Production of recombinant protein hLIF in static and dynamic systems of animal cell culture

Thesis for the Degree of Master of Science in Biotechnology Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Anthropocentric-based robotic and autonomous systems: assessment for new organisational options

Text based on the paper presented at the Conference "Autonomous systems: inter-relations of technical and societal issues" held at Monte de Caparica (Portugal), Universidade Nova de Lisboa, November, 5th and 6th 2009 and organized by IET-Research Centre on Enterprise and Work Innovation

Corporate networks in Poland: Interlocking directorates and business systems

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

How reporting and controlling systems can be effectively designed to support the decision-making process: The case of a Software SME

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Printable organic and inorganic materials for flexible electrochemical devices

Portuguese Science Foundation - project Electra PTDC/CTM/099124/2008 and the PhD grant SFRH/BD/45224. financial support: Professor E. Fortunato’s ERC 2008 Advanced Grant (INVISIBLE contract number 228144), “APPLE” FP7-NMP-2010-SME/262782-2 and “SMARTEC” FP7-ICT-2009.3.9/258203

How to improve urban mobility in Lisbon: intermodality and information and ticketing systems

Urban mobility is one of the main challenges facing urban areas due to the growing population and to traffic congestion, resulting in environmental pressures. The pathway to urban sustainable mobility involves strengthening of intermodal mobility. The integrated use of different transport modes is getting more and more important and intermodality has been mentioned as a way for public transport compete with private cars. The aim of the current dissertation is to define a set of strategies to improve urban mobility in Lisbon and by consequence reduce the environmental impacts of transports. In order to do that several intermodal practices over Europe were analysed and the transport systems of Brussels and Lisbon were studied and compared, giving special attention to intermodal systems. In the case study was gathered data from both cities in the field, by using and observing the different transport modes, and two surveys were done to the cities users. As concluded by the study, Brussels and Lisbon present significant differences. In Brussels the measures to promote intermodality are evident, while in Lisbon a lot still needs to be done. It also made clear the necessity for improvements in Lisbon’s public transports to a more intermodal passenger transport system, through integration of different transport modes and better information and ticketing system. Some of the points requiring developments are: interchanges’ waiting areas; integration of bicycle in public transport; information about correspondences with other transport modes; real-time information to passengers pre-trip and on-trip, especially in buses and trams. After the identification of the best practices in Brussels and the weaknesses in Lisbon the possibility of applying some of the practices in Brussels to Lisbon was evaluated. Brussels demonstrated to be a good example of intermodality and for that reason some of the recommendations to improve intermodal mobility in Lisbon can follow the practices in place in Brussels.

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Food waste valorization through the production of polyhydroxyalkanoates by mixed microbial cultures

Dissertação para obtenção do Grau de Mestre em Engenharia Química e Bioquímica

The role of s-nitrosothiols and rho-kinase 1 in glucose and lipid metabolism

RESUMO: Na sociedade contemporânea a diabetes tipo 2 e a obesidade estão a aumentar exponencialmente, representando um grave problema de saúde pública. De acordo com a IDF “A diabetes e a obesidade são o principal problema de saúde pública do século XXI’. Para além destas duas patologias, a prevalência de esteatose hepática não-alcoólica (NAFLD), entre a população obesa e diabética, é de cerca de 90%. O aumento da obesidade, diabetes e NAFLD tem uma forte correlação com o aumento do consumo de gorduras e açúcares, acompanhado de um decréscimo acentuado da actividade física. A obesidade, diabetes e NAFLD tem sido escrupolosamente investigada mas as terapêuticas disponíveis continuam a ser muito limitadas. Tendo em conta o número crescente e alarmante de obesos e diabéticos o conhecimento detalhado da patofisiologia da obesidade, diabetes e NAFLD, tendo em vista a necessidade extrema de desenvolvimento de novas estratégias terapêuticas, é da mais elevada urgência. O fígado é reconhecido como um orgão primordial no controlo da homeostase. No estado pós-prandial, o fígado converte a glucose em glicogénio e lípidos. Em contraste, no estado de jejum, o fígado promove a produção de glucose. Sistemas neuronais e hormonais, bem como o estado metabólico do fígado, controlam de forma muito precisa a alternância entre os diferentes substratos metabólicos, dependente do estado prandial. A insulina tem um papel central no controlo do metabolismo energético no fígado; se, por um lado, inibe a produção hepática de glucose e corpos cetónicos, por outro, promove a glicólise e a lipogénese. O metabolismo energético no fígado é também regulado por vários factores de transcrição e co-reguladores que, por sua vez, são regulados pela insulina, glucagina e outras hormonas metabólicas. Em conjunto, todos estes factores e reguladores vão controlar de forma muito estreita a gluconeogénese, a β-oxidação e a lipogénese, no fígado. Para além dos já conhecidos reguladores do metabolismo hepático, novas moléculas têm sido estudadas como tendo um papel fundamental na regulação do metabolismo energético no fígado. Qualquer desequilíbrio no metabolismo hepático vai contribuir para a insulino-resistência, NAFLD e diabetes tipo 2. O principal objectivo do trabalho de investigação aqui apresentado é o contributo para o estudo detalhado da patogénese da diabetes e obesidade, num contexto de dietas ricas em açúcares e gorduras, e com a perspectiva de explorar novas estratégias terapêuticas. Os objectivos específicos deste trabalho eram: primeiro, determinar se o tratamento com glutationo (GSH) e óxido nítrico (NO) era suficiente para melhorar a insulino-resistência associada ao elevado consumo de sacarose; segundo, determinar o papel da Rho-kinase 1 (ROCK1) na regulação do metabolismo hepático da glucose e dos lípidos; e terceiro, estudar o efeito do metilsulfonilmetano (MSM) em doenças metabólicas associadas à obesidade. Na primeira parte deste trabalho de investigação foram utilizados ratos Wistar machos sujeitos a uma dieta rica em sacarose (HS). Tal como esperado, estes animais apresentavam insulino-resistência e hiperinsulinémia. A dieta HS levou ao aumento dos níveis hepáticos de NO e ao decréscimo dos níveis de GSH no fígado. Em jejum, a administração intraportal de GSH e NO, a animais saudáveis promoveu um aumento significativo da sensibilidade à insulina. Também nestes animais, a administração intravenosa de S-nitrosotióis, compostos orgânicos que contém um grupo nitroso acoplado a um átomo de enxofre de um tiol, promoveu o aumento significativo da sensibilidade à insulina. Pelo contrário, em animais sujeitos à dieta HS, as doses padrão de GSH + NO e de S-nitrosotióis não conseguiram promover o aumento da sensibilidade à insulina. No entanto, ao aumentar a dose de S-nitrosotióis administrados por via intravenosa, foi possível observar o aumento da sensibilidade à insulina dependente da dose, indicando um possível papel dos S-nitrosotióis como sensibilizadores de insulina. O estudo detalhado do papel dos S-nitrosotióis na via de sinalização da insulina revelou que há um aumento da fosforilação do receptor da insulina (IR) e da proteína cinase B (Akt), sugerindo um efeito dos S-nitrosotióis nesta via de sinalização. Os resultados apresentados nesta primeira parte sugerem que os S-nitrosotióis promovem a correcta acção da insulina, podendo vir a ser importantes alvos terapêuticos. Na segunda parte deste trabalho de investigação utilizámos murganhos, com uma delecção específica da ROCK1 no fígado, e sujeitos a uma dieta rica em lípidos (HFD). Foi possível concluir que a ausência da ROCK1 no fígado previne a obesidade, melhora a sensibilidade à insulina e protege contra a esteatose hepática. A ausência de ROCK1 no fígado levou a um decréscimo significativo da expressão génica de genes associados à lipogénese, com uma diminuição acentuada do fluxo metabólico associado a esta via. Pelo contrário, a sobreexpressão de ROCK1, exclusivamente no fígado, promove a insulino-resistência e a esteatose hepática no contexto de obesidade induzida pela dieta. Para além disto, a delecção da ROCK1 no fígado de animais obesos e diabéticos, os murganhos deficientes em leptina, corroborou os dados obtidos no primeiro modelo animal, com a franca melhoria da hiperglicémia, hiperinsulinémia e esteatose hepática. Os dados que compõem esta parte do trabalho de investigação sugerem que a ROCK1 tem um papel crucial na regulação do metabolismo lipídico. Na terceira e última parte deste trabalho de investigação foi investigado o efeito do composto metilsulfunilmetano (MSM), um composto organosulfúrico naturalmente presente em plantas e utilizado também como suplemento dietético, em murganhos obesos e insulino-resistentes, por exposição a uma dieta rica em lípidos (DIO). O tratamento com MSM melhorou a insulino-resistência e protegeu contra a esteatose hepática. O conteúdo hepático em triglicéridos e colesterol também diminuíu de forma significativa nos animais DIO sujeitos ao tratamento com MSM, bem como a expressão génica associada à lipogénese. Para além disto, o tratamento com MSM levou a uma diminuição da expressão génica associada à inflamação. De realçar que o tratamento com MSM levou a uma melhoria do perfil hematopoiético destes animais, tanto na medula óssea como no sangue. Para comprovar o efeito benéfico do MSM na obesidade e insulino-resistência utilizámos murganhos deficientes no receptor da leptina, e por isso obesos e diabéticos, tendo observado um perfil semelhante ao obtido para murganhos sujeitos a uma dieta rica em lípidos e tratados com MSM. Concluímos, através dos dados recolhidos, que o MSM como suplemento pode ter efeitos benéficos na hiperinsulinémia, insulino-resistência e inflamação que caracterizam a diabetes tipo 2. Em resumo, os dados obtidos neste trabalho de investigação mostram que os S-nitrosotióis podem ter um papel importante como sensibilizadores da insulina, promovendo um aumento da sensibilidade à insulina num contexto de dietas ricas em sacarose. Para além disto, estudos in vitro, sugerem que os S-nitrosotióis regulam, especificamente, a via de sinalização da insulina. Este trabalho teve também como objectivo o estudo da ROCK1 como regulador do metabolismo da glucose e dos lípidos no fígado. Através do estudo de animais com uma delecção ou uma sobreexpressão da ROCK1 no fígado mostrou-se que esta tem um papel crucial na patogénese da obesidade e diabetes tipo 2, especificamente através do controlo da lipogénese de novo. Finalmente, foi também objectivo deste trabalho, explorar o efeito do MSM em animais DIO e deficientes em leptina. O tratamento com MSM protege de forma evidente contra a obesidade e insulino-resistência, com especial enfâse para a capacidade que esta molécula demonstrou ter na protecção contra a inflamação. Em conjunto os vários estudos aqui apresentados mostram que tanto os S-nitrosotióis como a ROCK1 têm um papel na patogénese da obesidade e diabetes tipo 2 e que a utilização de MSM como suplemento às terapêuticas convencionais pode ter um papel no tratamentos de doenças metabólicas.-------------------------------ABSTRACT: In modern western societies type 2 diabetes and obesity are increasing exponentially, representing a somber public concern. According to the International Diabetes Federation (IDF) ‘Diabetes and Obesity are the biggest public health challenges of the 21st century’. Aside from these the prevalence of nonalcoholic fatty liver disease (NAFLD), among the diabetic and obese population, is as high as 90%. It is now well established that the increase in obesity, diabetes and NAFLD strongly correlates with an increase in fat and sugar intake in our diet, alongside physical inactivity. The pathogenesis of obesity, diabetes and NAFLD has been thoroughly studied but the treatment options available are still narrow. Considering the alarming number in the obese and diabetic population the complete understanding of the pathogenesis, keeping in mind that new therapeutic strategies need to be attained, is of the highest urgency. The liver has been well established as a fundamental organ in regulating whole-body homeostasis. In the fed state the liver converts the glucose into glycogen and lipids. Conversely, in the fasted state, glucose will be produced in the liver. Neuronal and hormonal systems, as well as the hepatic metabolic states, tightly control the fast to fed switch in metabolic fuels. Insulin has a central role in controlling hepatic energy metabolism, by suppressing glucose production and ketogenesis, while stimulating glycolysis and lipogenesis. Liver energy metabolism is also regulated by various transcription factors and coregulators that are, in turn, regulated by insulin, glucagon and other metabolic hormones. Together, these regulators will act to control gluconeogenesis, β-oxidation and lipogenesis in the liver. Aside from the well-established regulators of liver energy metabolism new molecules are being studied has having a role in regulating hepatic metabolism. Any imbalance in the liver energy metabolism is a major contributor to insulin resistance, NAFLD and type 2 diabetes. The overall goal of this research work was to contribute to the understanding of the pathogenesis of diabetes and obesity, on a setting of high-sucrose and high-fat diets, and to explore potential therapeutic options. The specific aims were: first, to determine if treatment with glutathione (GSH) and nitric oxide (NO) was sufficient to ameliorate insulin resistance induced by high-sucrose feeding; second, to determine the physiological role of rho-kinase 1 (ROCK1) in regulating hepatic and lipid metabolism; and third, to study the effect of methylsulfonylmethane (MSM) on obesity-linked metabolic disorders. In the first part of this research work we used male Wistar rats fed a high-sucrose (HS) diet. As expected, rats fed a HS diet were insulin resistant and hyperinsulinemic. HS feeding increased hepatic levels of NO, while decreasing GSH. In fasted healthy animals administration of both GSH and NO, to the liver, was able to increase insulin sensitivity. Intravenous administration of S-nitrosothiols, organic compounds containing a nitroso group attached to the sulfur atom of a thiol, in fasted control animals also increased insulin sensitivity. Under HS feeding the standard doses of GSH + NO and S-nitrosothiols were unable to promote an increase in insulin sensitivity. However, the intravenous administration of increasing concentrations of S-nitrosothiols was able to restore insulin sensitivity, suggesting that S-nitrosothiols have an insulin sensitizing effect. Investigation of the effect of S-nitrosothiols on the insulin signaling pathway showed increased phosphorylation of the insulin receptor (IR) and protein kinase B (Akt), suggesting that S-nitrosothiols may have an effect on the insulin signaling pathway. Together, these data showed that S-nitrosothiols promote normal insulin action, suggesting that they may act as potential pharmacological tools. In the second part of this research work we used liver-specific ROCK1 knockout mice fed a high-fat (HF) diet. Liver-specific deletion of ROCK1 prevented obesity, improved insulin sensitivity and protected against hepatic steatosis. Deficiency of ROCK1 in the liver caused a significant decrease in the gene expression of lipogenesis associated gene, ultimately leading to decreased lipogenesis. Contrariwise, ROCK1 overexpression in the liver promoted insulin resistance and hepatic steatosis in diet-induced obesity. Furthermore, liver-specific deletion of ROCK1 in obese and diabetic mice, the leptin-deficient mice, improved the typical hyperglycemia, hyperinsulinemia and liver steatosis. Together, these data identify ROCK1 as a crucial regulator of lipid metabolism. In the third and final part of this research work we investigated the effect of MSM, an organosulfur compound naturally found in plants and used as a dietary supplement, on diet-induced obese (DIO) and insulin resistant mice. MSM treatment ameliorated insulin resistance and protected against hepatosteatosis. Hepatic content in triglycerides and cholesterol was significantly decreased by MSM treatment, as well as lipogenesis associated gene expression. Furthermore, MSM treated mice had decreased inflammation associated gene expression in the liver. Importantly, FACS analysis showed that MSM treatment rescued the inflammatory hematopoietic phenotype of DIO mice in the bone marrow and the peripheral blood. Moreover, MSM treatment of the obese and diabetic mice, the leptin-deficient mice, resulted in similar effects as the ones observed for DIO mice. Collectively, these data suggest that MSM supplementation has a beneficial effect on hyperinsulinemia, insulin resistance and inflammation, which are often found in type 2 diabetes. In conclusion, this research work showed that S-nitrosothiols may play a role as insulin sensitizers, restoring insulin sensitivity in a setting of high-sucrose induced insulin resistance. Furthermore, in vitro studies suggest that S-nitrosothiols specifically regulate the insulin signaling pathway. This research work also investigated the role of hepatic ROCK1 in regulation of glucose and lipid metabolism. Using liver-specific ROCK 1 knockout and ROCK1 overexpressing mice it was shown that ROCK1 plays a role in the pathogenesis of obesity and type 2 diabetes, specifically through regulation of the de novo lipogenesis pathway. Finally, this research work aimed to explore the effect of MSM in DIO and leptin receptor-deficient mice. MSM strongly protects against obesity and insulin resistance, moreover showed a robust ability to decrease inflammation. Together, the individual studies that compose this dissertation showed that S-nitrosothiols and ROCK1 play a role in the pathogenesis of obesity and type 2 diabetes and that MSM supplementation may have a role in the treatment of metabolic disorders.