A shared-disk parallel cluster file system

Dissertação apresentada para obtenção do Grau de Doutor em Informática Pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Determinants for the subcellular localization of the inner and outer spore coat hubs in Bacillus subtilis

Endospores, or spores for simplicity, are a highly resistant cell type produced by some bacterial species under adverse conditions. Two main protective layers contribute to the resilience of spores: the cortex, composed of peptidoglycan, and the outermost proteinaceous coat. In Bacillus subtilis, the coat comprises up to 80 different proteins, organized into four sublayers: the basement layer, the inner coat, the outer coat and the crust. These proteins are synthesized at different times during sporulation and deposited at the spore surface in multiple coordinated waves. Central to coat formation is a group of morphogenetic proteins that guide the assembly of the coat components. Targeting of the coat proteins to the surface of the developing spore is mainly controlled by the SpoIVA morphogenetic ATPase. In a second stage, the coat proteins fully encircle the spore, a process termed encasement that requires the morphogenetic protein SpoVID. Assembly of the inner coat requires SafA, whereas formation of the outer coat and the crust requires CotE. SafA interacts directly with the N terminus of SpoVID. (...)

Experimental study of proton induced nuclear reactions in 6,7 Li

This work presents the results of the experimental study of proton induced nuclear reactions in lithium, namely the 7Li(p,α) 4He, 6Li(p,α) 3He and 7Li(p,p)7Li reactions. The amount of 7Li and 6Li identified as primordial and observed in very old stars of the Milky Way galactic halo strongly deviates from the predictions of primordial nucleosynthesis and stellar evolution models which depend, among other factors, on the cross sections of reactions like 7Li(p,α) 4He and 6Li(p,α) 3He. These discrepancies have triggered a large amount of research in the fields of stellar evolution, cosmology, pre-galactic evolution and low energy nuclear reactions. Focusing on nuclear reactions, this work has measured the 7Li(p,α) 4He and 6Li(p,α) 3He reactions cross sections (expressed in terms of the astrophysical S -factor) with higher accuracy, and the electron screening effects in these reactions for different environments (insulators and metallic targets). The 7Li(p,α) 4He angular distributions were also measured. These measurementstook place in two laboratory facilities, in the framework of the LUNA (Laboratory for Undergroud Nuclear Astrophysics) international collaboration, namely the Laboratorio ´ de Feixe de Ioes ˜ in ITN (Instituto Tecnologico ´ e Nuclear) Sacavem, ´ Portugal, and the Dynamitron-TandemLaboratorium in Ruhr-Universitat¨ Bochum, Germany. The ITN target chamber was modified to measure these nuclear reactions, with the design and construction of new components, the addition of one turbomolecular pump and a cold finger. The 7Li(p,α) 4He and 6Li(p,α) 3He reactions were measured concurrently with seven and four targets, respectively. These targets were produced in order to obtain adequate and stable lithium depth profiles. In metallic environments, the measured electron screening potential energies are much higher than the predictions of atomic-physics models. The Debye screening model applied to the metallic conduction electrons is able to explain these high values. It is a simple model, but also very robust. Concerning primordial nucleosynthesis and stellar evolution models, these results are very important as they show that laboratory measurements are well controlled, and the model inputs from these cross sections are therefore correct. In this work the 7Li(p,p)7Li differential cross section was also measured, which is useful to describe the 7Li(p,α) 4He entrance channel.

Segmentation of striatal brain structures from high resolution pet images

Dissertation presented at the Faculty of Science and Technology of the New University of Lisbon in fulfillment of the requirements for the Masters degree in Electrical Engineering and Computers

Estabilização dinâmica em patologia degenerativa da coluna lombar: estado da arte e contributo pessoal

Resumo Este trabalho encontra-se dividido em três capítulos distintos. No primeiro, é caracterizada a doença degenerativa lombar, demorando-se o autor na descrição pormenorizada das alterações anatómicas, biomecânicas, e bioquímicas inerentes à sua ocorrência. Segue-se a descrição da evolução das diferentes formas de terapêutica, enumerando as que de forma clássica mais frequentemente são utilizadas (cirúrgicas e não cirúrgicas). No segundo capítulo, são referidos os mais recentes avanços tecnológicos nesta área, mencionando, nas suas vertentes biomecânicas, clínicas e terapêuticas, as particularidades das estabilizações dinâmicas interespinhosas e pediculares, bem como da artroplastia de disco. Após esta longa introdução, inicia-se o terceiro capítulo no qual se apresenta um estudo prospectivo da avaliação clínica, funcional, imagiológica e da variação da densidade mineral óssea vertebral em 20 doentes com patologia degenerativa, tratados com sistemas de estabilização dinâmica semi-rígida interespinhosa, e seguidos durante dois anos. Do estudo realizado conclui-se que os sistemas referidos são eficazes clínica e funcionalmente no tratamento de doentes com doença degenerativa lombar. Mais ainda, estes instrumentais proporcionam um aumento da altura do disco confirmado na incidência radiográfica de perfil no nível instrumentado. Constatámos ainda que a densidade mineral óssea vertebral dos doentes intervencionados, avaliada com sistema DXA, não demonstra diferenças com significância estatística ao longo do tempo, omparativamente à determinada em idêntica população mas sem qualquer patologia lombar. Acresce que se obteve uma correlação entre a funcionalidade física e a BMD radial, com significância estatística crescente nas duas medições realizadas. Abstract This study is divided in three different chapters. In the first one the author describes the anatomical, biomechanical and biochemical changes that go along with degenerative lumbar spine disease. The therapeutically possibilities are mentioned, mainly with the classic fusion and decompression as well as the non surgical options. Then, in the second chapter, the author describes, from the biomechanical, clinical and therapeutically point of view, the new techniques of dynamic stabilization, interspinous and pedicular systems, as well as disc replacement. After this introduction, in the third chapter a prospective clinical, functional, imagiologic and vertebral bone mineral density variation study is presented. Twenty patients with degenerative lumbar spine disease are selected, and operated with a semi rigid interspinous system device, and followed for a two year period. The author concludes that the interspinous semi rigid systems were clinically and functionally effective in lumbar degenerative patients. It was also founded that the disc height at the implant segment level increased after surgery. Bone density was assessed with a DXA system device. As far as vertebral bone density is concerned, the author found no differences what so ever inside the group during the study, or to an identical control group without any lumbar pathology. The correlation study between the BMD and physical function showed that there was only significant statistically data in radial BMD measurement, and this happened with growing correlation from year 2006 to 2007.

Burrows-wheeler transform in secondary memory

Master’s Thesis in Computer Engineering

Dynamics of cork mycobiota throughout stopper manufacturing process: from diversity to metabolite

Dissertation presented to obtain the Ph.D degree in Biology

Functional studies on BolA and related genes: increasing the understanding of a protein with pleiotropic effects

Dissertation presented to obtain a Doctoral degree in Biology by Instituto de Tecnologia Química e Biológica

Epidemiological characterization, antimicrobial resistance and virulence mechanisms of human and animal streptococci

Dissertação para obtenção do Grau de Doutor em Biologia

Proteínas recombinantes de Plasmodium Falciparum para deteção de malária por nanoimunoensaios

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Structural investigation of the Bacillus subtilis morphogenic factor RodZ

A thesis to obtain a Master degree in Structural and Functional Biochemistry

Creating greater value for biomass residues

Dissertation presented to obtain the Ph.D degree in Engineering Sciences and Technology

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.(...)

Follow the red road of triheme cytochromes in Geobacter sulfurreducens

The bacterium Geobacter sulfurreducens (Gs) is capable of oxidizing a large variety of compounds relaying electrons out of the cytoplasm and across the membrane in a process designated as extracellular electron transfer. The Gs genome was fully sequenced and a family composed by five periplasmic triheme cytochromes c7 (designated PpcA-E) was identified. These cytochromes play an important role in the reduction of extracellular acceptors. They contain approximately 70 amino acids, three heme groups with bis-histidinyl axial coordination, and share between 57 and 77% sequence identity. The triheme cytochrome PpcA is highly abundant in Gs and is most likely the reservoir of electrons destined for outer surface. In addition to its role in electron transfer pathways this protein can perform e-/H+ energy transduction, a process that is disrupted when the strictly conserved aromatic residue phenylalanine 15 is replaced by a leucine (PpcAF15L). This Thesis focuses on the expression, purification and characterization of these proteins using Nuclear Magnetic Resonance and ultraviolet-visible spectroscopy. The orientations of the heme axial histidine ring planes and the orientation of the heme magnetic axis were determined for each Gs triheme cytochrome. The comparison of the orientations obtained in solution with the crystal structures available showed significant differences. The results obtained provide the paramagnetic constraints to include in the future refinement of the solution structure in the oxidized state. In this work was also determined the solution structure and the pH-dependent conformational changes of the PpcAF15L allowing infer the structural origin for e-/H+ energy transduction mechanism as shown by PpcA. Finally, the backbone and side chain NH signals of PpcA were used to map interactions between this protein and the putative redox partner 9,10-anthraquinone-2,6-disulfonate (AQDS). In this work a molecular interaction was identified for the first time between PpcA and AQDS, constituting the first step toward the rationalization of the Gs respiratory chain.

Long-term characterization of air lime mortars with ceramic waste

Due to their exposure to environmental conditions, outer coatings composed by render and painting system are usually the first construction elements to deteriorate and require intervention. A correct conservation and rehabilitation of these materials is fundamental once they provide protection to other façade materials. It is known that old mortar renders were essentially air lime based mortars. To maintain the integrity of the whole wall-render elements, the image of the building and to avoid accelerated degradation, conservation and rehabilitation must be implemented with compatible mortars. As that, lime based mortars would be preferable. It was also common, in ancient renders, the incorporation of ceramic residues, which is, nowadays, an abundant material, especially in Central Region of Portugal. The reuse of these materials has great relevance once their landfilling causes serious environmental issues. In an attempt to combine the environmental and technical advantages of the use of ceramic waste in mortars’ production for rehabilitation purposes, a research has been developed at the University of Coimbra, in cooperation with Nova University of Lisbon, on the long term behaviour of air lime mortars with ceramic residues. In this paper the most significant up to one year results of an experimental campaign with air lime mortars with 1:3 and 1:2 volumetric proportions and ceramic residues are presented.