A phylogenetic method to perform genome-wide association studies in microbes

Genome-Wide Association Studies (GWAS) are designed to perform an unbiased search of genetic sequence data with the intent of identifying statistically significant associations with a phenotype or trait of interest. The application of GWAS methods to microbial organisms promises to improve the way we understand, manage, and treat infectious diseases. Yet, while microbial pathogens continue to undermine human health, wealth, and longevity, microbial GWAS methods remain unable to fully capitalise on the growing wealth of bacterial and viral genetic sequence data. Clonal population structure and homologous recombination in microbial organisms make it difficult for existing GWAS methods to achieve both the precision needed to reject false positive findings and the statistical power required to detect genuine associations between microbial genotypic and phenotypic variants. In this thesis, we investigate potential solutions to the most substantial methodological challenges in microbial GWAS, and we introduce a new phylogenetic GWAS approach that has been specifically designed for use in bacterial samples. In presenting our approach, we describe the features that render it robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Our approach is applicable to organisms ranging from purely clonal to frequently recombining, to sequence data from both the core and accessory genome, and to binary, categorical, and continuous phenotypes. We also describe the efforts taken to make our method efficient, scalable, and accessible in its implementation within the open-source R package we have created, called treeWAS. Next, we apply our GWAS method to simulated datasets. We develop multiple frameworks for simulating genotypic and phenotypic data with control over relevant parameters. We then present the results of our simulation study, and we use thorough performance testing to demonstrate the power and specificity of our approach, as compared to the performance of alternative cluster-based and dimension-reduction methods. Our approach is then applied to three empirical datasets, from Neisseria gonorrhoeae and Neisseria meningitidis, where we identify core SNPs associated with binary drug resistance and continuous antibiotic minimum inhibitory concentration phenotypes, as well as both core SNP and accessory genome associations with invasive and commensal phenotypes. These applications illustrate the versatility and potential of our method, demonstrating in each case that our approach is capable of confirming known resistance- or virulence-associated loci and discovering novel associations. Our thesis concludes with a review of the previous chapters and an evaluation of the strengths and limitations displayed by the current implementation of our phylogenetic approach to association testing. We discuss key areas for further development, and we propose potential solutions to advance the development of microbial GWAS in future work.Open Acces

Mapping poetry onto the visual arts : Carl Andre's Words

textAs innovative as his sculpture, Andre's visually oriented poetry, however, has yet to receive the same rigor of attention as his sculpture. His inventive use of poetic and visual form, which he described as poetry mapped onto the visual arts, provides a compelling example of the interrelationship of word and image, a practice, although often overlooked, that suffuses twentieth-century visual art and poetry. Whereas Andre produced approximately 1,500 poems over many decades, this project focuses on his Words installation, the largest permanently installed collection of Andre's poems in the world. In 1995, Andre gifted 465 pages of poetry to the Chinati Foundation in Marfa, Texas. Andre's experiments with genre, including lyrics, autobiographies, novels, odes, and operas, push literary convention to the edge of irreconcilability. Despite the array of genres, I argue that all of the disparate kinds of writing found in Words demonstrate Andre's poetic sensibility. Until recently the critical discussion of Andre's poems proceeded as a one-sided discourse, which advanced the notion that this large body of work was best suited to enhancing the understanding of Andre's sculptural practice. To redress the one-sidedness of the discourse requires approaching Andre not only as a sculptor who made poems, but also as a poet deeply engaged in the visual qualities of his poetics. Engaging the spirit of the "make it new" sensibility of modernist poetics, Andre developed his own practice by "mapping language on the conventions and usages of 20thcentury abstract art."¹ Andre's poetry operates in the space between art and language. In this space we find Andre's engagement with poetic history, particularly the innovations of Ezra Pound, his relationship to important poetic developments such as fragmentation and quotation, and his experimentation with poetry as a visual medium. An examination of Andre's poetic oeuvre, the publication and exhibition history of his poems, and the manner of critical attention given to the poems from the 1960s onward contextualizes Andre's practice of mapping poetry onto the visual arts, while also bridging the gap in discourse between the fields of art and poetry.Art Histor

The Five Stages of Team Development

Purpose: Provide students an introduction to existing business/psychology teachings on group dynamics and the five distinct stages of team development likely to be experienced in any group setting

Understanding PECAM-1-mediated mechanotransduction: from the protein to the vessel

Hemodynamic forces are critical for endothelial cell (EC) function and vessel health. Platelet endothelial cell adhesion-1 (PECAM-1) has been identified as a critical endothelial mechanosensor that is required for transducing mechanical signals into intracellular signaling events; however, molecular mechanisms of PECAM-1-mediated mechanotransduction remain elusive. This dissertation investigates mechanosignaling and cellular responses directly linked to force transduction via PECAM-1. In recent years, there has been increasing interest to understand how cells respond to tension on mechanosensitive proteins. Numerous studies investigating force-bearing integrins and have revealed that the cell responds to exogenous force by increasing cell-generated force that is proportional to the applied force. This change in cellular force manifests as an adaptive cellular stiffening response that allows the cell to resist the strain of the applied force. While much work has focused on cellular responses linked to integrins, other mechanosensitive proteins are now being probed. In Chapter II, I demonstrate that tension on PECAM-1 also results in an adaptive stiffening response. Furthermore, I demonstrate that, surprisingly, the PECAM-1-mediated mechanoresponse is not locally restricted to regions proximal to the site of force application, but rather global in nature. These data suggest that, contrary to previous thoughts, a localized mechanical perturbation can globally affect signaling cascades and cellular phenotype. Mechanosensitive signaling within the endothelium is greatly influenced by the subendothelial matrix composition. In Chapter III, I investigate how the extracellular matrix (ECM) identity influences PECAM-1 mechanosignaling and cellular response to force. I demonstrate that, contrary to cells adherent on fibronectin, adhesion to collagen suppresses mechanical responsiveness to tension on PECAM-1, including adaptive stiffening and focal adhesion growth. I further identify PKA-mediated inactivation of RhoA as critical signaling axis that influences endothelial cell mechanics in response to tension on PECAM-1 and the physiological stimulus of fluid shear stress in vitro and in vivo. Taken together, the work presented in this dissertation advances our understanding of how endothelial cells integrate mechanical and extracellular matrix-specific cues and provides insight into how these factors may contribute to cellular phenotype in vivo.Doctor of Philosoph

Participation in developing youth mental health services: ‘Cinderella Service’ to service re-design

Whilst there are pockets of excellence in the provision of Child and Adolescent Mental Health Services (CAMHS), many services fail to meet young people’s needs. Considering this, the current research aimed to ascertain perceptions of CAMHS provision in a rural county of the UK to inform re-design of youth mental health services. Design Methodology and Approach: The study comprised of two phases: phase one involved analysis of questionnaire data of youth views of CAMHS. Phase two involved analysis of the ‘Have Your Say’ event data which explored perceptions of CAMHS and future service re-design. Data were thematically analysed. Findings: Knowledge of the existence and purpose of CAMHS was variable. Participants wanted accessible information about services, rights, confidentiality and for this to be provided in multiple medias. Young people wanted staff that are easy to talk to, genuine, understanding and who value their insights. Participants wanted to be offered choice about appointments, location and timing. An ideal mental health service was described as a ‘one-stop-shop’ of co-locality and multi-agency collaboration. Young people clearly expressed a desire to influence the design and delivery of the radical re-design and to be embedded in its development. Practical Implications: The results highlighted multiple problems with CAMHS provision and provided a clear justification for the re-design of services. Originality/value: This was a novel approach demonstrating the importance, utility and power of effective participatory practices for informing the re-design of services

Regional gene repression by DNA double-strand breaks in G1 phase cells

DNA damage responses (DDR) to double-strand breaks (DSBs) alter cellular transcription programs at the genome-wide level. Through processes that are less well understood, DSBs also alter transcriptional responses locally, which may be important for efficient DSB repair. Here, we developed an approach to elucidate th

Hemodynamic forces in endothelial dysfunction and vascular aging

Aging is a key risk factor associated with the associated onset of cardiovascular disease. Notably, vascular aging and cardiovascular disease are both with endothelial dysfunction, or a marked decrease in production and bioavailability the vasodilator of nitric oxide (NO). As a result of decreased nitric oxide availability, aging vessels often exhibit endothelial cell senescence and increased oxidative stress. One of the most potent activators of NO production is fluid shear stress produced by blood flow. Interestingly, age-related decrease in NO production partially results from endothelial insensitivity to shear stress. While the endothelial cell response to fluid shear stress has been well characterized in recent years, the exact mechanisms of how the mechanical force of fluid shear stress is converted into intracellular biochemical signals are relatively unknown. Therefore, gaining a better knowledge of mechanosignaling events in endothelial cells may prove to be beneficial for developing potential therapies for cardiovascular diseases

Youth in motion: spatialising youth movement(s) in the social sciences

‘Youth in Motion: Spatialising Youth Movement(s) in the Social Sciences’ was a one-day interdisciplinary workshop convened by the University College London (UCL) Youth Geographies Research Group on Thursday 16 June 2011. The workshop attracted an international audience with participants from institutions in France, Finland, Italy, Canada and Australia, as well as around the UK. Although all attendees worked with youth in an academic context, many were also experienced youth work practitioners. Our primary objective was to provide an opportunity for social scientists working with youth in a diverse range of disciplinary contexts to consider how research accommodates the notion of movement(s) when exploring the spaces, places and everyday experiences of young lives. In this brief report, we aim to present some of the key themes that emerged over the course of the workshop and connect these with recent work asking ‘where next?’ for geographical research with youth..

Localized Tensional Forces on PECAM-1 Elicit a Global Mechanotransduction Response via the Integrin-RhoA Pathway

SummaryBackgroundMechanical forces regulate cell behavior and function during development, differentiation, and tissue morphogenesis. In the vascular system, forces produced by blood flow are critical determinants not only of morphogenesis and function, but also of pathological states such as atherosclerosis. Endothelial cells (ECs) have numerous mechanotransducers, including platelet endothelial cell adhesion molecule-1 (PECAM-1) at cell-cell junctions and integrins at cell-matrix adhesions. However, the processes by which forces are transduced to biochemical signals and subsequently translated into downstream effects are poorly understood.ResultsHere, we examine mechanochemical signaling in response to direct force application on PECAM-1. We demonstrate that localized tensional forces on PECAM-1 result in, surprisingly, global signaling responses. Specifically, force-dependent activation of phosphatidylinositol 3-kinase (PI3K) downstream of PECAM-1 promotes cell-wide activation of integrins and the small GTPase RhoA. These signaling events facilitate changes in cytoskeletal architecture, including growth of focal adhesions and adaptive cytoskeletal stiffening.ConclusionsTaken together, our work provides the first evidence of a global signaling event in response to a localized mechanical stress. In addition, these data provide a possible mechanism for the differential stiffness of vessels exposed to distinct hemodynamic force patterns in vivo