Embryonic stem cells (ESCs) are a special type of cell marked by two key properties: The capacity to create an unlimited number of identical copies of themselves (self-renewal) and the ability to give rise to differentiated progeny that can contribute to all tissues of the adult body (pluripotency). Decades of past research have identified many of the genetic determinants of the state of these cells, such as the transcription factors Pou5f1, Sox2 and Nanog. Many other transcription factors and, more recently, epigenetic determinants like histone modifications, have been implicated in the establishment, maintenance and loss of pluripotent stem cell identity. The study of these regulators has been boosted by technological advances in the field of high-throughput sequencing (HTS) that have made it possible to investigate the binding and modification of many proteins on a genome-wide level, resulting in an explosion of the amount of genomic data available to researchers. The challenge is now to effectively use these data and to integrate the manifold measurements into coherent and intelligible models that will actually help to better understand the way in which gene expression in stem cells is regulated to maintain their precarious identity. In this thesis, I first explore the potential of HTS by describing two pilot studies using the technology to investigate global differences in the transcriptional profiles of different cell populations. In both cases, I was able to identify a number of promising candidates that mark and, possibly, explain the phenotypic and functional differences between the cells studied. The pilot studies highlighted a strong requirement for specialised software to deal with the analysis of HTS data. I have developed GeneProf, a powerful computational framework for the integrated analysis of functional genomics experiments. This software platform solves many recurring data analysis challenges and streamlines, simplifies and standardises data analysis work flows promoting transparent and reproducible methodologies. The software offers a graphical, user-friendly interface and integrates expert knowledge to guide researchers through the analysis process. All primary analysis results are supplemented with a range of informative plots and summaries that ease the interpretation of the results. Behind the scenes, computationally demanding tasks are handled remotely on a distributed network of high-performance computers, removing rate-limiting requirements on local hardware set-up. A flexible and modular software design lays the foundations for a scalable and extensible framework that will be expanded to address an even wider range of data analysis tasks in future. Using GeneProf, billions of data points from over a hundred published studies have been re-analysed. The results of these analyses are stored in an web-accessible database as part of the GeneProf system, building up an accessible resource for all life scientists. All results, together with details about the analysis procedures used, can be browsed and examined in detail and all final and intermediate results are available and can instantly be reused and compared with new findings. In an attempt to elucidate the regulatory mechanisms of ESCs, I use this knowledge base to identify high-confidence candidate genes relevant to stem cell characteristics by comparing the transcriptional profiles of ESCs with those of other cell types. Doing so, I describe 229 genes with highly ESC-specific transcription. I then integrate the expression data for these ES-specific genes with genome-wide transcription factor binding and histone modification data. After investigating the global characteristics of these "regulatory inputs", I employ machine learning methods to first cluster subgroups of genes with ESC-specific expression patterns and then to define a "regulatory code" that marks one of the subgroups based on their regulatory signatures. The tightly co-regulated core cluster of genes identified in this analysis contains many known members of the transcriptional circuitry of ESCs and a number of novel candidates that I deem worthy of further investigations thanks to their similarity to their better known counterparts. Integrating these candidates and the regulatory code that drives them into our models of the workings of ESCs might eventually help to refine the ways in which we derive, culture and manipulate these cells - with all its prospective benefits to research and medicine.

Drug resistance to the current treatments on the market is on the rise, therefore there is strong interest in understanding what could be causing the resistance, how resistance could be spreading through the population, and finding some possible new drug targets. One protein of interest is Radiation Sensitive Protein 51 (Rad51). It is a protein that is involved in homologous recombination as well as other processes such as DNA damage repair. While Trichomonas vaginalis traditionally has been known to replicate via binary fission, a modified form of closed mitosis, there is some evidence that meiosis, or at least some form of genetic recombination, could occur in the organisms, possibly contributing to the resistance. The focus of my project was gaining an understanding of how the Trichomonas vaginalis Rad51 protein (TvRad51) could, either directly or indirectly, play a role in generating diversity that could lead to resistance. Since functional assays of purified Rad51 protein were previously unsuccessful, this study attempted to investigate TvRad51’s ability to interact with known binding partners via protein-protein interactions, while exploring new targets using yeast two-hybrid. Localization of TvRad51 showed that it behaves differently than the human version giving more information to understand how TvRad51 functions. Lastly, preliminary studies were conducted to evaluate the potential role of TvRad51 in telomere maintenance.

When biological information about an individual is produced in healthcare or research settings, ethical questions may arise about whether the individual herself should be able to access it. This thesis argues that the individual’s identity-related interests warrant serious attention in framing and addressing these questions. Identity interests are largely neglected in bioethical, policy and legal debates about information access – except where information about genetic parentage is concerned. Even there, the relationship between information and identity, and the interests involved, remain unclear. This thesis seeks to fill this conceptual gap and challenge this exceptionalism. It does so by developing a normative account of the roles that a wide range of information about our health, bodies and biological relationships – ‘personal bioinformation’ – can play in the construction of our self-conceptions. This account is developed in two steps. First, building on existing philosophical theories of narrative self-constitution, this thesis proposes that personal bioinformation has a critical role to play in the construction of identity narratives that remain coherent and support us in navigating our embodied experiences. Secondly, drawing on empirical literature reporting individuals’ attitudes to receiving three categories of personal bioinformation (about donor conception, genetic disease susceptibility, and neuroimaging-based psychiatric diagnoses), the thesis seeks to illustrate, demonstrate the plausibility of, and to refine this theoretically-based proposition. From these foundations, it is argued that we can have strong identity-related interests in whether and how we are able to access bioinformation about ourselves. The practical implications of this conclusion are then explored. It is argued that identity interests are not reducible to other interests (for example, in health protection) commonly weighed in information disclosure decisions. They, therefore, warrant attention in their own right. An ethical framework is developed to guide delivery of this. This framework sets out the ethical responsibilities of those who hold bioinformation about us to respond to our identity interests in information disclosure practices and policies. The framework is informed by indications from the illustrative examples that our interests engaged as much by how bioinformation is communicated as whether it is disclosed. Moreover, these interests are not uniformly engaged by all bioinformation in all circumstances and there is potential for identity detriment as well as benefit. The ethical framework highlights the opportunities for and challenges of responding to identity interests and the scope and limits of potential disclosers’ responsibilities to do so. It also makes recommendations as to the principles and characteristics of identity-supporting disclosure practices.