Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

The political philosophy of Miki Kiyoshi: A close reading of the philosophical foundations of cooperative communitarianism

The thesis is a historical and philological study of the mature political theory of Miki Kiyoshi (1897-1945) focused on Philosophical Foundations of Cooperative Communitarianism (1939), a full translation of which is included. As the name suggests, it was a methodological and normative communitarianism, which critically built on liberalism, Marxism and Confucianism to realise a regional political community. Some of Miki’s Western readers have wrongly considered him a fascist ideologue, while he has been considered a humanist Marxist in Japan. A closer reading cannot support either view. The thesis argues that the Anglophone study of Japanese philosophy is a degenerating research programme ripe for revolution in the sense of returning full circle to an original point. That means returning to the texts, reading them contextually and philologically, in principle as early modern European political theory is read by intellectual historians, such as the representatives of Cambridge School history of political thought. The resulting reading builds critically on the Japanese scholarship and relates it to contemporary Western and postcolonial political theory and the East Asian tradition, particularly neo-Confucianism. The thesis argues for a Cambridge School perspective radicalised by the critical addendum of geo-cultural context, supplemented by Geertzian intercultural hermeneutics and a Saidian ‘return to philology’. As against those who have seen radical reorientations in Miki’s political thought, the thesis finds gradual progression and continuity between his neo-Kantian, existentialist, Marxian anthropology, Hegelian and finally communitarian phases. The theoretical underpinnings are his philosophical anthropology, a structurationist social theory of praxis, and a critique of liberalism, Marxism, nationalism and idealism emphasising concrete as opposed to abstract theory and the need to build on existing cultural traditions to modernise rather than westernise East Asia. This post-Western fusion was imagined to be the beginning of a true and pluralistic universalism.

Investigations into the cellular and molecular changes in the amygdala in models of temporal lobe epilepsy and maternal immune activation

The amygdala is a limbic structure that is involved in many of our emotions and processing of these emotions such as fear, anger and pleasure. Conditions such as anxiety, autism, and also epilepsy, have been linked to abnormal functioning of the amygdala, owing to improper neurodevelopment or damage. This thesis investigated the cellular and molecular changes in the amygdala in models of temporal lobe epilepsy (TLE) and maternal immune activation (MIA). The kainic acid (KA) model of temporal lobe epilepsy (TLE) was used to induce Ammon’s-horn sclerosis (AHS) and to investigate behavioural and cytoarchitectural changes that occur in the amygdala related to Neuropeptide Y1 receptor expression. Results showed that KA-injected animals showed increased anxiety-like behaviours and displayed histopathological hallmarks of AHS including CA1 ablation, granule cell dispersion, volume reduction and astrogliosis. Amygdalar volume and neuronal loss was observed in the ipsilateral nuclei which was accompanied by astrogliosis. In addition, a decrease in Y1 receptor expressing cells in the ipsilateral CA1 and CA3 sectors of the hippocampus, ipsi- and contralateral granule cell layer of the dentate gyrus and ipsilateral central nucleus of the amygdala was found, consistent with a reduction in Y1 receptor protein levels. The results suggest that plastic changes in hippocampal and/or amygdalar Y1 receptor expression may negatively impact anxiety levels. Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the brain and tight regulation and appropriate control of GABA is vital for neurochemical homeostasis. GABA transporter-1 (GAT-1) is abundantly expressed by neurones and astrocytes and plays a key role in GABA reuptake and regulation. Imbalance in GABA homeostasis has been implicated in epilepsy with GAT-1 being an attractive pharmacological target. Electron microscopy was used to examine the distribution, expression and morphology of GAT-1 expressing structures in the amygdala of the TLE model. Results suggest that GAT-1 was preferentially expressed on putative axon terminals over astrocytic processes in this TLE model. Myelin integrity was examined and results suggested that in the TLE model myelinated fibres were damaged in comparison to controls. Synaptic morphology was studied and results suggested that asymmetric (excitatory) synapses occurred more frequently than symmetric (inhibitory) synapses in the TLE model in comparison to controls. This study illustrated that the amygdala undergoes ultrastructural alterations in this TLE model. Maternal immune activation (MIA) is a risk factor for neurodevelopmental disorders such as autism, schizophrenia and also epilepsy. MIA was induced at a critical window of amygdalar development at E12 using bacterial mimetic lipopolysaccharide (LPS). Results showed that MIA activates cytokine, toll-like receptor and chemokine expression in the fetal brain that is prolonged in the postnatal amygdala. Inflammation elicited by MIA may prime the fetal brain for alterations seen in the glial environment and this in turn have deleterious effects on neuronal populations as seen in the amygdala at P14. These findings may suggest that MIA induced during amygdalar development may predispose offspring to amygdalar related disorders such as heightened anxiety, fear impairment and also neurodevelopmental disorders.

Reading Lydgate's Troy Book: patronage, politics, and history in Lancastrian England

This thesis, Reading Lydgate's Troy Book: Patronage, Politics and History in Lancastrian England, discusses the relationship between John Lydgate as a court poet to his patron Henry V. I contend that the Troy Book is explored as a vehicle to propagate the idea that the House of Lancaster is the legitimate successor to King Richard II in order to smooth over the usurpation of 1399. Paul Strohm's England's Empty Throne was a key influence to the approach of this thesis' topic. I examine that although Chaucer had a definitive impact on Lydgate's writing, Lydgate is able to manipulate this influence for his own ambitions. In order to enhance his own fame, Lydgate works to promote Chaucer's canon so that as Chaucer's successor, he will inherit more prestige. The Trojan war is seen in context with the Hundred Years War, and can be applied contextually to political events. Lydgate presents characters that are vulnerable to human failings, and their assorted, complicated relationships. Lydgate modernises the Troy Book to reflect and enhance his Lancastrian society, and the thesis gives a contextual view of Lydgate's writing of the Troy Book. Lydgate writes for a more varied target audience than his thirteenth-century source, Guido delle Colonne, and there is a deliberation on the female characters of the Troy Book which promulgates the theory that Lydgate takes a proactive and empathetic interest in women's roles in society. Furthermore Lydgate has never really been accepted as a humanist, and I look at Lydgate's work from a different angle; he is a self-germinating humanist. Lydgate revives antiquity to educate his fifteenth-century audience, and his ambition is to create a memorial for his patron in the vernacular, and enhance his own fame as a poet separate from Chaucer's shadow.

Within the carnal: re-reading Merleau-Ponty through the language of drawing

In order to present visual art as a paradigm for philosophy, Merleau-Ponty investigated the creative processes of artists whose work corresponded closely with his philosophical ideas. His essays on art are widely valued for emphasising process over product, and for challenging the primacy of the written word in all spheres of human expression. While it is clear that he initially favoured painting, Merleau-Ponty began to develop a much deeper understanding of the complexities of how art is made in his late work in parallel with his advancement of a new ontology. Although his ontology remains unfinished and only exists as working notes and a manuscript entitled The Visible and Invisible, Merleau-Ponty had begun to appreciate the fundamental role drawing plays in the making of art and the creation of a language of expression that is as vital as the written or spoken word. Through an examination of Merleau-Ponty’s unfinished manuscript and working notes my thesis will investigate his working methods and use of materials and also explore how he processed his ideas by using my own art practice as the basis of my research. This research will take the form of an inquiry into how the unfinished and incomplete nature of text and artworks, while they are still ‘works in progress’, can often reveal the more human and carnal components of creative processes. Applying my experience as a practitioner and a teacher in an art school, I focus on the significance of drawing practice for Merleau-Ponty’s later work, in order to rebalance an overemphasis on painting in the literature. Understanding the differences between these two art forms, and how they are taught, can offer an alternative engagement with Merleau-Ponty’s later work and his struggle to find a language to express his developing new ontology. In addition, by re-reading his work through the language of drawing, I believe we gain new insights which reaffirm Merleau-Ponty's relevance to contemporary art making and aesthetics.