Investigation of the regulation mechanisms for bioplastics production from industrial residues

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Disclosing Carbon Monoxide Protection in Cerebral Ischemia: Insights into the cellular mechanisms

Dissertation presented to obtain the PhD degree in Biochemistry, Neurosciences

Identification of atmospheric pollutants control mechanisms during co-combustion of coal and non-toxic wastes

Doctoral dissertation for Ph.D. degree in Sustainable Chemistry

A system’s approach to cache hierarchy-aware decomposition of data-parallel computations

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Using cilia mutants to study left-right asymmetry in zebrafish

A thesis submitted in fulfillment of the requirements for the degree of the Masters in Molecular Genetics and Biomedicine

Optimization of breast tomosynthesis image reconstruction using parallel computing

Breast cancer is the most common cancer among women, being a major public health problem. Worldwide, X-ray mammography is the current gold-standard for medical imaging of breast cancer. However, it has associated some well-known limitations. The false-negative rates, up to 66% in symptomatic women, and the false-positive rates, up to 60%, are a continued source of concern and debate. These drawbacks prompt the development of other imaging techniques for breast cancer detection, in which Digital Breast Tomosynthesis (DBT) is included. DBT is a 3D radiographic technique that reduces the obscuring effect of tissue overlap and appears to address both issues of false-negative and false-positive rates. The 3D images in DBT are only achieved through image reconstruction methods. These methods play an important role in a clinical setting since there is a need to implement a reconstruction process that is both accurate and fast. This dissertation deals with the optimization of iterative algorithms, with parallel computing through an implementation on Graphics Processing Units (GPUs) to make the 3D reconstruction faster using Compute Unified Device Architecture (CUDA). Iterative algorithms have shown to produce the highest quality DBT images, but since they are computationally intensive, their clinical use is currently rejected. These algorithms have the potential to reduce patient dose in DBT scans. A method of integrating CUDA in Interactive Data Language (IDL) is proposed in order to accelerate the DBT image reconstructions. This method has never been attempted before for DBT. In this work the system matrix calculation, the most computationally expensive part of iterative algorithms, is accelerated. A speedup of 1.6 is achieved proving the fact that GPUs can accelerate the IDL implementation.

Coordinating development: uncovering the mechanisms that coordinate organ growth and patterning with the development of the whole body

Organisms produce correctly patterned structures across a wide range of organ and body sizes. Despite considerable work revealing the mechanisms that regulate the growth and patterning of organs, those responsible for coordinating organ development with whole-body development are still largely unknown.(...)

Analysis of the interaction of polycyclic aromatic compounds in a model organism: integration of genotoxic and histopathological effects

Due to their toxicity, especially their carcinogenic potential, polycyclic aromatic hydrocarbons (PAHs) became priority pollutants in biomonitoring programmes and environmental policy, such as the European Water Framework Directive. The model substances tested in this study, namely benzo[b]fluoranthene (B[b]F), considered potentially carcinogenic to humans and an effector carcinogenic PAH to wildlife, and phenanthrene (Phe), deemed a non-carcinogenic PAH, are common PAHs in coastal waters, owning distinct properties reflected in different, albeit overlapping, mechanisms of toxicity. Still, as for similar PAHs, their interaction effects remain largely unknown. In order to study the genotoxic effects of caused by the interaction of carcinogenic and non-carcinogenic PAHs, and their relation to histopathological alterations, juvenile sea basses, Dicentrarchus labrax, a highly ecologically- and economically-relevant marine fish, were injected with different doses (5 and 10 μg.g-1 fish ww) of the two PAHs, isolated or in mixture, and incubated for 48 h. Individuals injected with B[b]F and the PAH mixture exhibited higher clastogenic/aneugenic effects and DNA strand breakage in blood cells, determined through the erythrocytic nuclear abnormalities (ENA) and Comet assays, respectively. Also, hepatic histopathological alterations were found in all animals, especially those injected with B[b]F and the PAH mixture, relating especially to inflammation. Still, Phe also exhibited genotoxic effects in sea bass, especially in higher doses, revealing a very significant acute effect that was accordant with the Microtox test performed undergone in parallel. Overall, sea bass was sensitive to B[b]F (a higher molecular weight PAH), likely due to efficient bioactivation of the pollutant (yielding genotoxic metabolites and reactive oxygen species), when compared to Phe, the latter revealing a more significant acute effect. The results indicate no significant additive effect between the substances, under the current experimental conditions. The present study highlights the importance of understanding PAH interactions in aquatic organisms, since they are usually present in the aquatic environment in complex mixtures.

Development of novel ionic liquids based on biological molecules

Ionic Liquids (ILs) belong to a class of compounds with unusual properties: very low vapour pressure; high chemical and thermal stability and the ability to dissolve a wide range of substances. A new field in research is evaluating the possibility to use natural chiral biomolecules for the preparation of chiral ionic liquids (CILs). This important challenge in synthetic chemistry can open new avenues of research in order to avoid some problems related with the intrinsic biodegradability and toxicity associated to conventional ILs. The research work developed aimed for the synthesis of CILs, their characterization and possible applications, based on biological moieties used either as chiral cations or anions, depending on the synthetic manipulation of the derivatives. Overall, a total of 28 organic salts, including CILs were synthesized: 9 based on L-cysteine derivatives, 12 based on L-proline, 3 based on nucleosides and 4 based on nucleotides. All these new CILs were completely characterized and their chemical and physical properties were evaluated. Some CILs based on L-cysteine have been applied for discrimination processes, including resolution of racemates and as a chiral catalyst for asymmetric Aldol condensation. L-proline derived CILs were also studied as chiral catalysts for Michael reaction. In parallel, the interactions of macrocyclic oligosugars called cyclodextrins (CDs) with several ILs were studied. It was possible to improve the solubility of CDs in water and serum. Additionally, fatty acids and steroids showed an increase in water solubility when ILs-CDs systems were used. The development of efficient and selective ILs-CDs systems is indispensable to expand the range of their applications in host-guest interactions, drug delivery systems or catalytic reactions. Novel salts derived from nucleobases were used in order to enhance the fluorescence in aqueous solution. Additionally, preliminary studies regarding ethyl lactate as an alternative solvent for asymmetric organocatalysis were performed.

Unraveling intrinsic mechanisms of Nerve Regeneration

Unlike injury to the peripheral nervous system (PNS), where injured neurons can trigger a regenerative program that leads to axonal elongation and in some cases proper reinnervation, after injury to the central nervous system (CNS) neurons fail to produce the same response. The regenerative program includes the activation of several injury signals that will lead to the expression of genes associated with axonal regeneration. As a consequence, the spawned somatic response will ensure the supply of molecular components required for axonal elongation. The capacity of some neurons to trigger a regenerative response has led to investigate the mechanisms underlying neuronal regeneration. Thus, non-regenerative models (like injury to the CNS) and regenerative models (such as injury to the PNS) were used to understand the differences underlying those two responses to injury. To do so, the regenerative properties of dorsal root ganglion (DRG) neurons were addressed. This particular type of neurons possesses two branches, a central axon, that has a limited capacity to regenerate; and a peripheral axon, where regeneration can occur over long distances. In the first paradigm used to understand the neuronal regeneration mechanisms, we evaluated the activation of injury signals in a non-regenerative model. Injury signals include the positive injury signals, which are described as being enhancers of axonal regeneration by activating several transcription factors. The currently known positive injury signals are ERK, JNK and STAT3. To evaluate whether the lack of regeneration following injury to the central branch of DRG neurons was due to inactivation of these signals, activation of the transcription factors pELK-1, p-c-jun (downstream targets of ERK and JNK, respectively) and pSTAT3 were examined. Results have shown no impairment in the activation of these signals. As a consequence, we further proceed with evaluation of other candidates that could participate in axonal regeneration failure. By comparing the protein profiles that were triggered following either injury to the central branch of DRG neurons or injury to their peripheral branch, we were able to identify high levels of GSK3-β, ROCKII and HSP-40 after injury to the central branch of DRG neurons. While in vitro knockdown of HSP-40 in DRG neurons showed to be toxic for the cells, evaluation of pCRMP2 (a GSK3-β downstream target) and pMLC (a ROCKII downstream target), which are known to impair axonal regeneration, revealed high levels of both proteins following injury to the central branch when comparing with injury to their peripheral one. Altogether, these results suggest that activation of positive injury signals is not sufficient to elicit axonal regeneration; HSP-40 is likely to participate in the cell survival program; whereas GSK3-β and ROCKII activity may condition the regenerative capacity following injury to the nervous system.(...)

Exploring ionic liquids′ unique stimuli to elucidate uncharacterised cellular and molecular mechanisms in filamentous fungi

The emergence of new fungal pathogens, either of plants or animals, and the increasing number of reported cases of resistant human pathogenic strains to the available antifungal drugs reinforces the need for better understanding the biology of filamentous fungi. Conventional drugs target components of the fungal membrane or cell wall, therefore identifying novel intracellular targets, yet unique to fungi, is a global priority.(...)

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.

A public transport bus assignment problem: parallel metaheuristics assessment

Combinatorial Optimization Problems occur in a wide variety of contexts and generally are NP-hard problems. At a corporate level solving this problems is of great importance since they contribute to the optimization of operational costs. In this thesis we propose to solve the Public Transport Bus Assignment problem considering an heterogeneous fleet and line exchanges, a variant of the Multi-Depot Vehicle Scheduling Problem in which additional constraints are enforced to model a real life scenario. The number of constraints involved and the large number of variables makes impracticable solving to optimality using complete search techniques. Therefore, we explore metaheuristics, that sacrifice optimality to produce solutions in feasible time. More concretely, we focus on the development of algorithms based on a sophisticated metaheuristic, Ant-Colony Optimization (ACO), which is based on a stochastic learning mechanism. For complex problems with a considerable number of constraints, sophisticated metaheuristics may fail to produce quality solutions in a reasonable amount of time. Thus, we developed parallel shared-memory (SM) synchronous ACO algorithms, however, synchronism originates the straggler problem. Therefore, we proposed three SM asynchronous algorithms that break the original algorithm semantics and differ on the degree of concurrency allowed while manipulating the learned information. Our results show that our sequential ACO algorithms produced better solutions than a Restarts metaheuristic, the ACO algorithms were able to learn and better solutions were achieved by increasing the amount of cooperation (number of search agents). Regarding parallel algorithms, our asynchronous ACO algorithms outperformed synchronous ones in terms of speedup and solution quality, achieving speedups of 17.6x. The cooperation scheme imposed by asynchronism also achieved a better learning rate than the original one.