The past five years has seen the discovery of a wealth of genetics variants associated with an incredible range of diseases and traits that have been identified in genome- wide association studies (GWAS). These GWAS have typically been performed in in- dividuals of European descent, prompting a call for such studies to be conducted over a more diverse range of populations. These include groups such as African Ameri- cans and Latinos as they are recognised as bearing a disproportionately large burden of disease in the U.S. population. The variation in ancestry among such groups must be correctly accounted for in association studies to avoid spurious hits arising due to differences in ancestry between cases and controls. Such ancestral variation is not all problematic as it may also be exploited to uncover loci associated with disease in an approach known as admixture mapping, or to estimate recombination rates in admixed individuals. Many models have been proposed to infer genetic ancestry and they differ in their accuracy, the type of data they employ, their computational efficiency, and whether or not they can handle multi-way admixture. Despite the number of existing models, there is an unfulfilled requirement for a model that performs well even when the ancestral populations are closely related, is extendible to multi-way admixture scenarios, and can handle whole- genome data while remaining computationally efficient. In this thesis we present a novel method of ancestry estimation named MULTIMIX that satisfies these criteria. The underlying model we propose uses a multivariate nor- mal to approximate the distribution of a haplotype at a window of contiguous SNPs given the ancestral origin of that part of the genome. The observed allele types and the ancestry states that we aim to infer are incorporated in to a hidden Markov model to capture the correlations in ancestry that we expect to exist between neighbouring sites. We show via simulation studies that its performance on two-way and three-way admixture is competitive with state-of-the-art methods, and apply it to several real admixed samples of the International HapMap Project and the 1000 Genomes Project.

Hypoxia-inducible factor (HIF) is the master regulator of genes involved in adaptation to hypoxia. The stability and transcriptional activity of HIF are regulated by post-translational hydroxylations: prolyl hydroxylation by the prolyl hydroxylase domain-containing enzymes PHD1 – 3 earmarks HIF for proteasomal degradation, whilst asparaginyl hydroxylation by factor inhibiting HIF (FIH) blocks the interaction of HIF with the transcriptional coactivators p300/CBP. The PHDs and FIH hydroxylate HIF directly from molecular oxygen and are therefore oxygen sensors. Recent literature shows that FIH also hydroxylates a number of proteins containing an ankyrin-repeat domain (ARD). Together with reports suggesting that the PHDs are involved in HIF-independent pathways, this suggests that the HIF hydroxylases may have a wide range of non-HIF targets. This thesis describes my investigations into novel substrates of the HIF hydroxylases. This work has characterized the FIH-dependent hydroxylation of the ARD-containing protein Notch1, and defined a consensus sequence for hydroxylation that corresponds to the ankyrin-repeat consensus. Using this consensus potential sites of hydroxylation in a novel ARD FIH substrate, myosin phosphatase targeting subunit 1 (MYPT1), were identified then subsequently confirmed and characterized. Notch1 competes with HIF for FIH hydroxylation. My experiments show that this occurs because Notch1 is a more efficient substrate than HIF, whilst studies on MYPT1 and other proteins indicate that competitive inhibition of FIH may be a general property of ARDs. There are more than 300 ARD proteins in the human genome, and this thesis demonstrates that FIH may hydroxylate a significant percentage of these. In addition to the analysis of ARD hydroxylation a proteomic investigation into novel PHD3 substrates has identified two candidate proteins, suggesting that the PHDs may also have multiple targets. These results have important implications for oxygen sensing, and indicate that post-translational hydroxylation is likely to be a widespread modification in cell biology.

Failure to process prelamin A, by the enzyme ZMPSTE24, leads to the build up of farnesylated prelamin A, which has been implicated in causing the symptoms experienced in laminopathies and HIV therapy. A common feature to these conditions is the development of an irregular nuclear boundary, often including deep invaginations that form a nucleoplasmic reticulum. Additionally, dysregulated lipid synthesis is frequently associated with improper lamin A processing and I set out to address the molecular mechanisms behind these two features that could explain lipoatrophy experienced in patients. By using siRNA targeted against Zmpste24 I utilised an array of biochemical, molecular and imaging techniques to uncover a mechanism that leads to the production of a nucleoplasmic reticulum that was dependent on both the farnesylated tail of prelamin A and the phosphatidylcholine synthesising enzyme CCTα. The morphology of this structure consisted of an invagination of both the inner and outer nuclear membranes with a cytoplasmic core or just invagination of the inner nuclear membrane. Serial section dual axis electron tomography provided a new insight into the ultrastructural changes at the nuclear periphery that revealed novel structural features. The dysregulation of lipid synthesis was assessed by investigating the effects farnesylated prelamin A has on the distribution and dynamics of the transcription factor SREBP-1 and assessment of the downstream consequences this has on its targets that regulate adipocyte differentiation potential. Finally, the metabolomic profile of an HIV protease inhibitor that leads to prelamin A build up was generated and revealed increases in lipolysis, glycolysis and mediators of inflammation. The research presented offers a new insight into the development of a convoluted nuclear boundary and nucleoplasmic reticulum, in the context of lamin A mutants and how dysregulated lipid synthesis, caused by farnesylated prelamin A, leads to lipoatrophy.

Topoisomerase 2α (Topo2α) is an essential protein with DNA decatenating enzymatic properties, indispensable for chromosome decatenation and segregation. It is a target for a plethora of antitumour drugs and Topo2α protein levels have been associated with the success of treatment, but also drug resistance and secondary malignancies. Although unique in its ability to resolve catenated chromosomes, the role of Topo2α in other steps of DNA metabolism, such as DNA replication elongation and termination have been elusive. A thorough understanding of the role of Topo2α in the cell will not only allow for increased insight into the mechanisms it is involved in, but it will also shed light on proteins and pathways that can act as back-up in its absence, and therefore hopefully expand the basis on which to improve treatment options. Through a synthetic lethal interaction (SLI) screen with an siRNA library targeting 200 DNA repair and signalling genes, Topo2α emerged as being synthetic lethal to Werner protein (WRN), a RecQ helicase involved in maintaining genome integrity mainly in S phase, and the loss of which leads to Werner Syndrome (WS), a segmental progeroid syndrome. The screen was performed in WRN deficient cells, with the initial aim to find proteins that act to buffer against loss of viability, which is the central idea in the concept of synthetic lethality in the absence of WRN. The screen revealed an SLI between WRN and Topo2α and although we were unable to fully validate this, it spurred the question of Topo2α’s role in DNA replication. The findings in this thesis suggest that Topo2α is not required for DNA elongation and timely completion of S phase, and that simultaneous loss of the closely related isoform Topo2β does not affect replication, suggesting that these proteins do not act in parallel back-up pathways during replication. Interestingly, cells accumulate in the polyploid fraction after both depletion and inhibition of Topo2α, albeit with different kinetics. The mechanistic basis of this phenotype remains to be understood through further research, but it is highly interesting as aneuplidity and polyploidy are implicated in the initial stages of tumour development.

RNA interference (RNAi) is a post transcriptional gene silencing mechanism that allows potent and specific silencing of cognate mRNA transcripts. Selective silencing can be used to dissect complex polygenic diseases, elucidate the function of known genes and provide a tool for genetic therapy. Its use in the case of dominant inherited disorders including disorders of the central nervous system, depends on its ability to confer single nucleotide discrimination between normal and mutant gene alleles. In this thesis the ability of RNAi effector molecules to provide single nucleotide specificity was examined by targeting two dominant inherited mutations of the acetylcholine receptor that cause slow-channel syndrome. Allele-specific silencing was achieved for one mutation. The other mutation was also silenced but not in an allele specific way despite employing known techniques for increasing single-nucleotide specificity. The model used in this thesis is the congenital myasthenia slow-channel syndrome. This is a dominant inherited disorder of the neuromuscular junction which is both well-characterised and more readily accessible compared to the central nervous system, thus provides a prototype for development of allele-specific RNAi therapeutics. Here we describe a new transgenic animal model of the slow-channel syndrome and show good representation of the human disorder. The need for defining the characteristics that determine the effectiveness and the specificity of RNAi effectors at single-nucleotide level, along with the future uses of the newly described animal model are discussed.

This thesis examines the role and relationship of standardization and advocacy in humanitarian aid planning processes within the emergent field of education and instability. Standardization refers to the aid industry’s increasing emphasis on establishing ‘universal’ principles and normative frameworks. Advocacy refers to transnational-policy-network activities that move forward the global standardization agenda. The study focuses on the purposes and practices of knowledge creation by an education-and-instability ‘epistemic community’: the Inter-Agency Network for Education in Emergencies (INEE). Drawing on global-level interviews with key figures, participant observations, and documentary analysis, the research explores how this epistemic community promotes its core tenets: that education is an inherent human right and that educational provision should be a frontline humanitarian response on par with food distribution and shelter construction. The thesis analyzes the consensus-making process that resulted in the publication of the 2004 INEE Minimum Standards handbook, the then-epitome of the epistemic community’s knowledge. Next, the thesis examines the local application and adaptation of such global standardization processes in post-conflict Uganda. The case study presents the relationships among international and local ‘development partner’ institutions concerned with educational planning as a complex and contradictory story of power dynamics and knowledge circulation. These ‘partnerships’ are characterized by a shared quest for adherence to the knowledge encapsulated within standardized global frameworks and their normative principles. For Ugandan institutions, fluency in this discourse is a powerful tool to appropriate for their own ends. For international institutions, the knowledge is at once a technical resource and a means to bring ever more stakeholders into the wider epistemic community concerned with humanitarian aid. I argue that, through judicious use of standardization and advocacy mechanisms, INEE seeks to legitimize the education sector’s existence within the humanitarian aid industry and expand support for (or ‘conversion’ to) the education-and-instability epistemic community’s core beliefs.

This dissertation focuses on international actors' response to the ethnic cleansing perpetrated during the 1992 – 1995 Bosnian War. The work illuminates the multilateral attempt to reverse one of the outcomes of ethnic cleansing following the war, through the return of displaced people. The policy emphasis on "re-mixing" people, interpreted through a strategy of minority returns, and supported and coordinated on an international scale, was unprecedented. This dissertation asks: why did powerful states and international organizations pursue a re-mixing policy as a response to ethnic cleansing in Bosnia? At first glance, the choice seems counterintuitive. The policy was expensive. Post-1989, the West no longer needed "to keep Yugoslavia afloat." Furthermore, reversal required a degree and duration of international involvement that, at the time, was thought to be politically, militarily, and financially impossible. There are two existing explanations for this surprising phenomenon: international moralism and norm evolutionism. International moralists posit that international actors were moved to re-mix Bosnians out of a sense of guilt. Norm evolutionists argue that international norms governing appropriate responses to ethnic cleansing have shifted during the twentieth century towards support for re-mixing. In contrast to these two dominant views, this dissertation argues that the re-mixing policy initially emerged as a practical fix to a series of pressing, context-specific political challenges. State policymakers justified the re-mixing policy, however, on normative grounds. Though not the original incentive for action, international organizations on the ground then adopted the policy, empowered by states' normative justifications and thereby transformed the political rhetoric into concrete action. This dissertation corrects a common assumption that the origins and motivations behind the re-mixing policy were normative in nature, it contributes to a better understanding of how normative discourses emerge, mature, and transform into policy and it offers policy recommendations based on lessons learnt from this important and seemingly contradictory case.

T-lymphocytes are an essential cell type of the adaptive immune system. Due to their importance in immune responses and disorders, the molecular mechanisms leading to T-lymphocyte activation have been the subject of extensive research which has translated into important therapeutic developments. Early signalling events involving tyrosine phosphorylation are well characterised. However, later events involving other post-translational modifications are less well understood. Several studies have provided evidence suggesting a role for protein arginine methylation in T-lymphocyte activation. Arginine methylation is an essential post-translational modification in mammals and yet has not been extensively studied. No large scale analysis of arginine methylation sites has been performed. To gain insight into the role of protein arginine methylation in T-lymphocyte activation, the aims of this work were to: 1. Establish whether levels of arginine methylation are altered during Tlymphocyte activation 2. Use mass spectrometry based proteomics to identify arginine methylated proteins in the T-lymphocyte proteome 3. Further characterise an arginine methylated protein important to Tlymphocyte activation Arginine methylation was found to be induced after long term (>20 hours) stimulation of primary T-lymphocytes. Large increases in the main protein arginine methyltransferase, PRMT1, were also observed. Enrichment and labelling methods were developed to detect arginine methylated peptides from T-lymphocytes by mass spectrometry. This resulted in the identification of 265 unique arginine methylation sites in 141 proteins. 204 of the methylation sites were novel and 103 of the proteins had not previously been described as arginine methylated. Individual arginine methylation sites were characterised before and after activation of T-lymphocytes, with some sites showing significant changes in abundance. Among the novel arginine methylated proteins discovered were Dynamin II, WASp and WIPF1. These proteins are involved in re-organisation of the actin cytoskeleton at the immunological synapse formed between a Tlymphocyte and an antigen presenting cell. The functional consequences of the arginine methylation sites inWASp were characterised. WASp is essential for T-lymphocyte activation and some initial evidence showed that one of the arginine methylation sites is important for WASp activation.

Internally Displaced Persons ('IDPs') outnumber refugees by two to one and often have the same fears, needs and wants as refugees recognised as such under international law. However, refugee status entails international protection, while IDPs are left to the protection of their own state, which may, but by no means necessarily, be the very entity that has forced them to flee in the first place. In recent years, there have been significant developments in the realm of IDP protection. This includes the conclusion of two regional treaties on the protection of IDPs, the development of relevant soft law instruments, and the reformed 'Cluster Approach' of humanitarian response. Although the increased focus on IDP protection is a welcome development, the UNHCR has expressed the fear that 'activities for the internally displaced may be (mis)interpreted as obviating the need for international protection and asylum.' This thesis represents the first legal analysis of the relationship between the protection of IDPs and International Refugee Law. It will discuss five key challenges in this respect. First, the challenge of drawing the attention of the international community to the plight of IDPs; second, the challenge of developing an appropriate framework for the protection of IDPs; third, the challenge of ensuring that internal protection is not interpreted as a substitute for asylum; fourth; the challenge of determining the relationship between complementary protection and internal displacement; and fifth, the challenge of ensuring that IDP protection in an inter-agency context does not trigger the application of Article 1D of the Refugee Convention, rendering the Convention inapplicable to the recipients of that protection. This thesis will conclude by setting out the future challenges in the relationship between IDP protection and International Refugee Law, by identifying questions left open for further research, and by illustrating the overall impact and importance of this thesis' findings.

Avanços na área da tecnologia de informação proporcionaram mudanças em diversas áreas da atividade humana. A comunicaço cientifica e uma destas áreas. Periódicos científicos, que tradicionalmente utilizam como meio de divulgação a mídia impressa, possuem agora como alternativa a midia eletrônica. Alguns periódicos científicos lançados no final do século XX estão disponíveis exclusivamente no formato eletrônico. Esta tese de Doutorado analisa de forma específica as dinâmicas de acesso e uso dos periódicos científicos eletônicos brasileiros na área da Ciência da Informação. Discutem-se diversos tópicos fundamentais para a compreensão deste assunto. O estudo do acesso dos usuários aos periódicos foi realizado através da análise dos arquivos de log de acesso gerados pelos servidores web onde estão hospedados os periódicos selecionados para a pesquisa. O estudo relacionado ao uso que os usuários fazem dos periódicos foi realizado através da análise de um questionário enviado para os docentes dos programas de pós-graduação em Ciência da Informação, credenciados pela Coordenação de Aperfeicoamento de Pessoal de Nível Superior CAPES, até a data de 30 de junho de 2001. A pesquisa identifica vários comportamentos dos usários quando do acesso aos periódicos científicos eletrônicos brasileiros, bem como algumas barreiras para uma utilização mais efetiva deste recurso. As conclusões da pesquisa sao relevantes para a elaboraço de novos periódicos cientificos eletrônicos. O prototipo de um sistema de informação eletrônico, voltado para o gerenciamento do processo de elaboração de um periódico científico eletrônico, e apresentado em sugestões para futuras pesquisas. Este protótipo materializa algumas das idéias discutidas ao longo do texto. / Electronic journals, Scientific Communication, Information Science, Information Technology