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

Thermo-hydro-mechanical analysis of CO2 injection into deep aquifers

One of the biggest challenges for humanity is global warming and consequently, climate changes. Even though there has been increasing public awareness and investments from numerous countries concerning renewable energies, fossil fuels are and will continue to be in the near future, the main source of energy. Carbon capture and storage (CCS) is believed to be a serious measure to mitigate CO2 concentration. CCS briefly consists of capturing CO2 from the atmosphere or stationary emission sources and transporting and storing it via mineral carbonation, in oceans or geological media. The latter is referred to as carbon capture and geological storage (CCGS) and is considered to be the most promising of all solutions. Generally it consists of a storage (e.g. depleted oil reservoirs and deep saline aquifers) and sealing (commonly termed caprock in the oil industry) formations. The present study concerns the injection of CO2 into deep aquifers and regardless injection conditions, temperature gradients between carbon dioxide and the storage formation are likely to occur. Should the CO2 temperature be lower than the storage formation, a contractive behaviour of the reservoir and caprock is expected. The latter can result in the opening of new paths or re-opening of fractures, favouring leakage and compromising the CCGS project. During CO2 injection, coupled thermo-hydro-mechanical phenomena occur, which due to their complexity, hamper the assessment of each relative influence. For this purpose, several analyses were carried out in order to evaluate their influences but focusing on the thermal contractive behaviour. It was finally concluded that depending on mechanical and thermal properties of the pair aquifer-seal, the sealing caprock can undergo significant decreases in effective stress.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Impacto do programa nacional de acreditação em saúde : comparação de indicadores entre unidades de saúde familiar acreditadas e não acreditadas

RESUMO - A qualidade é actualmente um factor incontornável do posicionamento das instituições de saúde, independentemente da sua estrutura de financiamento. A prestação de cuidados de qualidade é globalmente entendida como custo-efectiva. A acreditação das instituições de saúde é a forma mais utilizada como garantia dessa mesma qualidade. A aplicação da acreditação nos CSP tem um percurso mais recente, existindo na literatura opiniões distintas quanto aos seus efeitos. Nos últimos anos, Portugal implementou uma reforma estrutural dos CSP, com a criação das Unidades de Saúde Familiar. Paralelamente, o Departamento da Qualidade em Saúde, sob jurisdição da Direcção Geral da Saúde, implementou o Programa Nacional de Acreditação em Saúde. A acreditação das USF é hoje em dia uma realidade. ! Objectivos: Este trabalho pretende estudar o impacto do Programa Nacional de Acreditação em Saúde ao nível dos CSP, através da comparação dos indicadores de desempenho das Unidades de Saúde Familiar no ano de 2012. Metodologia: Para analisar as diferenças entre USF, identificaram-se os resultados dos indicadores de desempenho disponíveis para o ano 2012, das sete USF Acreditadas. Foram seleccionadas 7 USF Não Acreditadas, tendo como objectivo a criação de pares de USF (Acreditada + Não Acreditada), mantendo a maior homogeneidade possível entre cada unidade. Para cada par, foram identificadas as situações que apresentavam diferenças significativas no desempenho. Da mesma forma, analisaram-se as diferenças significativas por indicador, região e dimensão do desempenho. Procedeu-se à avaliação do grau de cumprimento das metas propostas, identificando desvios face ao objectivo contratualizado. Resultados e Conclusões: As USF Acreditadas apresentam resultados significativamente superiores em 12% das situações e inferiores em 10% das vezes. Não existem diferenças significativas em 4 dos 14 indicadores estudados. As USF Acreditadas são tendencialmente melhores, apresentando contudo diferenças marginais.

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.

Detection of purkinje images for automatic positioning of fixation target and interferometric measurements of anterior eye chamber

In cataract surgery, the eye’s natural lens is removed because it has gone opaque and doesn’t allow clear vision any longer. To maintain the eye’s optical power, a new artificial lens must be inserted. Called Intraocular Lens (IOL), it needs to be modelled in order to have the correct refractive power to substitute the natural lens. Calculating the refractive power of this substitution lens requires precise anterior eye chamber measurements. An interferometry equipment, the AC Master from Zeiss Meditec, AG, was in use for half a year to perform these measurements. A Low Coherence Interferometry (LCI) measurement beam is aligned with the eye’s optical axis, for precise measurements of anterior eye chamber distances. The eye follows a fixation target in order to make the visual axis align with the optical axis. Performance problems occurred, however, at this step. Therefore, there was a necessity to develop a new procedure that ensures better alignment between the eye’s visual and optical axes, allowing a more user friendly and versatile procedure, and eventually automatizing the whole process. With this instrument, the alignment between the eye’s optical and visual axes is detected when Purkinje reflections I and III are overlapped, as the eye follows a fixation target. In this project, image analysis is used to detect these Purkinje reflections’ positions, eventually automatically detecting when they overlap. Automatic detection of the third Purkinje reflection of an eye following a fixation target is possible with some restrictions. Each pair of detected third Purkinje reflections is used in automatically calculating an acceptable starting position for the fixation target, required for precise measurements of anterior eye chamber distances.

Geographical distribution of Trypanosoma cruzi in triatomine vectors in the State of Mato Grosso do Sul, Brazil

Introduction This work presents the initial findings of a molecular epidemiological investigation of Trypanosoma cruzi in triatomine insects in State of Mato Grosso do Sul. Methods A total of 511 triatomines from different regions of the state were examined. Deoxyribonucleic acid (DNA) was extracted from the intestinal contents of the insects using phenol-chloroform-isoamyl alcohol (25:24:1). Polymerase chain reaction (PCR) using primers 121/122 targeting DNA kinetoplast (kDNA) was then performed to identify T. cruzi, and positive samples were subjected to PCR using the primer pair TcSC5D-F/R followed by restriction fragment length polymorphism (RFLP) with the restriction enzymes SphI and HpaI (1 U/reaction), cloning and sequencing. Results One hundred samples were positive for T. cruzi, and three discrete typing units (DTUs) were identified (TcI, TcII, and TcBat). Triatoma sordida had the highest T. cruzi occurrence (83.3%), and DTUs were found in three samples: 58.3% of the samples were TcI, 33.3% were TcII and 8.3% were TcBat. There was a clear geographical distribution of the DTUs throughout the state, with TcI, TcII and TcBat located in the center, TcI located in the east, and TcII located in the west. Conclusions This study showed the occurrence of overlapping DTUs in State of Mato Grosso do Sul. The distributions of the DTUs were different, with TcI, TcII and TcBat in the center of the state, TcI predominantly in the east, and TcII in the west. Further studies may reveal a more defined mosaic distribution of DTUs in MS.

Clinical and serological outcomes with different surgical approaches for human hepatic hydatidosis

ABSTRACTINTRODUCTION:Hydatidosis is the result of infection with the larval stages of some species of the genus Echinococcus. Treatment approaches for hydatid cysts include the use of albendazole, surgery, and/or medico-surgical procedures. The choice of the therapeutic surgical approach depends on the cyst number and localization, surgeon expertise, and presence of complications. The present study aimed to compare the outcomes of the following therapeutic approaches for the treatment of hepatic hydatid cysts: pericystectomy; the puncture, aspiration, injection, and reaspiration (PAIR) technique; and the PAIR technique followed by deroofing, evacuation of cysts, and omentoplasty.METHODS:The 54 patients were divided into 3 groups: Group I (14 patients) who underwent pericystectomy, Group II (23 patients) who underwent the PAIR technique, and Group III (17 patients) who underwent the PAIR technique followed by deroofing and omentoplasty. The diagnosis of hydatid cysts was based on serological testing using enzyme-linked immunosorbent assay, abdominal ultrasound, and parasitological examination of the cyst contents. Morbidity, mortality, length of hospital stay, recurrence, and postoperative complications were evaluated.RESULTS:Postoperative bleeding, infection, and recurrence were reported in Groups I and II; Group III did not experience postoperative infection and had shorter hospital stays. Recurrence and postoperative complications did not occur in Group III.CONCLUSIONS:The partial surgical procedure with deroofing, evacuation of the cysts, and omentoplasty, as performed in the present study, is recommended as a safe and effective method for elimination of the entire parasite with minimal possibility for intra-peritoneal spillage.

Determinants of mortality in oncology patients colonized or infected with Staphylococcus aureus

Oxacillin-resistant Staphylococcus aureus (ORSA) infection is an important cause of hospital morbidity and mortality. The objective of this study was to identify the main factors associated with death in patients colonized or infected with Staphylococcus aureus in a cancer center. A matched-pair case-control study enrolled all patients infected or colonized with ORSA (cases) admitted to the Hospital do Câncer in Rio de Janeiro from 01/01/1992 to 12/31/1994. A control was defined as a patient hospitalized during the same period as the case-patients and colonized or infected with oxacillin-susceptible Staphylococcus aureus (OSSA). The study enrolled 95 cases and 95 controls. Patient distribution was similar for the two groups (p > or = 0.05) with respect to gender, underlying diseases, hospital transfer, prior infection, age, temperature, heart and respiratory rates, neutrophil count, and duration of hospitalization. Univariate analysis of putative risk factors associated with mortality showed the following significant variables: admission to the intensive care unit (ICU), presence of bacteremia, use of central venous catheter (CVC), ORSA colonization or infection, pneumonia, use of urinary catheter, primary lung infection, prior use of antibiotics, mucositis, and absence of cutaneous abscesses. Multivariate analysis showed a strong association between mortality and the following independent variables: admission to ICU (OR [odds ratio]=7.2), presence of Staphylococcus bacteremia (OR=6.8), presence of CVC (OR=5.3), and isolation of ORSA (OR=2.7). The study suggests a higher virulence of ORSA in comparison to OSSA in cancer patients.

Engineered MRI nanoprobes based on superparamagnetic iron oxide nanoparticles

This project aimed to engineer new T2 MRI contrast agents for cell labeling based on formulations containing monodisperse iron oxide magnetic nanoparticles (MNP) coated with natural and synthetic polymers. Monodisperse MNP capped with hydrophobic ligands were synthesized by a thermal decomposition method, and further stabilized in aqueous media with citric acid or meso-2,3-dimercaptosuccinic acid (DMSA) through a ligand exchange reaction. Hydrophilic MNP-DMSA, with optimal hydrodynamic size distribution, colloidal stability and magnetic properties, were used for further functionalization with different coating materials. A covalent coupling strategy was devised to bind the biopolymer gum Arabic (GA) onto MNPDMSA and produce an efficient contrast agent, which enhanced cellular uptake in human colorectal carcinoma cells (HCT116 cell line) compared to uncoated MNP-DMSA. A similar protocol was employed to coat MNP-DMSA with a novel biopolymer produced by a biotechnological process, the exopolysaccharide (EPS) Fucopol. Similar to MNP-DMSA-GA, MNP-DMSA-EPS improved cellular uptake in HCT116 cells compared to MNP-DMSA. However, MNP-DMSA-EPS were particularly efficient towards the neural stem/progenitor cell line ReNcell VM, for which a better iron dose-dependent MRI contrast enhancement was obtained at low iron concentrations and short incubation times. A combination of synthetic and biological coating materials was also explored in this project, to design a dynamic tumortargeting nanoprobe activated by the acidic pH of tumors. The pH-dependent affinity pair neutravidin/iminobiotin, was combined in a multilayer architecture with the synthetic polymers poy-L-lysine and poly(ethylene glycol) and yielded an efficient MRI nanoprobe with ability to distinguish cells cultured in acidic pH conditions form cells cultured in physiological pH conditions.

Design of bio-inspired ionic liquids for protein stabilisation

Ionic Liquids (ILs) consist in organic salts that are liquid at/or near room temperature. Since ILs are entirely composed of ions, the formation of ion pairs is expected to be one essential feature for describing solvation in ILs. In recent years, protein - ionic liquid (P-IL) interactions have been the subject of intensive studies mainly because of their capability to promote folding/unfolding of proteins. However, the ion pairs and their lifetimes in ILs in P-IL thematic is dismissed, since the action of ILs is therefore the result of a subtle equilibrium between anion-cation interaction, ion-solvent and ion-protein interaction. The work developed in this thesis innovates in this thematic, once the design of ILs for protein stabilisation was bio-inspired in the high concentration of organic charged metabolites found in cell milieu. Although this perception is overlooked, those combined concentrations have been estimated to be ~300 mM among the macromolecules at concentrations exceeding 300 g/L (macromolecular crowding) and transient ion-pair can naturally occur with a potential specific biological role. Hence the main objective of this work is to develop new bio-ILs with a detectable ion-pair and understand its effects on protein structure and stability, under crowding environment, using advanced NMR techniques and calorimetric techniques. The choline-glutamate ([Ch][Glu]) IL was synthesized and characterized. The ion-pair was detected in water solutions using mainly the selective NOE NMR technique. Through the same technique, it was possible to detect a similar ion-pair promotion under synthetic and natural crowding environments. Using NMR spectroscopy (protein diffusion, HSQC experiments, and hydrogen-deuterium exchange) and differential scanning calorimetry (DSC), the model protein GB1 (production and purification in isotopic enrichment media) it was studied in the presence of [Ch][Glu] under macromolecular crowding conditions (PEG, BSA, lysozyme). Under dilute condition, it is possible to assert that the [Ch][Glu] induces a preferential hydration by weak and non-specific interactions, which leads to a significant stabilisation. On the other hand, under crowding environment, the [Ch][Glu] ion pair is promoted, destabilising the protein by favourable weak hydrophobic interactions , which disrupt the hydration layer of the protein. However, this capability can mitigates the effect of protein crowders. Overall, this work explored the ion-pair existence and its consequences on proteins in conditions similar to cell milieu. In this way, the charged metabolites found in cell can be understood as key for protein stabilisation.

The Mechanism of Centriole Inactivation in Starfish Oocytes

The centrosome is the major organizing center in a cell, composed by two centrioles, one mother and one daughter, and surrounded by a pericentriolar material, which nucleates microtubules. Centriole duplication and segregation is tightly coupled to cell cycle, which guarantees that centriole number is maintained over generations. During the somatic cell cycle, a pair of centrioles duplicates, after which each daughter cell receives a pair, forming a closed cycle. However, during fertilization, if both cells were to contribute with their pair of centrioles, gamete fusion would result in the double of the normal centriole number.(...)

Aprendizagem baseada na resolução de problemas: uma experiência pedagógica com alunos de um Curso de Especialização Tecnológica

Relatório de estágio de mestrado em Ensino de Informática

Aprender a debater: o debate como atividade de interação e de participação democrática

Relatório de estágio de mestrado em Ensino de Inglês e de Espanhol no 3º Ciclo do Ensino Básico e no Ensino Secundário

Brasergasilus mamorensis sp. n. (Copepoda: Ergasilidae) from the Nasal cavities of Hydrolycus pectoralis (Guenther, 1866) (Characiformes: Cynodontidae) from the Brazilian Amazon, and considerations about Abergasilinae

Brasergasilus mamorensis sp. n., collected from the nasal cavities of Hydrolycus pectoralis (Guenther, 1866) in the Mamoré River, Rondônia State, Brazil, is described. This is the first time that a species from the genus Brasergasilus has been collected in the nasal cavities. This new species is the only one that has a spine on the first segment of the antenna, a simple seta on the basipodites of the first three pairs of legs and one pair of vestigial legs (leg 5 ) on the sixth thoracic somite.