Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.

Nanoscale electronic properties of conjugated polymers and nanocrystals

The objective of this thesis is the exploration and characterisation of the nanoscale electronic properties of conjugated polymers and nanocrystals. In Chapter 2, the first application of conducting-probe atomic force microscopy (CP-AFM)-based displacement-voltage (z-V) spectroscopy to local measurement of electronic properties of conjugated polymer thin films is reported. Charge injection thresholds along with corresponding single particle gap and exciton binding energies are determined for a poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] thin film. By performing measurements across a grid of locations on the film, a series of exciton binding energy distributions are identified. The variation in measured exciton binding energies is in contrast to the smoothness of the film suggesting that the variation may be attributable to differences in the nano-environment of the polymer molecules within the film at each measurement location. In Chapter 3, the CP-AFM-based z-V spectroscopy method is extended for the first time to local, room temperature measurements of the Coulomb blockade voltage thresholds arising from sequential single electron charging of 28 kDa Au nanocrystal arrays. The fluid-like properties of the nanocrystal arrays enable reproducible formation of nanoscale probe-array-substrate junctions, allowing the influence of background charge on the electronic properties of the array to be identified. CP-AFM also allows complementary topography and phase data to be acquired before and after spectroscopy measurements, enabling comparison of local array morphology with local measurements of the Coulomb blockade thresholds. In Chapter 4, melt-assisted template wetting is applied for the first time to massively parallel fabrication of poly-(3-hexylthiophene) nanowires. The structural characteristics of the wires are first presented. Two-terminal electrical measurements of individual nanowires, utilising a CP-AFM tip as the source electrode, are then used to obtain the intrinsic nanowire resistivity and the total nanowire-electrode contact resistance subsequently allowing single nanowire hole mobility and mean nanowire-electrode barrier height values to be estimated. In Chapter 5, solution-assisted template wetting is used for fabrication of fluorene-dithiophene co-polymer nanowires. The structural characteristics of these wires are also presented. Two-terminal electrical measurements of individual nanowires indicate barrier formation at the nanowire-electrode interfaces and measured resistivity values suggest doping of the nanowires, possibly due to air exposure. The first report of single conjugated polymer nanowires as ultra-miniature photodetectors is presented, with single wire devices yielding external quantum efficiencies ~ 0.1 % and responsivities ~ 0.4 mA/W under monochromatic illumination.

The study of molecular variation in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.)

Polymorphic microsatellite DNA loci were used here in three studies, one on Salmo salar and two on S. trutta. In the case of S. salar, the survival of native fish and non-natives from a nearby catchment, and their hybrids, were compared in a freshwater common garden experiment and subsequently in ocean ranching, with parental assignment utilising microsatellites. Overall survival of non-natives was 35% of natives. This differential survival was mainly in the oceanic phase. These results imply a genetic basis and suggest local adaptation can occur in salmonids across relatively small geographic distances which may have important implications for the management of salmon populations. In the first case study with S trutta, the species was investigated throughout its spread as an invasive in Newfoundland, eastern Canada. Genetic investigation confirmed historical records that the majority of introductions were from a Scottish hatchery and provided a clear example of the structure of two expanding waves of spread along coasts, probably by natural straying of anadromous individuals, to the north and south of the point of human introduction. This study showed a clearer example of the genetic anatomy of an invasion than in previous studies with brown trout, and may have implications for the management of invasive species in general. Finally, the genetics of anadromous S. trutta from the Waterville catchment in south western Ireland were studied. Two significantly different population groupings, from tributaries in geographically distinct locations entering the largest lake in the catchment, were identified. These results were then used to assign very large rod caught sea trout individuals (so called “specimen” sea trout) back to region of origin, in a Genetic Stock Identification exercise. This suggested that the majority of these large sea trout originated from one of the two tributary groups. These results are relevant for the understanding of sea trout population dynamics and for the future management of this and other sea trout producing catchments. This thesis has demonstrated new insights into the population structuring of salmonids both between and within catchments. While these chapters look at the existence and scale of genetic variation from different angles, it might be concluded that the overarching message from this thesis should be to highlight the importance of maintaining genetic diversity in salmonid populations as vital for their long-term productivity and resilience.