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.

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.

Straw - structured reading, analysis and writing in humanities disciplines

Technology provides a range of tools which facilitate parts of the process of reading, analysis and writing in humanities, but these tools are limited and poorly integrated. Methods of providing students with the skills to make good use of a range of tools to create an integrated, structured process of writing in the disciplines are examined, compared and critiqued. Tools for mindmapping and outlining are examined both as reading tools and as tools to structure knowledge and explore ontology creation. Interoperability between these and common wordprocessors is examined in order to explore how students may be taught to develop a structured research and writing process using currently available tools. Requirements for future writing tools are suggested

The Kyoto School and Confucianism: a Confucian reading of the philosophy of history and political thought of Masaaki Kosaka

This dissertation examines the philosophy of Masaaki Kōsaka (1900-1969) from the East Asian perspective of Confucianism, which I believe is the most appropriate moral paradigm for comprehending his political speculations. Although largely neglected in post-war scholarship, Kōsaka was a prominent member of the Kyoto School during the 1930s and 40s. This was a group of Japanese thinkers strongly associated with the philosophies of Kitarō Nishida and Hajime Tanabe. Kōsaka is now best known for his participation in the three Chūō Kōron symposia held in 1941 and 1942. These meetings have been routinely denounced by liberal historians due to the participants’ support for the Pacific War and the Co-Prosperity Sphere. However, many of these liberal portrayals have failed to take into account the full extent of the group’s resistance to the military junta of Hideki Tōjō. Adopting the methods and techniques of the empirical disciplines of academic history and Orientalism, I develop an interpretative framework that is more receptive to the political values that mattered to Kōsaka as a Confucian inspired intellectual. This has necessitated the rejection of moral history, which typically prioritises modern liberal values brought a priori to the historical record of wartime Japan, as well as recognition of the different ontological foundations that inform the unique political theories of the East Asian intellectual tradition. Reinforced by the prior research of Michel Dalissier and Graham Parkes, as well as my own reading of the Confucian canon, I adopt David Williams’s thesis of ‘Confucian Revolution’ as my principle schema of interpretation. This, I believe, is better able to reconcile Kōsaka’s support for the war with his strong condemnation of the imperialist practices of the Japanese military. Moreover, acknowledging the importance of Confucianism allows us to fully appreciate Kōsaka’s strong affinity for Kant’s practical metaphysics, Hegel’s political philosophy and Ranke’s historiography.