Measuring chromosome-end fusions in fission yeast

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

The role of electron transfer in DNA building blocks: evaluation of strand breaks and their implications

Dissertação para obtenção do Grau de Doutor em Engenharia Física

Development of an affinity pair “Tag-Receptor” for recombinant protein expression and purification

Dissertação apresentada para a obtenção do Grau de Mestre em Biotecnologia, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Development of population-specific function assessment intrument in Lebanon

RESUMO: Contexto: O funcionamento tem sido reconhecido como um dos principais indicadores de resultados para avaliar se as pessoas beneficiam das intervenções destinadas a melhorar a sua saúde mental. O funcionamento refere-se à forma como um indivíduo consegue responder às suas tarefas e solicitações, dos seus familiares e da sua comunidade, de acordo com os requisitos do local e a cultura em que vive (eg, tarefa de cozinhar e limpar para as mulheres em algumas culturas ). O funcionamento é altamente dependente da cultura - por isso, tem sido recomendado o desenvolvimento de medidas de funcionamento específicas de cada cultura. Desenvolver localmente os instrumentos de medida evita problemas de adequação, associados com a adaptação de instrumentos ocidentais. Embora os instrumentos criados desta forma sejam específicos de um meio cultural, eles são simultaneamente "transculturais", no sentido em que cada um se refere às tarefas mais importantes para a população local . Esta abordagem mostrou-se útil para investigadores e agências de ajuda (eg, ONGs) que trabalham em países não-ocidentais . Este estudo descreve o trabalho da agência International Medical Corps (IMC) na criação e validação de um questionário de funcionamento específico nas dimensões cultura e gênero, no Líbano, destinado a avaliar eventuais melhorias em pessoas que receberam intervenções de para problemas de saúde mental, a nível dos cuidados primários de saúde. Método: O instrumento foi desenvolvido usando um método que é uma alternativa à abordagem existente de adaptação de instrumentos ocidentais a outras culturas e situações; esta abordagem é rápida e exequível, tendo já demonstrado ser útil no desenvolvimento de instrumentos válidos e fidedignos. Inicialmente, foi solicitado que as pessoas identificassem, de uma lista livre, as tarefas mais importantes para cuidar de si próprias, da sua família e da sua comunidade; as tarefas identificadas foram posteriormente usadas como base para um instrumento de avaliação de funcionamento culturalmente válido. A partir daqui, foram desenvolvidos questionários específicos da comunidade em questão, posteriormente testados no terreno nas vertentes da validade (de conteúdo, facial e de constructo) e da fiabilidade (teste-reste e inter-entrevistadores). Resultados. O estudo resultou na criação e validação de um questionário de funcionamento específico de cultura e gênero capaz de medir efectivamente a capacidade de execução de tarefas importantes do quotidiano,como parte da avaliação de resultados levada a cabo por profissionais da CSP previamente treinados na identificação, suporte e encaminhamento de pessoas com problemas de saúde mental no Líbano. Conclusão. Neste trabalho descreve-se o desenvolvimento de um questionário de funcionamento específico de cultura e gênero, orientado para a avaliação de resultados, num contexto mais lato de um sistema abrangente de avaliação e monitorização de um serviço comunitário. --------------ABSTRACT: Background. Functioning has been recognized as one of the most important key outcomes to assess whether people benefit from interventions aimed to improve their mental health. Functioning refers to how well na individual can complete the tasks and demands for themselves, their family, and their community which are required by them depending on the setting and the culture they live in (e.g. task of cooking and cleaning for women in some cultures). Functioning is highly dependent on culture. Therefore, it has been recommended to develop culture-specific measures of function. Developing instruments locally avoids the problems of limited local relevance and appropriateness associate with adapting western instruments. Although each instrument created in this way is culturally bound, they are “cross cultural” in the sense that each refers to the tasks most important to local people. This approach proves useful for both researchers and aid agencies working in non-western countries. This study describes International Medical Corps’ (IMC) work in Lebanon to create and validate a culture and gender specific functioning questionnaire to assess improvements in people who received treatment interventions for mental health problems at the primary health care (PHC) level. Method. The measure was developed using a method that is an alternative to the existing approach of adapting western function instruments to other cultures and situations; an approach which has been demonstrated as rapid, feasible and which can yield valid and reliable instruments. Function was assessed by first asking local people what tasks are important to care for themselves, their family and their community using free listing, then using these tasks as the basis for a culturally valid function assessment instrument. Community specific function questionnaires based on these tasks were then created, and field-tested for validity using content, face and construct validity methods, and also field tested for reliability using inter-rater and test retest reliability methods. Results. The study resulted in the creation and validation of a culture and gender specific functioning questionnaire that would effectively measure the ability to do tasks important to daily existence, as part of assessing client level outcomes where PHC providers were trained in the identification, management and referral of people with mental health problems in Lebanon. Conclusion. The paper describes a successful pilot for developing culture and gender specific functioning questionnaires that evaluate client level outcomes as part of a more comprehensive system for monitoring and evaluation of community based case management supports and services.

Humor and the framing of the public sphere and public opinion in Portugal (1797-1834)

In his Answer to the Question: What is Enlightenment (1784), Kant puts forward his belief that the vocation to think freely, which humankind is endowed with, is bound to make sure that “the public use of reason” will at last act “even on the fundamental principles of government and the state [will] find it agreeable to treat man – who is now more than a machine – in accord with his dignity”. The critical reference to La Mettrie (1747), by opposing the machine to human dignity, will echo, in the dawn of the 20th century, in Bergson’s attempt to explain humor. Besides being exclusive to humans, humor is also a social phenomenon. Freud (1905) assures that pleasure originated by humor is collective, it results from a “social process”: jokes need an audience, a “third party”, in order to work and have fun. Assuming humor as a social and cultural phenomenon, this paper intends to sustain that it played a role in the framing of the public sphere and of public opinion in Portugal during the transition from Absolute Monarchy to Liberalism. The search for the conditions which made possible the critical exercise of sociability is at the root of the creation of the public sphere in the sense developed by Habermas (1962), whose perspective, however, has been questioned by those who point 2 out the alleged idealism of the concept – as opposed, for example, to Bakhtin (1970), whose work stresses diversity and pluralism. This notwithstanding, the concept of public sphere is crucial to the building of public opinion, which is, in turn, indissoluble from the principle of publicity, as demonstrated by Bobbio (1985). This paper discusses the historical evolution of the concept of public opinion from Ancient Greece doxa, through Machiavelli’s “humors” (1532), the origin of the expression in Montaigne (1580) and the contributions of Hobbes (1651), Locke (1690), Swift (1729), Rousseau (1762) or Hume (1777), up to the reflection of Lippman (1922) and Bourdieu’s critique (1984). It maintains that humor, as it appears in Portuguese printed periodicals from 1797 (when Almocreve de Petas was published for the first time) to the end of the civil war (1834) – especially in those edited by José Daniel Rodrigues da Costa but also in O Piolho Viajante, by António Manuel Policarpo da Silva, or in the ones written by José Agostinho de Macedo, as well as in a political “elite minded” periodical such as Correio Braziliense –, contributed to the framing of the public sphere and of public opinion in Portugal.

Deciphering the genome of Desulfovibrio gigas: the role of the hydrogenases

The work presented in this thesis describes the functional characterization of hydrogenases in the overall energy metabolism of the sulfate reducing bacterium Desulfovibrio gigas. With the complete annotation of the D. gigas genome, we were able to verify that only the two previously described hydrogenases are present in this organism, the periplasmic [NiFe] HynAB and the cytoplasmic membrane-bound [NiFe] Ech.(...)

Development of an integrative approach for the characterization of ecological risk on marine transition ecosystems: the Sado Estuary as a case study

Estuaries and other transitional waters are complex ecosystems critically important as nursery and shelter areas for organisms. Also, humans depend on estuaries for multiple socio-economical activities such as urbanism, tourism, heavy industry, (taking advantage of shipping), fisheries and aquaculture, the development of which led to strong historical pressures, with emphasis on pollution. The degradation of estuarine environmental quality implies ecologic, economic and social prejudice, hence the importance of evaluating environmental quality through the identification of stressors and impacts. The Sado Estuary (SW Portugal) holds the characteristics of industrialized estuaries, which results in multiple adverse impacts. Still, it has recently been considered moderately contaminated. In fact, many studies were conducted in the past few years, albeit scattered due to the absence of true biomonitoring programmes. As such, there is a need to integrate the information, in order to obtain a holistic perspective of the area able to assist management and decision-making. As such, a geographical information system (GIS) was created based on sediment contamination and biomarker data collected from a decade-long time-series of publications. Four impacted and a reference areas were identified, characterized by distinct sediment contamination patterns related to different hot spots and diffuse sources of toxicants. The potential risk of sediment-bound toxicants was determined by contrasting the levels of pollutants with available sediment quality guidelines, followed by their integration through the Sediment Quality guideline Quotient (SQG-Q). The SQG-Q estimates per toxicant or class was then subjected to georreferencing and statistical analyses between the five distinct areas and seasons. Biomarker responses were integrated through the Biomarkers Consistency Indice and georreferenced as well through GIS. Overall, in spite of the multiple biological traits surveyed, the biomarker data (from several organisms) are accordant with sediment contamination. The most impacted areas were the shipyard area and adjacent industrial belt, followed by urban and agricultural grounds. It is evident that the estuary, although globally moderately impacted, is very heterogeneous and affected by a cocktail of contaminants, especially metals and polycyclic aromatic hydrocarbon. Although elements (like copper, zinc and even arsenic) may originate from the geology of the hydrographic basin of the Sado River, the majority of the remaining contaminants results from human activities. The present work revealed that the estuary should be divided into distinct biogeographic units, in order to implement effective measures to safeguard environmental quality.

From Consciousness to Knowledge – The Explanatory Power of Revelation

Epistemology in philosophy of mind is a difficult endeavor. Those who believe that our phenomenal life is different from other domains suggest that self-knowledge about phenomenal properties is certain and therefore privileged. Usually, this so called privileged access is explained by the idea that we have direct access to our phenomenal life. This means, in contrast to perceptual knowledge, self-knowledge is non-inferential. It is widely believed that, this kind of directness involves two different senses: an epistemic sense and a metaphysical sense. Proponents of this view often claim that this is due to the fact that we are acquainted with our current experiences. The acquaintance thesis, therefore, is the backbone in justifying privileged access. Unfortunately the whole approach has a profound flaw. For the thesis to work, acquaintance has to be a genuine explanation. Since it is usually assumed that any knowledge relation between judgments and the corresponding objects are merely causal and contingent (e.g. in perception), the proponent of the privileged access view needs to show that acquaintance can do the job. In this thesis, however, I claim that the latter cannot be done. Based on considerations introduced by Levine, I conclude that this approach involves either the introduction of ontologically independent properties or a rather obscure knowledge relation. A proper explanation, however, cannot employ either of the two options. The acquaintance thesis is, therefore, bound to fail. Since the privileged access intuition seems to be vital to epistemology within the philosophy of mind, I will explore alternative justifications. After discussing a number of options, I will focus on the so called revelation thesis. This approach states that by simply having an experience with phenomenal properties, one is in the position to know the essence of those phenomenal properties. I will argue that, after finding a solution for the controversial essence claim, this thesis is a successful replacement explanation which maintains all the virtues of the acquaintance account without necessarily introducing ontologically independent properties or an obscure knowledge relation. The overall solution consists in qualifying the essence claim in the relevant sense, leaving us with an appropriate ontology for phenomenal properties. On the one hand, this avoids employing mysterious independent properties, since this ontological view is physicalist in nature. On the other hand, this approach has the right kind of structure to explain privileged self-knowledge of our phenomenal life. My final conclusion consists in the claim that the privileged access intuition is in fact veridical. It cannot, however, be justified by the popular acquaintance approach, but rather, is explainable by the controversial revelation thesis.

The influence of carbohydrates in the interaction of Paracoccidioides brasiliensis with CCL-6 cells in vitro

INTRODUCTION: Little is known about the early events in the interaction between Paracoccidioides brasiliensis and its host. To understand the effect of carbohydrates in the interaction between the fungus and epithelial cell in culture, we analyzed the influence of different carbohydrate solutions on the adhesion of P. brasiliensis yeast cells to CCL-6 cells in culture. METHODS: Fungal cells were cultivated with the epithelial cell line, and different concentrations of D-fucose, N-acetyl-glucosamine, D-mannose, D-glucosamine, D-galactosamine, sorbitol and fructose were added at the beginning of the experiment. Six hours after the treatment, the cells were fixed and observed by light microscopy. The number of P. brasiliensis cells that were adhered to the CCL-6 monolayer was estimated. RESULTS: The number of adhesion events was diminished following treatments with D-fucose, N-acetyl-glucosamine, D-mannose, D-glucosamine and D-galactosamine as compared to the untreated controls. Sorbitol and fructose-treated cells had the same adhesion behavior as the observed in the control. P. brasiliensis propagules were treated with fluorescent lectins. The FITC-labeled lectins WGA and Con-A bound to P. brasiliensis yeast cells, while SBA and PNA did not. CONCLUSIONS: The perceptual of adhesion between P. brasiliensis and CCL-6 cells decreased with the use of D-mannose, N-acetyl-glucosamine and D-glucosamine. The assay using FITC-labeled lectins suggests the presence of N-acetyl-glucosamine, α-mannose and α-glucose on the P. brasiliensis cell surface. An enhanced knowledge of the mediators of adhesion on P. brasiliensis could be useful in the future for the development of more efficient and less harmful methods for disease treatment and control.

Effects of quantitative easing on the USA economy: A test for policy effectiveness

The catastrophic disruption in the USA financial system in the wake of the financial crisis prompted the Federal Reserve to launch a Quantitative Easing (QE) programme in late 2008. In line with Pesaran and Smith (2014), I use a policy effectiveness test to assess whether this massive asset purchase programme was effective in stimulating the economic activity in the USA. Specifically, I employ an Autoregressive Distributed Lag Model (ARDL), in order to obtain a counterfactual for the USA real GDP growth rate. Using data from 1983Q1 to 2009Q4, the results show that the beneficial effects of QE appear to be weak and rather short-lived. The null hypothesis of policy ineffectiveness is not rejected, which suggests that QE did not have a meaningful impact on output growth.

Electron driven reactions in sulphur containing biological prototypes

The interaction of ionising radiation with living tissues may direct or indirectly generate several secondary species with relevant genotoxic potential. Due to recent findings that electrons with energies below the ionisation threshold can effectively damage DNA, radiation-induced damage to biological systems has increasingly come under scrutiny. The exact physico-chemical processes that occur in the first stages of electron induced damage remain to be explained. However, it is also known that free electrons have a short lifetime in the physiological medium. Hence, electron transfer processes studies represent an alternative approach through which the role of "bound" electrons as a source of damage to biological tissues can be further explored. The thesis work consists of studying dissociative electron attachment (DEA) and electron transfer to taurine and thiaproline. DEA measurements were executed in Siedlce University with Prof. Janina Kopyra under COST action MP1002 (Nanoscale insights in ion beam cancer therapy). The electron transfer experiments were conducted in a crossed atom(potassium)-molecule beam arrangement. In these studies the anionic fragmentation patterns were obtained. The results of both mechanisms are shown to be significantly different, unveiling that the damaging potential of secondary electrons can be underestimated. In addition, sulphur atoms appear to strongly influence the dissociation process, demonstrating that certain reactions can be controlled by substitution of sulphur at specific molecular sites.

Construção de uma responsabilidade europeia além-fronteiras

The suppression of internal border controls has led the European Union to establish a mechanism for determining the Member State responsible for examining each asylum application, with the main intention of deterring asylum seekers from lodging multiple applications and guaranteeing that it will be assessed by one of the States – the Dublin System. Even though it holds on a variety of criteria, the most commonly used is the country of first entrance in the EU. The growing migrating flows coming mainly from Northern Africa have thus resulted in an incommensurable burden over the border countries. Gradually, countries like Greece, Bulgaria and Italy have lost capability of providing adequate relief to all asylum seekers and the records of fundamental rights violations related to the provision of housing and basic needs or inhuman detention conditions started piling up. To prevent asylum seekers who had already displaced themselves to other Member States from being transferred back to countries where their human dignity is questionable, the European Court of Human Rights and the Court of Justice have developed a solid jurisprudence determining that when there is a risk of serious breach of fundamental rights all transfers to that country must halt, especially when it is identified with systemic deficiencies in the asylum system and procedures. This reflexion will go through the jurisprudence that influenced very recent legislative amendments, in order to identify which elements form part of the obligation not to transfer under the Dublin System. At last, we will critically analyze the new rising obligation, that has clearly proven insufficient in light of the international fundamental rights framework that the Member States and the EU are bound to respect, proposing substantial amendments with a view to reach a future marked by high solidarity and global responsibility from the European Union.

O âmbito de aplicação material da legislação de proteção de dados pessoais e o tratamento de imagem por pessoa singular

Images have gained a never before seen importance. Technological changes have given the Information Society extraordinary means to capture, treat and transmit images, wheter your own or those of others, with or without a commercial purpose, with no boundaries of time or country, without “any kind of eraser”. From the several different ways natural persons may engage in image processing with no commercial purpose, the cases of sharing pictures through social networks and video surveillance assume particular relevance. Consequently there are growing legitimate concerns with the protection of one's image, since its processing may sometimes generate situations of privacy invasion or put at risk other fundamental rights. With this in mind, the present thesis arises from the question: what are the existent legal instruments in Portuguese Law that enable citizens to protect themselves from the abusive usage of their own pictures, whether because that image have been captured by a smartphone or some video surveillance camera, whether because it was massively shared through a blog or some social network? There is no question the one's right to not having his or her image used in an abusive way is protected by the Portuguese constitution, through the article 26th CRP, as well as personally right, under the article 79th of the Civil Code, and finally through criminal law, articles 192nd and 193rd of the Criminal Code. The question arises in the personal data protection context, considering that one's picture, given certain conditions, is personal data. Both the Directive 95/46/CE dated from 1995 as well as the LPD from 1998 are applicable to the processing of personal data, but both exclude situations of natural persons doing so in the pursuit of activities strictly personal or family-related. These laws demand complex procedures to natural persons, such as the preemptive formal authorisation request to the Data Protection National Commission. Failing to do so a natural person may result in the application of fines as high as €2.500,00 or even criminal charges. Consequently, the present thesis aims to study if the image processing with no commercial purposes by a natural person in the context of social networks or through video surveillance belongs to the domain of the existent personal data protection law. To that effect, it was made general considerations regarding the concept of video surveillance, what is its regimen, in a way that it may be distinguishable from Steve Mann's definition of sousveillance, and what are the associated obligations in order to better understand the concept's essence. The application of the existent laws on personal data protection to images processing by natural persons has been analysed taking into account the Directive 95/46/CE, the LPD and the General Regulation. From this analysis it is concluded that the regimen from 1995 to 1998 is out of touch with reality creating an absence of legal shielding in the personal data protection law, a flaw that doesn't exist because compensated by the right to image as a right to personality, that anyway reveals the inability of the Portuguese legislator to face the new technological challenges. It is urgent to legislate. A contrary interpretation will evidence the unconstitutionality of several rules on the LPD due to the obligations natural persons are bound to that violate the right to the freedom of speech and information, which would be inadequate and disproportionate. Considering the recently approved General Regulation and in the case it becomes the final version, the use for natural person of video surveillance of private spaces, Google Glass (in public and private places) and other similar gadgets used to recreational purposes, as well as social networks are subject to its regulation only if the images are shared without limits or existing commercial purposes. Video surveillance of public spaces in all situations is subject to General Regulation provisions.

A maritimidade portuguesa : a extensão da plataforma continental

As potencialidades da plataforma continental estendida são enormes e variadas, desde as que podem ser obtidas através de sectores tradicionais – como portos e marinas ou turismo náutico – até as que advirão de novos sectores como a exploração dos fundos do mar ou a energia das ondas, entre outras. Com efeito, devido ao alargamento resultante das negociações nas Nações Unidas, é praticamente garantido que Portugal passe a controlar um espaço marítimo, acrescido de 2.1 milhões de km2, isto é, vinte vezes a extensão da sua superfície terrestre. A maritimidade de Portugal constitui um traço profundamente marcado na sua história, bem como nas suas tradicionais práticas económicas, sociais e simbólicas. Na verdade, os últimos anos testemunharam a criação de um amplo consenso quanto ao papel determinante que o desenvolvimento costeiro, a superfície e o comprimento dos limites do “Mar Português” terá no futuro do país. Da articulação entre o Território Nacional, o Oceano Atlântico e o Continente Europeu, associada à confluência das vias de comunicação marítimas que ligam a Europa à América do Norte e do Sul configurar-e-ão os aspectos essenciais do designado “Espaço Estratégico de Interesse Nacional Permanente”. A área geográfica prioritária para o desenvolvimento das acções militares de Defesa Nacional e dos interesses vitais permanentes inclui assim – para além do Território Nacional – o Espaço Interterritorial, o Mar Territorial (MT), o espaço aéreo sob responsabilidade nacional e a Zona Económica Exclusiva (ZEE). O País é titular de soberania no território continental e nos arquipélagos da Madeira dos Açores, para além de estar comprometido com alguns Estados da CPLP, que têm no Atlântico Sul uma importante e poderosa presença. Pela geografia e pela definição dos interesses dos Estados e dos grandes espaços em que estão incluídos, Portugal está na articulação da segurança do Atlântico Norte com a segurança do Atlântico Sul. Esta realidade acarreta novos desafios para a Defesa Nacional, assumindo como preocupações acrescidas o terrorismo, o tráfico e a pirataria marítimas, entre outras.