the phage display selected antibodies, unveiling molecular details. hJag2DE3 and hDll1DE6 proteins were purified from refolded inclusion bodies or mammalian cell culture supernatants, respectively, and purity was confirmed by SDS-PAGE (>95%). Protein produced in mammalian cells showed to be more stable, apparently with the physiological disulfide pattern, contrary to what was observed in the refolded protein. Several nano-scale crystallization experiments were set up in 96-well plates, but no positive result was obtained. We will continue to pursue for the best expression for the Notch ligand constructs in both expression systems.

Assembly and function of a protein cross-linking enzyme during bacterial spore morphogenesis

Sporulation in Bacillus subtilis culminates with the formation of a dormant endospore. The endospore (or spore) is one of the most resilient cell types known and can remain viable in the environment for extended periods of time. Contributing to the spore’s resistance and its ability to interact with and monitor its immediate environment is the coat, the outermost layer of B. subtilis spores. The coat is composed by over 70 different proteins, which are produced at different stages in sporulation and orderly assembled around the developing spore.(...)

Avaliação da instabilidade de vertentes e processos de erosão superficial na zona de Castelo Branco, Furnas, ilha de São Miguel, Açores

A presente dissertação tem como objetivo identificar e avaliar os elementos de instabilidade geotécnica das vertentes e terrenos da zona do Vanzinho (Castelo Branco, Furnas, ilha de São Miguel), com vista a propor medidas de estabilização das vertentes e controlo da erosão superficial dos terrenos. Com este objetivo foi definida uma metodologia de trabalho em cinco etapas que consistiu: (i) a primeira etapa, no levantamento de dados bibliográficos, integração da informação geológica/geomorfológica em SIG (sistema de informação geográfica) e na observação e levantamento de campo das superfícies de instabilidade geotécnica; (ii) a segunda etapa, na recolha de amostras de solo, remexidas e não remexidas, para caracterização das propriedades físicas e mecânicas dos materiais; (iii) a terceira etapa, na realização de ensaios laboratoriais para a determinação das propriedades físicas e mecânicas dos solos e respetiva classificação; (iv) uma quarta etapa, que consistiu no tratamento estatístico multivariado de dados, nomeadamente, a aplicação dos métodos de análise fatorial das correspondências e de classificação hierárquica com vista à caracterização da tipologia dos materiais e eventual correlação com as evidências de instabilidade; (v) a quinta etapa consistiu na projeção de um conjunto de medidas estruturais e não estruturais (medidas biológicas) a implementar para a estabilização de vertentes e controlo dos processos de erosão superficial observados na área do Vanzinho. Para a estimação da distribuição espacial das diferentes tipologias de solo foi utilizado o método geoestatístico da krigagem multifásica. Para cada elemento de instabilidade cartografado foi criada uma ficha que caracteriza a tipologia da ocorrência, a dimensão, a forma e o coberto vegetal do meio envolvente. O trabalho realizado teve por base a integração de toda a informação num SIG, o que possibilita a atualização de eventuais novas ocorrências, bem como o fácil manuseamento e análise dos dados, a utilizar em trabalhos futuros.

Análise experimental das condições de escoamento superficial em zonas urbanas na presença de viaturas

As cheias em zonas urbanas representam um fenómeno natural que parece ocorrer cada vez com mais frequência, provocando muitas vezes a inundação de caves, estações de metropolitano e, em alguns casos extremos, a perda de vidas humanas. Estas cheias ocorrem quando os sistemas artificiais de recolha de águas pluviais deixam de ter capacidade de vazão suficiente para os caudais afluídos e parte do escoamento começa a fazer-se à superfície. Deste modo, o objetivo principal deste trabalho consiste na avaliação da influência que o grau de obstrução, causado pela presença de viaturas nas vias públicas, tem no agravamento das alturas de água nos arruamentos. Para isso, foram realizados ensaios laboratoriais num modelo à escala 1:12, nos quais se procurou simular as condições reais de escoamento de caudais de cheia, em vias urbanas. Os ensaios foram feitos para 20 cenários, para os quais se combinaram diferentes quantidades e disposições de veículos, a que correspondem diferentes graus de obstrução ao escoamento. Durante as medições das alturas de água, em todos os cenários, fizeram-se variar as inclinações do fundo entre 0,005 e 0,030 m/m para uma gama de caudais compreendida entre 10 e 40 m3/h. Posteriormente, com os valores das medições obtidas, inferiram-se quais os cenários mais críticos, ou seja, quais as situações onde se observaram maiores incrementos nas alturas de água de escoamento nos arruamentos. A partir da variação entre as alturas de escoamento do cenário base, sem a presença de veículos, e as alturas dos diferentes cenários com obstáculos, obtiveram-se as sobrelevações da altura de água, tanto em valor absoluto como em valor relativo. Por fim, mas não menos importante, procurou-se obter padrões e consequentemente relações entre os diversos parâmetros em estudo, principalmente a relação entre a percentagem de obstrução e a sobrelevação da altura de água nos arruamentos. Da análise dos resultados obtidos procurou-se por último extrair conclusões e tecer algumas recomendações tendo em vista a minimização de algumas consequências deste tipo de situações extremas.

PROTEIN FOLDING AND DISEASE THE MITOCHONDRIAL PROTEIN FRATAXIN

This dissertation focuses on the study of frataxin, a small mitochondrial protein whose deficiency is associated with the neurodegenerative disease Friedreich's ataxia (FRDA). Aiming at a better understanding of frataxin conformational and functional properties, two lines of research were followed: first, the effect of FRDA-related mutations in human frataxin (FXN) were studied and the role of oxidative stress related modification addressed; second, yeast frataxin (Yfh1) orthologue was used to explore the conformational and functional properties of the protein.(...)

Gas tungsten arc welding of NiTi shape memory alloy

Shape memory alloys are characterized by the ability of recovering their initial shape after being deformed and by superelasticity. Since the discovery of these alloys, a new field of interest emerged not only for the scientific community but also to many industries. However, these alloys present poor machinability which constitute a constrain in the design of complex components for new applications. Thus, the demand for joining techniques able to join these alloys without compromising their properties became of great importance to enlarge the complexity of existing applications. Literature shows that these alloys are joined mainly using laser welding. In the present study, similar NiTi butt joints, were produced using TIG welding. The welds were performed in 1.5 mm thick plates across the rolling direction. A special fixture and gas assist device was designed and manufactured. Also a robot arm was adapted to accommodate the welding torch to assure the repeatability of the welding parameters. Welds were successfully achieved without macroscopic defects, such as pores and distortions. Very superficial oxidation was seen on the top surface due to insufficient shielding gas flow on the weld face. The welded joints were mechanically tested and structurally characterized. Testing methods were used to evaluate macro and microstructure, as well as the phase transformation temperatures, the mechanical single and cyclic behaviour and the shape recovery ability. Differential Scanning Calorimetry (DSC), Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), microhardness measurements were techniques also used to evaluate the welded joints. A depletion in Ni in the fusion zone was seen, as well as a shift in Ms temperature. For strain values of 4% the accumulated irrecoverable strain was of about 30% and increased with the strain imposed during cycling. Nevertheless, a complete recovery of initial shape was observed when testing the shape memory effect on a dedicated device that introduces a deformation of 6.7%. That is, the welding procedure does not remove the ability of the specimens to recover their initial shape.

Manipulation of host cell functions by Salmonella: the role of the bacterial effector protein SteA

Salmonella enterica serovars are Gram-negative facultative intracellular bacterial pathogens that infect a wide variety of animals. Salmonella infections are common in humans, causing usually typhoid fever and gastrointestinal diseases. Salmonella enterica serovar Typhimurium (S. Typhimurium), which is a leading cause of human gastroenteritis, has been extensively used to study the molecular pathogenesis of Salmonella, because of the availability of sophisticated genetic tools, and of suitable animal and tissue culture models mimicking different aspects of Salmonella infections.(...)

Inhibition of SNF1-related protein kinase1 by trehalose 6-phosphate and other metabolites and the interrelation with plant gorwth

All life forms need to monitor carbon and energy availability to survive and this is especially true for plants which must integrate unavoidable environmental conditions with metabolism for cellular homeostasis maintenance. Sugars, in the heart of metabolism, are now recognized as crucial signaling molecules that translate those conditions. One such signal is trehalose 6- phosphate (T6P), a phosphorylated dimer of glucose molecules which levels correlate well with those of sucrose (Suc). Central integrators of stress and energy regulation include the conserved plant Snf1-related kinase1 (SnRK1) which respond to low cellular energy levels by up-regulating energy conserving and catabolic metabolism and down-regulating energy consuming processes. In 2009 T6P was shown to inhibit SnRK1. The in vitro inhibition of SnRK1 by T6P was confirmed in vivo through the observation that genes normally induced by SnRK1 were repressed by T6P and vice-versa, promoting growth processes. These observations provided a model for the regulation of growth by sugar.(...)