Aggregations of fused in sarcoma (FUS), a multifunctional RNA processing protein, define a pathological subtype of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), whilst mutations in the FUS gene are causative for ALS. To model the impact of FUS mutations, expression vectors containing the entire genomic sequence of FUS, up and downstream regions, and native promoter sequences have been generated. The constructs have been tagged with an mCherry fluorescent tag, and three separate pathological mutations (R244C, R521C, and P525L) have been separately inserted. Transgenic mice have been generated using the WT and P525L FUS vectors to provide a highly physiological model of FUS in disease. Within transfected HEK293 cells, insertion of the P525L and R521C FUS mutations leads to relocalisation of FUS from the nucleus to the cytoplasm. R521C and P525L mutant FUS incorporates into cytoplasmic aggregations of untranslated mRNA and RNA binding proteins known as stress granules. The strong relocalisation seen with P525L-FUS is associated with a gain of cytotoxicity. Reversal of this cytoplasmic relocalisation by demethylation of FUS rescues this cytotoxicity, suggesting a toxic gain of cytoplasmic function in the majority of FUS mutations. By contrast, insertion of the R244C mutation leads to neither relocalisation, stress granule association, nor cytotoxicity. Notably the R244C mutation, located away from the nuclear localization domain in which the majority of FUS mutations are found, leads to the presence of smaller FUS fragments in western blot analyses. These fragments appear not to be due to splicing defects in FUS but rather are due to post-translational modifications or aberrant protein cleavage. These data suggest an alternative pathway for FUS toxicity based upon a nuclear loss of function.

Breast cancer type 1 susceptibility protein (BRCA1) has been established as an important tumour suppressor protein and its loss of function is associated with hereditary breast and ovarian cancer. An emerging body of work suggests that BRCA1 is involved in sporadic cases of breast and ovarian cancers and may also have a role in other cancers, indicating a more global role in tumourigenesis. BRCA1-mutated cancers can be early-onset and are characterised by being highly aggressive with a propensity to metastasize, thus from a clinical perspective there is a requirement to understand the molecular mechanisms in order to be able to tailor treatments and develop therapeutics. BRCA1 has numerous cellular functions, many ascribed to its role in maintenance of genome integrity, transcription and checkpoint control. More recently, a number of extra-nuclear roles have been established. An interesting novel function is the role of the E3 ubiquitin ligase activity on cell motility. Abrogation of the ubiquitin ligase activity of BRCA1 results in cells exhibiting a hypermotile, invasive phenotype which may help to account for the metastatic nature of BRCA1-mutated tumours. Our aim was to further elucidate BRCA1’s role in cell motility, starting with the identification of relevant candidate ubiquitin ligase substrates. To date, there has yet to be a systematic approach to identify BRCA1’s ubiquitin ligase substrates. Thus we undertook an unbiased proteomic approach to identify extra-nuclear candidates by comparing the profiles of ubiquitinated proteins in breast cancer epithelial cells expressing either functional BRCA1 or ubiquitin ligase-dead BRCA1. We identified 55 candidates which were differentially enriched between the two cell lines and through pathway analysis we determined a significant proportion were cytoskeletal and translation related proteins. Using an ubiquitin-remnant profiling approach, we also identified the site(s) of ubiquitination for many of the candidates. To assess the role of these candidates in cell motility initially we adopted an in silico approach. We used existing time-lapse movies from the online database (www.mitocheck.org) which systematically siRNA knocked down every single gene in the human genome. We developed a series of algorithms which track cell motility from these movies and used these to analyse 192,000 movies containing 3.5 billion cell steps. We have produced a complete database containing motility information after siRNA knockdown of every gene in the human genome, which has been annotated with gene ontologies, KEGG families, Gene Descriptions, SwissProt, Ensembl IDs and siRNA information. In addition to providing motility data of our candidates, we also carried out gene set enrichment analysis on the whole dataset to uncover structural or functional families that may be involved in up-regulating motility when knocked down by siRNA. This is the first report of a genome-wide motility database. Based on overlaps between the results from these two large-scale unbiased proteomic and in silico datasets, we selected 4 candidates, namely, ezrin, moesin, fermitin-2 and delta-catenin. Through monolayer wound healing, cell spreading and single cell motility assays, we determined that ezrin was a particularly relevant and informative candidate. The hypermotile phenotype observed in cells expressing ubiquitin ligase dead BRCA1 was rescued through siRNA knockdown of ezrin and thus we suggest that BRCA1 may regulate cell motility through effects on ezrin. This thesis has investigated candidate BRCA1’s role in cell motility, identified candidate substrates for the E3 ubiquitin ligase activity, established a genome-wide motility database and proposed a possible pathway through which BRCA1 may mediate cell motility and by extension metastasis.

This thesis examines the relationship between environmental stress and human mobility with a view to understanding the impacts of climate change on human migration. Using a conjuncture of political ecology and migration theory, it firstly explores the literature on 'environmental refugees' identifying a distinction between general agreement on the existence of a relationship between environmental stress and migration, and debate over the appropriateness of the 'environmental refugee' as a suitable means for representing that relationship. Secondly this conjuncture is used to examine accounts from farmers and migrants in northern Ethiopia, with a focus on understanding how environmental and non-environmental factors interact to shape mobility decisions in a context of environmental stresses, thought analogous to those predicted to accompany future climate change. The principal finding of the study is that although environmental stress matters in mobility decisions, it does so due to the context of non-environmental factors in which it occurs, not in spite of them. With this in mind the work provides a framework of additive, vulnerability, enabling and barrier effects as a means for elaborating our understanding of how environmental and non-environmental factors interact to determine mobility strategies in a context of environmental stress. Focussing on the role of non-environmental factors, the work reveals that while biophysical features operate at a macro-scale to shape mobility decisions, these decisions are determined by non-environmental features operating at a micro-scale. The research then traces differences in the existence of these micro-scale, non-environmental, factors across two field sites, finding that their origins lie in both historical and contemporary forces of regional and global political economy. As such, the work concludes that understanding the relationship between climate change and human migration will require a contextualisation of that relationship within this broader framework.

Mucolipidosis type IV (MLIV) is a rare, autosomal recessive, neurodegenerative, lysosomal storage disorder. MLIV is caused by mutations in a gene (MCOLN1) encoding a TRP channel family member known as Mucolipin 1 or TRPML1. TRPML1 is a lysosomal transmembrane protein that appears to be required for normal lysosomal pH regulation, recycling of molecules and membrane reorganisation including lysosomal biogenesis, fusion and exocytosis. The exact function of the channel is unknown but it is permeable to multiple ions including Ca²⁺, Na⁺ and K⁺, possibly also Fe²⁺ and Zn²⁺. How normal TRPML1 function regulates lysosomal processes is not clearly understood. Mutations in the MCOLN1 gene can lead to complete loss of TRPML1 function, partial loss of function or mislocalisation, all of which lead to lysosomal dysfunction, lysosomal lipid storage and ultimately neurodegeneration. The disease processes that lead to neurodegeneration are poorly understood and at present no therapy exists for MLIV. We have discovered that TRPML1 results in regulating lysosomal Ca²⁺ homeostasis that is the opposite of the Ca²⁺ dysregulation associated with Niemann-Pick type C disease (NPC). Our findings indicate that disrupted function of TRPML1 leads to enhanced Ca²⁺ release via the NAADP receptor, recently shown to be the lysosomal two-pore channel TPC2. This indicates that TRPML1 is not the NAADP receptor as suggested by others, indeed NAADP mediated Ca²⁺ release is enhanced with multiple NAADP induced lysosomal Ca²⁺ release events occurring in TRPML1 null cells compared to single releases in normal cells. This phenotype appears to be responsible for the cellular dysfunction associated with MLIV disease cells, enhanced lysosomal fusion, defective endocytosis and potentially even altered lysosomal pH. Several of these phenotypes are normalised by the NAADP receptor specific antagonist Ned-19. These findings illustrate that the NAADP receptor is central to MLIV disease pathology and may be a novel candidate for disease therapy.

Environmental governance is a challenging topic in development contexts. On the one hand, the traditional development paradigm is based on economic growth through environmental exploitation; on the other, environmental degradation reduces vulnerable populations’ options for development. In the last thirty years numerous attempts to integrate environmental concerns in development policies have proved unsuccessful, raising questions as to whether the current governance system can address the challenge. The literature on environmental management has focused on identifying rules for successful governance, leaving little space to explore the complexities of the interactions between actors and their environments, wherein the reasons for sustained degradation might lie. The questions that this thesis asks are: How do diverse groups of actors rationalize and interact with degraded ecosystems? And what role does the governance system play in codifying these interactions? To answer these questions, the thesis engages in an institutional study of Lake Titicaca, between Peru and Bolivia. The lake has witnessed a degradation of its bay in the last thirty years, as a result of urban and mining development in the region. A complex web of organizations that go from the bi-national to the community level manages Lake Titicaca. The investigation of the questions asked is particularly relevant in the current context, as the countries to which the lake belongs put forward significantly different visions of the environment. By drawing on the strengths of social-ecological systems frameworks proposed by the two mains schools – the Resilience Alliance and Bloomington Workshop – and filling some of their deficiencies using insights from the sociological literatures on negotiation and justification, I hope to have created a composite framework with which to give an insightful account of the complexity and diversity at play in the field. The thesis adopts a broad range of qualitative methods (observation, interviews, document analysis) completed with descriptive statistics for budget analysis. The thesis argues that the actors’ approaches to the ecosystem are complex, diverse and constitutive of social-ecological systems wherein relationships are negotiated between actors, between actors and the ecosystem and ‘within’ actors as they hold competing visions and strategies. Some of the variables shaping these negotiations are crafted through the interaction between social and ecological elements, which also influence the actors’ understanding of the system. Others are determined by parameters crafted in the social sphere, and the ways in which social-ecological interactions fit with those. Policy interventions to improve the condition of Lake Titicaca need a more sophisticated understanding of these social-ecological systems.

The CCCTC-binding factor (CTCF) is a versatile, multifunctional zinc-finger protein involved in a broad spectrum of cellular functions. In mammalian cells, CTCF functions together with the Cohesin complex, an essential regulator of sister chromatid cohesion. Together, CTCF and Cohesin have been shown to regulate gene expression at a genome-wide level in mammalian cells. In the yeast Saccharomyces pombe, Cohesin has been implicated in transcription termination of convergently transcribed genes, in a cell cycle dependent manner. The aim of this thesis was to investigate the possibility of direct transcriptional involvement of CTCF and Cohesin in human cells. The first model system applied for this experimental purpose was the β-globin gene with introduced canonical CTCF-binding sites replacing the endogenous Co- Transcriptional Cleavage (CoTC) element downstream of β-globin. The results obtained indicate that recruitment of CTCF to the β-globin 3` flanking region does not prevent read-through transcription. However, CTCF-binding does mediate RNA Polymerase II (Pol II) pausing at the site of recruited CTCF. This results in more efficient pre-mRNA 3` end processing and therefore rescues β-globin mRNA to wild type levels. Cohesin was not detected at the introduced CTCF-binding sites. These results are a contribution to our understanding of the spatio-temporal requirements for cotranscriptional events like 3` end pre-mRNA processing and Pol II kinetics. The second part of my thesis presents an investigation on the involvement of CTCF and Cohesin in lipopolysaccharide (LPS)-induced Tumor Necrosis Factor α (TNFα) gene expression regulation in human monocytes and differentiated M1- and M2-type macrophages. These studies provide first evidence of Cohesin recruitment to the TNFα gene body and its regulatory NFκB-binding sites. Differences in the recruitment profiles obtained indicate potential regulatory differences of TNFα among the three cell types. Preliminary data provide an insight into the effects on TNFα mRNA levels upon down-regulation of Cohesin subunits.

Population displacement has long been a controversial companion of development. The central tension has been between the position challenging the kind of development that removes people from their homes, livelihoods and communities, and a managerial position that the impoverishment risks of displacement can be mitigated through an effective intervention. Whereas recent research has been devoted to unpacking a rather unsuccessful performance of involuntary resettlement as a mitigation measure, this study aims to question the assumption of mitigation itself by expanding the concept of development impacts beyond the realm of displacement. Through an empirical study of a railway project in Metro Manila, the Philippines, I examine how urban residents are affected by a large-scale demolition and displacement that took place in their locality. Semi-structured interviews were conducted along the railway tracks after the land was cleared of informal settlements since the study placed particular focus on residents who were not physically displaced. They are identified in my research as non-displaced people. Few studies have addressed the possibility that other people might have been adversely affected in situ and this is particularly so in urban areas. Empirical findings reveal that the physical environment and socio-economic relationships in the locality were significantly transformed through the clearance; impacting the tenure status, livelihoods and social milieu of non-displaced people. Tenure security was important for avoiding displacement but was not a definitive factor as a number of people are still informal settlers who continue to be faced with other eviction threats. For the non-displaced, the physical change of the locality became relevant when their productive capital, notably, a second house or business space, was affected. The loss or erosion of physical capital had a secondary impact on livelihoods, which was compounded by the rupture in the local livelihood network following a mass population outflow. Whereas the income of locally-based businesses decreased substantially, livelihoods that operate beyond the locality remain relatively resilient. Differentiated experiences of a local change are also reflected in a range of evaluations that describe local social ambiance before and after the event. Diverse ways in which non-displaced people were affected underline that the current conceptualisation of impacts is limited to one dimension of displacement. This raises the need to adopt a more holistic and disaggregated approach to understanding the complexities of development impacts. A discussion on whether and how they can be mitigated would benefit further from such a comprehensive study.

This work concerns itself with understanding the organisation of cellular immune responses to three major human pathogens - HIV, CMV and Hepatitis C (HCV). Each was studied to form three projects, each undertaken with a different approach - arrived at independently - and largely owing their origins to opportunity and circumstance as much as design. Each project led to exploration of a particular aspect of T-cell phenotype (that is the expression of particular molecular markers on T-cells) and its’ broader biological significance. I found that T-cell phenotype was strongly linked to the magnitude of T-cell responses (CMV) and the ability of T-cells to control infection (HIV). Finally I explored the significance of expression of a molecule known as CD161 on the surface of HCV specific CD8+ T-cells, indicating a phenotype of T-cell that may not follow the ‘normal rules’ applicable to T-cells in general.

The purpose of this thesis is to develop a vertex model framework that can be used to perform computational experiments related to the dynamics of epithelial tissues in developmental systems. We focus on three example systems: the Drosophila wing imaginal disc, the Drosophila epidermis and the visceral endoderm of the mouse embryo. Within these systems, key questions pertaining to size-control mechanisms and coordination of cell migration remain unanswered and are amenable to computational testing. The vertex model presented here builds upon existing frameworks in three key ways. Firstly, we include novel force terms, representing, for example, the reaction of a cell to being compressed and its shape becoming distorted during a highly dynamic process such as cell migration. Secondly, we incorporate a model of diffusing morphogenetic growth factors within the vertex framework, using an arbitrary Lagrangian-Eulerian formulation of the diffusion equation and solving with the finite-element method (FEM). Finally, we implement the vertex model on the surface of an ellipsoid, in order to simulate cell migration in the mouse embryo. Throughout this thesis, we validate our model by running simple simulations. We demonstrate convergence properties of the FEM scheme and discuss how the time taken to solve the system scales with tissue size. The model is applied to biological systems and its utility demonstrated in several contexts. We show that when growth is dependent on morphogen concentration in the Drosophila wing disc, proliferation occurs preferentially in regions of high concentration. In the Drosophila epidermis, we show that a recently proposed mechanism of compartment size-control, in which a growth-factor is released in limited amounts, is viable. Finally, we examine the phenomenon of rosettes in the mouse embryo, which occur when five or more cells meet at a common vertex. We show, by running simulations both with and without rosettes, that they are crucial facilitators of ordered migration, and are thus critical in the patterning of the early embryo.

The high-throughput technologies developed in the last decade have revolutionized the speed of data accumulation in the life sciences. As a result we have very rich and complex data that holds great promise to solving many complex biological questions. One such technology that is very well established and widespread is DNA microarrays, which allows one to simultaneously measure the expression levels of tens of thousands of genes in a biological tissue. This thesis aims to contribute to the development of statistics that allow the end users to obtain robust and meaningful results from DNA microarrays for further investigation. The methodology, implementation and pragmatic issues of two important and related topics – sample size estimations for designing new studies and meta-analysis of existing studies – are presented here to achieve this aim. Real life case studies and guided steps are also given. Sample size estimation is important at the design stage to ensure a study has sufficient statistical power to address the stated objective given the financial constraints. The commonly used formula for estimating the number of biological samples, its short-comings and potential amelioration are discussed. The optimal number of biological samples and number of measurements per sample that minimizes the cost is also presented. Meta-analysis or the synthesis of information from existing studies is very attractive because it can increase the statistical power by making comprehensive and inexpensive use of available information. Furthermore, one can also easily test the generalizability of findings (i.e. the extent of results from a particular valid study can be applied to other circumstances). The key issues in conducting a meta-analysis for microarrays studies, a checklist and R codes are presented here. Finally, the poor availability of raw data in microarray studies is discussed here with recommendations for authors, journal editors and funding bodies. Good availability of data is important for meta-analysis in order to avoid biased results and for sample size estimation.