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.

Quaternary geology of the German North Sea and Western Irish Sea Mud Belt: revised stratigraphies, geotechnical properties, sedimentology and anthropogenic impacts

The climatic development of the Mid to Late Quaternary (last 400,000 years) is characterised by fluctuation between glacial and interglacial periods leading to the present interglacial, the Holocene. In comparison to preceding periods it was believed the Holocene represented a time of relative climatic stability. However, recent work has shown that the Holocene can be divided into cooler periods such as the Little Ice Age alternating with time intervals where climatic conditions ameliorated i.e. Medieval Warm Period, Holocene Thermal Optimum and the present Modern Optimum. In addition, the Holocene is recognised as a period with increasing anthropogenic influence on the environment. Onshore records recording glacial/interglacial cycles as well as anthropogenic effects are limited. However, sites of sediment accumulation on the shallow continental shelf offer the potential to reconstruct these events. Such sites include tunnel valleys and low energy, depositional settings. In this study we interrogated the sediment stratigraphy at such sites in the North Sea and Irish Sea using traditional techniques, as well as novel applications of geotechnical data, to reconstruct the palaeoenvironmental record. Within the German North Sea sector a combination of core, seismic and in-situ Cone Penetration Testing (CPT) data was used to identify sedimentary units, place them within a morphological context, relate them to glacial or interglacial periods stratigraphically, and correlate them across the German North Sea. Subsequently, we were able to revise the Mid to Late Quaternary stratigraphy for the North Sea using this new and novel data. Similarly, Holocene environmental changes were investigated within the Irish Sea at a depositional site with active anthropogenic influence. The methods used included analyses on grain-size distribution, foraminifera, gamma spectrometry, AMS 14C and physical core logging. The investigation revealed a strong fluctuating climatic signal early in the areas history before anthropogenic influence affects the record through trawling.