Target recognition by multi-domain RNA-binding proteins

Multi-functional RNA binding proteins regulate and coordinate the many steps of RNA metabolism. Accurate functioning of these processes is vital in cells and misregulation has been linked to many human diseases. RNA binding proteins contain multiple RNA binding domains. The ability to perform multiple functions depends on the recognition of a diverse range of targets and domains are used combinatorially to achieve this. In this thesis I ask how the sequence specificity of low affinity RNA-binding domains and the interplay between said domains plays a role in RNA target selectivity. Within this question I focus on three proteins; TUT4, a uridyl transferase involved in the regulation of both non-coding RNAs and histone mRNA; FMRP, a translational repressor whose loss in cells is the cause of Fragile X Syndrome; and RBM10 a regulator of alternative splicing and miRNA biogenesis. I found that through the use of separate RNA binding domains both TUT4 and RBM10 are able to exert flexibility in target recognition; TUT4 by using two CCHC-type zinc fingers, working independently to recognise short RNA stretches; and RBM10 by using different subsets of domains to recognise either specific high affinity splice site sequences or pre-miRNAs. In FMRP the determination of the sequence specificity of KH1 allowed us to isolate its contribution to target selection. In a secondary objective, looking at methodologies used in RNA-protein interaction, SIA was improved to make it both less laborious and to reduce the sample requirements, and with FMRP a novel mutational strategy was used in combination with SIA to determine the sequence specificity of this low affinity domain. In summary these data extend our understanding of the RNA binding mechanisms of the three systems studied and introduces improved or novel methodologies to the future study of protein-RNA interactions

Wave energy converter arrays: Motion response of inter-connected array

Compact wave energy converter (WEC) arrays are a promising option in terms of opti-mizing energy output per unit area of marine space, realizing synergies in O&M tasks and auxiliary installations (substations, export cables, etc.), and achieving economies of scale. Four different levels of connectivity between five OWC spar buoys in a compact array—corresponding to as many mooring configurations—were tested in the Ocean Basin at the University of Plymouth. We find considerable implications of the inter-connectivity on the frequency of heave motion response, with interconnected cases yielding a higher natural frequency and an increase in magnitude compared to the baseline (non-connected) arrangement. This indicates the importance of a holistic inter-connected system design approach required in the early design stages with respect to the wave climate at the deployment site. For instance, for a site off Leixões (Portugal), the frequency upshift obtained through inter-connectivity may be beneficial

Human-in-the-Loop Mixup

Aligning model representations to humans has been found to improve robustness and generalization. However, such methods often focus on standard observational data. Synthetic data is proliferating and powering many advances in machine learning; yet, it is not always clear whether synthetic labels are perceptually aligned to humans - rendering it likely model representations are not human aligned. We focus on the synthetic data used in mixup: a powerful regularizer shown to improve model robustness, generalization, and calibration. We design a comprehensive series of elicitation interfaces, which we release as HILL MixE Suite, and recruit 159 participants to provide perceptual judgments along with their uncertainties, over mixup examples. We find that human perceptions do not consistently align with the labels traditionally used for synthetic points, and begin to demonstrate the applicability of these findings to potentially increase the reliability of downstream models, particularly when incorporating human uncertainty. We release all elicited judgments in a new data hub we call H-Mix

A questionnaire to identify patellofemoral pain in the community: an exploration of measurement properties

Background Community-based studies of patellofemoral pain (PFP) need a questionnaire tool that discriminates between those with and those without the condition. To overcome these issues, we have designed a self-report questionnaire which aims to identify people with PFP in the community. Methods Study designs: comparative study and cross-sectional study. Study population: comparative study: PFP patients, soft-tissue injury patients and adults without knee problems. Cross-sectional study: adults attending a science festival. Intervention: comparative study participants completed the questionnaire at baseline and two weeks later. Cross-sectional study participants completed the questionnaire once. The optimal scoring system and threshold was explored using receiver operating characteristic curves, test-retest reliability using Cohen’s kappa and measurement error using Bland-Altman plots and standard error of measurement. Known-group validity was explored by comparing PFP prevalence between genders and age groups. Results Eighty-four participants were recruited to the comparative study. The receiver operating characteristic curves suggested limiting the questionnaire to the clinical features and knee pain map sections (AUC 0.97 95 % CI 0.94 to 1.00). This combination had high sensitivity and specificity (over 90 %). Measurement error was less than the mean difference between the groups. Test–retest reliability estimates suggest good agreement (N = 51, k = 0.74, 95 % CI 0.52–0.91). The cross-sectional study (N = 110) showed expected differences between genders and age groups but these were not statistically significant. Conclusion A shortened version of the questionnaire, based on clinical features and a knee pain map, has good measurement properties. Further work is needed to validate the questionnaire in community samples

Results of a multicentre UK-wide compassionate use programme evaluating the efficacy of idelalisib monotherapy in relapsed, refractory follicular lymphoma.

Follicular lymphoma (FL) is an indolent B-cell malignancy with a variable course. Standard immuno-chemotherapy incorporate alkylator and anti-CD20 monoclonal antibody as first line (Rummel et al, 2013) commonly followed by 24 months rituximab maintenance (Salles et al, 2008). Anthracycline, purine analogue, and alkylator combination are used at relapse and younger patients may have remissions consolidated with autologous or allogeneic stem-cell transplantation (alloSCT) (Kothari et al, 2014). Relapsed or refractory (R/R) FL in patients unfit for transplantation or post-transplantation is incurable, and remains an unmet need

The New COAST Laboratory of Plymouth University: a World-Class Facility for Marine Energy

During the development of coastal, ocean engineering and marine renewables technology, physical modelling must be undertaken. The new COAST laboratory at Plymouth University comprises two wave basins and two wave flumes that can all produce waves and currents together. Initial commissioning experiments of the facilities show that the design specifications were met in the majority of cases or exceeded. Despite the newness of the laboratory, experiments to investigate the motion response of a wave energy converter and to investigate wave impacts on moored structures have been undertaken in collaboration with both universities and commercial clients

Modelling of the buckling of a diaphragm–spine structure for a wave energy converter

publisher: Elsevier articletitle: Modelling of the buckling of a diaphragm–spine structure for a wave energy converter journaltitle: Materials & Design articlelink: http://dx.doi.org/10.1016/j.matdes.2017.01.041 content_type: article copyright: © 2017 Published by Elsevier Ltd

Protein-RNA specificity by high-throughput principal component analysis of NMR spectra

Defining the RNA target selectivity of the proteins regulating mRNA metabolism is a key issue in RNA biology. Here we present a novel use of principal component analysis (PCA) to extract the RNA sequence preference of RNA binding proteins. We show that PCA can be used to compare the changes in the nuclear magnetic resonance (NMR) spectrum of a protein upon binding a set of quasi-degenerate RNAs and define the nucleobase specificity. We couple this application of PCA to an automated NMR spectra recording and processing protocol and obtain an unbiased and high-throughput NMR method for the analysis of nucleobase preference in protein–RNA interactions. We test the method on the RNA binding domains of three important regulators of RNA metabolism

Engaging with community researchers for exposure science: lessons learned from a pesticide biomonitoring study

A major challenge in biomonitoring studies with members of the general public is ensuring their continued involvement throughout the necessary length of the research. The paper presents evidence on the use of community researchers, recruited from local study areas, as a mechanism for ensuring effective recruitment and retention of farmer and resident participants for a pesticides biomonitoring study. The evidence presented suggests that community researchers' abilities to build and sustain trusting relationships with participants enhanced the rigour of the study as a result of their on-the-ground responsiveness and flexibility resulting in data collection beyond targets expected