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 balance between the pro-inflammatory effect of plasma noradrenaline and the anti-inflammatory effect of neuronal noradrenaline determines the peripheral effect of noradrenaline

Perfusion experiments on an isolated, canine lateral saphenous vein segment preparation have shown that noradrenaline causes potent, flow dependent effects, at a threshold concentration comparable to that of plasma noradrenaline, when it stimulates the segment by diffusion from its microcirculation (vasa vasorum). The effects caused are opposite to those neuronal noradrenaline causes in vivo and that, in the light of the principle that all information is transmitted in patterns that need contrast to be detected – star patterns need darkness, sound patterns, quietness – has generated the hypothesis that plasma noradrenaline provides the obligatory contrast tissues need to detect and respond to the regulatory information encrypted in the diffusion pattern of neuronal noradrenaline. Based on the implications of that hypothesis, the controlled variable of the peripheral noradrenergic system is believed to be the maintenance of a set point balance between the contrasting effects of plasma and neuronal noradrenaline on a tissue. The hypothalamic sympathetic centres are believed to monitor that balance through the level of afferent sympathetic traffic they receive from a tissue and to correct any deviation it detects in the balance by adjusting the level of efferent sympathetic input it projects to the tissue. The failure of the centres to maintain the correct balance, for reasons intrinsic or extrinsic to themselves, is believed to be responsible for degenerative and genetic disorders. When the failure causes the balance to be polarised in favour of the effect of plasma noradrenaline that is believed to cause inflammatory diseases like dilator cardiac failure, renal hypertension, varicose veins and aneurysms; when it causes it to be polarised in favour of the effect of neuronal noradrenaline that is believed to cause genetic diseases like hypertrophic cardiopathy, pulmonary hypertension and stenoses and when, in pregnancy, a factor causes the polarity to favour plasma noradrenaline in all the maternal tissues except the uterus and conceptus, where it favours neuronal noradrenaline, that is believed to cause preeclampsia.

Echoes of existentialism in the works of Carlos Fuentes

In this thesis I have set out to trace the echoes of existentialism in the work of the Mexican novelist, Carlos Fuentes scrutinizing, in particular, La región más transparente, La muerte de Artemio Cruz and Cambio de piel. In the opening segment of the thesis I outline the essential tenets of existentialist thought and how it became the predominant philosophical and literary movement of the early part of the twentieth-century. Stemming from the work of Sören Kierkegaard in Denmark towards the end of the nineteenth-century, it challenged the arid philosophies of previous generations and provided a new way of looking at man and the human condition. In this opening chapter, I study the works of the more important philosophers in this regard such as Heidegger, Sartre, Jaspers, Marcel, Unamuno, and Ortega y Gasset and show how each in his own way contributed to the further development of the new philosophy. Chapter 2 is concerned with the spread of existentialism to the Latin American continent. In the early part of the twentieth-century, Mexico was emerging from a turbulent revolutionary period and seeking a solution to the fractured nature of its society. The Spanish philosopher, Ortega y Gasset, and the many Spanish intellectuals who sought refuge from Franco’s dictatorship in Mexico, helped to popularise the new philosophy and these lively debates about existentialism served to underpin ideas around mexicanidad or Mexican national identity. Carlos Fuentes was deeply immersed in the debate of his time, positioned as he was as a prominent public intellectual. In La muerte de Artemio Cruz he shows us how great wealth and power are a poor recompense for the loss of love and compassion and lead only to alienation and selfishness. In his other best known novel, La región más transparente, he explores the rise of modern Mexico and its society – an inauthentic society that is corrupted by a scramble for wealth and self-aggrandizement. The final chapter is devoted to the study of Cambio de piel which is concerned with violence and alienation as central pillars of existence. The violence depicted here precipitates a crisis in the human condition and an accompanying sense of alienation. The thesis seeks to establish that existentialism is central not only to Fuentes’s literary concerns but also forms a part of his ethics as an artist.