Studies on the wine spoilage yeast Brettanomyces bruxellensis: 4-ethylphenol production and improved detection

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Pyruvate kinase and glucose-6-phosphate dehydrogenase deficies and their association with malaria - population genetics and proteomic studies

A malária é reconhecida como uma das principais forças selectivas a actuar na história recente no genoma humano. Inúmeros polimorfismos genéticos têm sido descritos como protectores contra a gravidade da malária, como o alelo HbS (designado de traço falciforme) e o alelo G6PD A- (associado à deficiência de G6PD). Mais recentemente, também a deficiência de PK foi associada com a protecção contra a malária. Evidências desta associação foram obtidas em estudos com modelos de roedor e estudos in vitro utilizando GV humanos deficientes em PK. Até à data, não foram obtidos dados em populações humanas que revelem esta associação: ainda não foi identificada uma variante de PK com uma prevalência elevada em regiões endémicas de malária e não foram identificadas marcas de selecção na região do gene que codifica para a PK (gene PKLR). Além disso, os mecanismos subjacentes à protecção contra a malária por deficiências enzimáticas dos GV não estão bem esclarecidos. Assim, os objectivos do presente estudo foram: investigar os polimorfismos genéticos humanos com associação com a malária em Cabo Verde; pesquisar marcas de selecção da malária na região do gene PKLR em populações Africanas; determinar a frequência da deficiência em PK e identificar uma eventual variante da enzima que possa estar sob selecção positiva em regiões endémicas de malária; avaliar o efeito das duas deficiências enzimáticas (PK e G6PD) na invasão e maturação do parasita em culturas in vitro de Plasmodium usando GV normais e deficientes; e analisar o perfil proteómico de GV infectados e não infectados, normais e com deficiência (em PK e G6PD), bem como de parasitas isolados de GV tanto deficientes como normais. Em Cabo Verde (área epidémica), não foram identificadas marcas de selecção pela malária, através da análise dos vários polimorfismos. No entanto, quando a análise foi realizada em dois países endémicos (Angola e Moçambique), foram detectadas várias marcas de selecção: a genotipagem de microssatélites (STRs) e polimorfismos de base única (SNPs) localizados na vizinhança do gene PKLR revelou uma diferenciação consideravelmente maior entre as populações Africana e Europeia (Portuguesa), do que a diferenciação determinada aquando da utilização de marcadores genéticos neutros. Além disso, uma região genómica de maior amplitude apresentou um Desequilíbrio de Ligação (LD) significativo no grupo de malária não grave (e não no grupo de malária grave), sugerindo que a malária poderá estar a exercer pressão selectiva sobre a região do genoma humano que envolve o gene PKLR. No estudo que incidiu na determinação da prevalência da deficiência de PK no continente Africano (realizado em Moçambique), esta revelou-se elevada - 4,1% - sendo o valor mais elevado descrito até ao momento a nível mundial para esta enzimopatia. Na pesquisa de mutações que pudessem estar na causa deste fenótipo (baixa actividade de PK), foi identificada uma mutação não sinónima 829G>A (277Glu>Lys), significativamente associada à baixa actividade enzimática. Esta mutação foi também identificada em Angola, São Tomé e Príncipe e Guiné Equatorial, onde a frequência de portadores heterozigóticos foi entre 2,6 e 6,7% (valores que se encontram entre os mais elevados descritos globalmente para mutações associadas à deficiência em PK). Não foi possível concluir acerca da associação entre a deficiência de PK e o grau de severidade da malária e da associação entre o alelo 829A e a mesma, devido ao baixo número de amostras. Os resultados dos ensaios de invasão/maturação do parasita sugeriram que, nos GV com deficiência de PK ou G6PD, a invasão (onde está envolvida a membrana do GV hospedeiro e o complexo apical do parasita) é mais relevante para a eventual protecção contra a malária do que a maturação. Os resultados da análise proteómica revelaram respostas diferentes por parte do parasita nas duas condições de crescimento (GV com deficiência de PK e GV com deficiência de G6PD). Esta resposta parece ser proporcional à gravidade da deficiência enzimática. Nos parasitas que cresceram em GV deficientes em G6PD (provenientes de um indivíduo assintomático), a principal alteração observada (relativamente às condições normais) foi o aumento do número de proteínas de choque térmico e chaperones, mostrando que os parasitas responderam às condições de stress oxidativo, aumentando a expressão de moléculas de protecção. Nos parasitas que cresceram em condições de deficit de PK (GV de indivíduo com crises hemolíticas regulares, dependente de transfusões sanguíneas), houve alteração da expressão de um maior número de proteínas (relativamente ao observado em condições normais), em que a maioria apresentou uma repressão da expressão. Os processos biológicos mais representados nesta resposta do parasita foram a digestão da hemoglobina e a troca de proteínas entre hospedeiro e parasita/remodelação da superfície do GV. Além disso, uma elevada percentagem destas proteínas com expressão alterada está relacionada com as fendas de Maurer, que desempenham um papel importante na patologia da infecção malárica. É colocada a hipótese de que a protecção contra a malária em GV deficientes em PK está relacionada com o processo de remodelação da membrana dos GV pelo parasita, o que pode condicionar a invasão por novos parasitas e a própria virulência da malária. Os resultados da análise do proteoma dos GV contribuirão para confirmar esta hipótese.

Functional and structural studies of two enzymes: membrane bound kinase and Z-DNA/Z-RNA-binding protein

Dissertação para obtenção do Grau de Doutor em Sistemas de Bioengenharia

Crystallographic studies on membrane and cytoplasmic enzymes

Dissertation presented to obtain the Ph.D degree in Biochemistry, Structural Biochemistry

Studies of the assembly of the Streptococcus pneumoniae capsular polysaccharide

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

Understanding the microbial ecology and ecophysiology of enhanced biological phosphorus removal processes through metabolic modelling and experimental studies

Dissertation to obtain the degree of Master in Chemical and Biochemical Engineering

Controlling gene expression in enterobacteriaceae: studies on sRNAs and strategies for synthetic biology

Dissertation presented to obtain the Master Degree in Molecular, Genetics and Biomedicine

Functional and structural studies of a mini-ferritin protein

Dissertação para obtenção do Grau de Mestre em Bioquímica

Studies towards modified chitooligosaccharides: a new approach to NAG-NAM moiety

Dissertação para obtenção do Grau de Mestre em Bioorgânica

Upgrade of an experimental volumetric unit for gas adsorption equilibrium studies

In this work, a volumetric unit previously assembled by the research group was upgraded. This unit revamping was necessary due to the malfunction of the solenoid valves employed in the original experimental setup, which were not sealing the gas properly leading to erroneous adsorption equilibrium measurements. Therefore, the solenoid valves were substituted by manual ball valves. After the volumetric unit improvement its operation was validated. For this purpose, the adsorption equilibrium of carbon dioxide (CO2) at 323K and 0 - 20 bar was measured on two different activated carbon samples, in the of extrudates (ANG6) and of a honeycomb monolith (ACHM). The adsorption equilibrium results were compared with data previously measured by the research group, using a high-pressure microbalance from Rubotherm GmbH (Germany) – gravimetric. The results obtained using both apparatuses are coincident thus validating the good operation of the volumetric unit upgraded in this work. Furthermore, the adsorption equilibrium of CO2 at 303K and 0 - 10 bar on Metal-Organic Frameworks (MOFs) Cu-BTC and Fe-BTC was also studied. The CO2 adsorption equilibrium results for both MOFs were compared with the literature results showing good agreement, which confirms the good quality of the experimental results obtained in the new volumetric unit. Cu-BTC sample showed significantly higher CO2 adsorption capacity when compared with the Fe-BTC sample. The revamping of the volumetric unit included a new valve configuration in order to allow testing an alternative method for the measurement of adsorption equilibrium. This new method was employed to measure the adsorption equilibrium of CO2 on ANG6 and ACHM at 303, 323 and 353K within 0-10 bar. The good quality of the obtained experimental data was testified by comparison with data previously obtained by the research group in a gravimetric apparatus.

Double-walled PLLA/PLGA particles for the sustained release of Meloxicam: preparation, characterisation and contolled release studies

There were two main objectives in this thesis investigation, first, the production, characterisation, in vitro degradation and release studies of double walled microspheres for drug release control. The second one, and the most challenging, was the production of double walled nanospheres, also for drug control delivery. The spheres were produced using two polymers, the Poly(L-lactide)Acid, PLLA, and the Poly(L-lactide-co-glycolic)Acid, PLGA.Afterwards, a model drug, Meloxicam, which is an antiinflammatory drug, was encapsulated into the particles. Micro and nanospheres were produced by the solvent extraction/evaporation method, where perfect spherical particles were obtained. By varying the polymers PLLA/PLGA mass ratio, different core and shell composition, as well as several shell and core thickness were observed. In the particles with a PLLA/PLGA mass ratio 1:1, the shell is composed by PLLA and the core by PLGA. It was also verified that the Meloxicam has a tendency to be distributed in the PLGA layer. Micro and nanoparticles were characterised in morphology, size, polymer cristalinity properties and drug distribution. Particles degradation studies was performed, where the particles in a PVA solution of pH 7,4 where placed in an incubator, during approximately 40 days, at 120rpm, and 37ºC, simulating, as much as possible, the human body environment. From these studies, the conclusion was that particles containing a PLGA shell and a PLLA core degrade more rapidly, due to the fact that PLLA is more hydrophobic than the PLGA. Concerning the drug release controlled results, done also for 40 and 50 days, they showed that the microspheres containing a shell of PLLA release more slowly than when the shell is composed of PLGA. This result was predictable, since the drug is solubilised in the PLGA polymer and so, in that case, the PLLA shell works like a barrier between the drug and the outer medium. Another positive aspect presented by this study is the lower initial burst effect, obtained when using double walled particles, which is one of the advantages of the same. In a second part of this investigation, the production of the nanospheres was the main goal, since it was not yet accomplished by other authors or investigators. After several studies, referring to the speed, time and type of agitation, as well as, the concentration and volume of the first aqueous solution of poly-vinyl-alcohol (PVA) during the process of solvent extraction/evaporation it was possible to obtain double walled nanospheres.(...)

Structural and functional studies of a high activity NiFeSe Hydrogenase

Theawareness that fossil fuels exist in limited quantities has stimulated research into energy production from renewable sources. Future energy sources! should! be! plentiful! with! negligible! impact! on! the! environment.! Hydrogen!has!the!potential!to!satisfy!these!requirements.!Nevertheless,!current! methods! of! H2! production! rely! on! nonOrenewable! resources.! Biological! H2! production! from! sunlight! or! biomass! is! an! appealing! alternative! to! current! production!methods.!!(...)

Crystallographic studies of proteins involved in the mRNA localization mechanisms in Drosophila melanogaster and amidation of the peptidoglycan residues in Staphylococcus aureus

Part of the work described in this chapter, was the subject of the following publication: D. Vieira, T. a. Figueiredo, A. Verma, R. G. Sobral, A. M. Ludovice, H. de Lencastre, and J. Trincao, “Purification, crystallization and preliminary X-ray diffraction analysis of GatD, a glutamine amidotransferase-like protein from Staphylococcus aureus peptidoglycan,” Acta Crystallogr. Sect. F Struct. Biol. Commun., vol. 70, no. 5, pp. 1–4, Apr. 2014.

Foresight exercises as a tool for decision-making: the example of two case studies in health

Based on the report for the unit “Foresight Methods Analysis” of the PhD programme on Technology Assessment at the Universidade Nova de Lisboa, under the supervision of Prof. Dr. António B. Moniz

Experimental and modeling studies on reverse electrodialysis for sustainable power generation

A potentially renewable and sustainable source of energy is the chemical energy associated with solvation of salts. Mixing of two aqueous streams with different saline concentrations is spontaneous and releases energy. The global theoretically obtainable power from salinity gradient energy due to World’s rivers discharge into the oceans has been estimated to be within the range of 1.4-2.6 TW. Reverse electrodialysis (RED) is one of the emerging, membrane-based, technologies for harvesting the salinity gradient energy. A common RED stack is composed by alternately-arranged cation- and anion-exchange membranes, stacked between two electrodes. The compartments between the membranes are alternately fed with concentrated (e.g., sea water) and dilute (e.g., river water) saline solutions. Migration of the respective counter-ions through the membranes leads to ionic current between the electrodes, where an appropriate redox pair converts the chemical salinity gradient energy into electrical energy. Given the importance of the need for new sources of energy for power generation, the present study aims at better understanding and solving current challenges, associated with the RED stack design, fluid dynamics, ionic mass transfer and long-term RED stack performance with natural saline solutions as feedwaters. Chronopotentiometry was used to determinate diffusion boundary layer (DBL) thickness from diffusion relaxation data and the flow entrance effects on mass transfer were found to avail a power generation increase in RED stacks. Increasing the linear flow velocity also leads to a decrease of DBL thickness but on the cost of a higher pressure drop. Pressure drop inside RED stacks was successfully simulated by the developed mathematical model, in which contribution of several pressure drops, that until now have not been considered, was included. The effect of each pressure drop on the RED stack performance was identified and rationalized and guidelines for planning and/or optimization of RED stacks were derived. The design of new profiled membranes, with a chevron corrugation structure, was proposed using computational fluid dynamics (CFD) modeling. The performance of the suggested corrugation geometry was compared with the already existing ones, as well as with the use of conductive and non-conductive spacers. According to the estimations, use of chevron structures grants the highest net power density values, at the best compromise between the mass transfer coefficient and the pressure drop values. Finally, long-term experiments with natural waters were performed, during which fouling was experienced. For the first time, 2D fluorescence spectroscopy was used to monitor RED stack performance, with a dedicated focus on following fouling on ion-exchange membrane surfaces. To extract relevant information from fluorescence spectra, parallel factor analysis (PARAFAC) was performed. Moreover, the information obtained was then used to predict net power density, stack electric resistance and pressure drop by multivariate statistical models based on projection to latent structures (PLS) modeling. The use in such models of 2D fluorescence data, containing hidden, but extractable by PARAFAC, information about fouling on membrane surfaces, considerably improved the models fitting to the experimental data.