VictorJuiz/thesis huggingface dataset:
Investigating the neuroprotective function of TLDc proteins

A recent World Health Organisation Global Burden of Disease study reports a yearly increase in the prevalence of neurodegenerative diseases, with more than 100 million people worldwide expected to be living with dementia by 2050. These disorders represent a range of neurological conditions characterised by selective neuronal cell death; no effective treatments have been developed, with the available therapy only able to reduce the symptoms in some cases. Although etiology of neurodegenerative diseases is not well understood, some common pathological features are shared between them, including protein aggregation and oxidative stress. Identification of the molecular mechanisms underlying these processes would therefore deepen our understanding of the disease pathogenesis and help in the search for new therapeutic targets. Members of a conserved protein family (TLDc) have been shown in recent years to protect neurons from oxidative insults in vitro and in vivo and play a role in oxidative stress response regulation via unknown mechanism. In addition, TLDc mutations are causative in range of neurological disorders, some characterised by neurodegeneration. Therefore, further analysis of this particular protein family may provide new insights into fundamental protective mechanisms that could be harnessed in the future.
The aim of this thesis was to investigate the mechanism of action of the TLDc protein oxidation resistance 1 (Oxr1) in oxidative stress protection and in the maintenance of neural tissue homeostasis. Using a combination of in vitro assays and in animal models with disruption or overexpression of Oxr1, I have shown that Oxr1 interacts with the potent antioxidant enzyme peroxiredoxin-2 where it regulates its post-translational modifications and oligomerisation in a brain-region specific manner. I have also for the first time discovered a molecular function of Oxr1 by showing it possesses holdase chaperone activity in vitro, suggesting it acts as a putative chaperone. Next, to understand the cause of neurodegeneration in the Oxr1 knockout mouse, transcriptional profiling was carried out, revealing an induction of presymptomatic neuroinflammatory markers, suggesting Oxr1 is critical for the normal inflammatory response in the brain. I have also produced preliminary data suggesting a role for Oxr1 in autophagy. Finally, computational analysis of transcriptional activity and regulation of TLDc family members suggests high degree of functional conservation between TLDc genes and their involvement in processes throughout the body, proposing novel directions for future studies. Together, my results contribute to our understanding of the functions of TLDc genes in the CNS and the role of Oxr1 in oxidative stress protection and proteostasis.

Keywords: cerebellum
oxidative stress
neurodegeneration
Advisor: Oliver, P
Davies, K
Dissecting the upstream regulation of the GATA genes during heart development

The cardiac GATA transcription factors (TFs) play vital roles in the developing myocardium and potentially during regeneration. While their function as cardiac effectors has been well studied, the precise molecular mechanisms driving their activity have yet to be parsed. Here, I have investigated the upstream regulation of the cardiac GATA factors during cardiogenesis in zebrafish by interrogating their cis-regulatory genomic landscapes. Using cardiomyocyte-specific ATAC-Seq datasets, I have identified putative enhancers around the gata4, 5 and 6 loci that are accessible during cardiac development and regeneration and tested their activity in vivo using a novel, highly efficient reporter system in zebrafish.
I observed heart-specific reporter activity driven by the majority of the newly identified putative gata5 and gata6 enhancers, within particular subpopulations of these TFs domains of expression. The reported activity of Tg(Gata5-E5-mCherry) was of particular interest. I characterised Gata5-E5-mCherry positive populations using a combination of microscopic and transcriptomic analyses. I then tested the requirement of overrepresented TF binding site motifs for the activity of Gata5-E5 by assessing changes in enhancer-driven reporter expression after binding site perturbation. Gata5-E5 was active in a population of extracardiac cells adjacent to the inflow tract that expressed epithelial markers, hypothesised to act as support cells for second heart field progenitor cells. Gata5-E5 was also active in a population of CMs in the inflow tract region that expressed the hallmarks of cardiac conduction system cells. Binding site studies revealed a potential upstream regulation by Gata5, Nkx2.5/Nkx2.7 and Tbx2a/2b/5a to drive the activity of gata5 in these cells. Gata5-E5 was also active in CMs throughout the atrium and ventricle and binding site studies suggested an upstream role for Gata5, Meis1b, Nkx2.5/Nkx2.7 and Tbx20 in regulating Gata5-E5 activity in this subpopulation of CMs.
Future experiments will involve ChIP-Seq to test the direct interactions suggested by binding site perturbation studies, and Capture-C to investigate topologically associating domains, ultimately revealing the functional interaction between these enhancers and their regulated GATA genes. Taken together, my work has begun to uncover the exact upstream spatiotemporal regulation of the cardiac GATA factors in various subpopulations of the heart during early cardiogenesis at high resolution. Comprehension of these complex networks is critical to understand the molecular basis of GATA-related congenital heart defects.

Advisor: Simoes, F
Riley, P
Patient, R
Genomic analyses of polysaccharide capsules in Neisseria species

Neisseria meningitidis is one of several Neisseria species that asymptomatically colonise the human nasopharynx. Occasionally, N. meningitidis invades the bloodstream, resulting in invasive meningococcal disease (IMD). In most settings, expression of a serogroup A, B, C, W, X or Y polysaccharide capsule is essential for IMD. Previously, capsules were considered unique to N. meningitidis, among the Neisseria, possibly acquired by horizontal genetic transfer (HGT). In this thesis, genomic analyses further investigate the distribution and evolution of capsules in Neisseria species.
Chapter 2 identifies orthologues of conserved capsule export genes in 13 nonpathogenic Neisseria species. Novel capsule synthesis genes are further characterised and found to resemble those present in other encapsulated bacteria including N. meningitidis, Actinobacillus and Haemophilus. Preliminary 1H NMR results are consistent with some of the structural predictions arising from these comparisons.
Phylogenetic analyses in Chapter 3 indicate that the meningococcal capsule has undergone HGT with other Neisseria species on at least two occasions. Sequence analyses are consistent with hypotheses postulating that the meningococcal capsule was acquired de novo through HGT, with Neisseria subflava identified as a potential donor, but are not sufficient to definitively prove that such an event occurred.
Finally, Chapter 4 explores a more contemporary example of HGT within the meningococcal capsule locus. Capsule switching from serogroup E to serogroup B is shown to be responsible for cases of IMD in clonal complexes cc60 and cc1157. This example is further explored to discuss the interaction between the capsule and the wider genetic profile of meningococci, and their association with IMD.
These analyses expand on previous understanding of the distribution and evolution of the polysaccharide capsule in the Neisseria, and the implications for the epidemiology of IMD. Discussions of this important virulence-associated factor address its enigmatic existence in organisms that principally colonise the nasopharynx without causing disease.

Keywords: bacteria
virulence
evolution
commensals
genomes
Advisor: Maiden, M
Sequelae of selected gastrointestinal infections: incidence, risk factors and economic impact on the National Health Service in England

Background Sequelae of reactive arthritis (ReA), irritable bowel syndrome (IBS), Guillain-Barré syndrome (GBS), ulcerative colitis (UC), Crohn’s disease (CD) and Rheumatoid arthritis (RA) following gastrointestinal (GI) infections can occur. Evidence suggests proton pump inhibitors (PPI) or antibiotics can increase the risk of GI infections, but their role in sequelae onset is unclear. Further, the impact on the National Health Service (NHS) of GI infections sequelae is unknown.
Methods Four studies were conducted in this thesis. First, a systematic review (SR) to determine the association between prior use of PPI or treatment with antibiotics and the onset of ReA and IBS amongst patients with Campylobacter or non-typhoidal Salmonella (NTS) infections. Second, a population-based study of routinely collected linked primary care, hospital, deprivation and deaths data (2000-2015) to determine the incidence of ReA, IBS, GBS, UC, CD, and RA in the 12 months following Campylobacter or NTS infection. Third, a retrospective cohort study to assess the role of antibiotics or PPI in the onset of sequelae amongst patients with Campylobacter infection. Fourth, an economic assessment to determine the impact of sequelae of the selected GI infections on the volume, type and costs of all health care encounters in the periods’ pre- and post-infection.
Results In the SR, only one study reported an elevated risk in the onset of ReA amongst patients with the selected GI infections who had prior PPI prescription. There was no clear association between antibiotics and sequelae onset. In the population-based study, less than two per cent of the patients developed sequelae. Patients with sequelae were mainly females in comparison with those with GI infection only. Of all the sequelae considered, the incidence of IBS was highest in the 12 months post-infection (1.2%). Female Campylobacter patients on PPI were two and a half times more likely to develop IBS. There was no association with antibiotics and the onset of sequelae of campylobacteriosis. Sequelae significantly impacted the NHS with an additional £1.3 million in expenditure on average annually. Males, older people (65+), and those with underlying health conditions incurred the highest costs.
Conclusions The findings raise the need to emphasise the negative consequences of Campylobacter and NTS infections. It highlights the significant impact of sequelae on the NHS and the patient groups with excess expenditure. This is vital in the evaluation of public health interventions to reduce the overall burden of these GI infections. Further evidence to determine the existence of a dose-response relationship between PPI and Campylobacter infection in the onset of IBS is warranted.

Keywords: Sequelae
direct costs
Proton pump inhibitors
Salmonellosis
Campylobacter
Antibiotics
Campylobacteriosis
Advisor: Fanshawe, T
McCarthy, N
Perera, R
Violato, M
Assessing early postoperative recovery following lower limb joint replacement

Improving perioperative recovery is critical to enhance patient care, ensure timely discharge from the patient, clinician and hospital perspective and improve short and long-term outcomes after surgery.
A systematic review was performed examining tools for early post-operative recovery after elective lower limb joint replacement. It showed that no fully-validated, patient-reported tools existed. Currently used measures included pain scores, opioid usage, length of stay and surgical satisfaction.
In order to address this need, a patient-reported outcome measure (PROM) and change measure for use in the first six weeks following surgery have been developed. A five-phased, best practice, iterative approach was used.
Planning Phase - Qualitative interviews (n=22) were performed with orthopaedic healthcare professionals, ascertaining if and how clinicians would use such a PROM. These helped determine the views of potential users, and guide structure and layout.
Phase One - Qualitative patient-interviews (n=30) from the day of surgery to nine weeks postoperatively were completed. Analysis of these interviews identified important patient-reported factors in early recovery.
Phase Two - The factors provided from Phase One interviews were used to find questionnaire themes. Items were then generated and pilot questionnaires developed. Items were tested and refined in the context of cognitive debrief interviews (n=34) for potential inclusion in the final tools.
Phase Three - Final testing of questionnaire properties with item reduction (n=168). The Oxford Arthroplasty Early Recovery Score (OARS) is a 14-item PROM measuring health status at the time of testing. The Oxford Arthroplasty Early Change Score (OACS) is a 14-item measure to assess change.
Phase Four - Validation: The OARS and OACS were administered to consecutive patients (n=155) in an independent cohort. Validity and reliability were assessed. Psychometric testing showed positive results, good validity and sensitivity to change.
The OARS and OACS were then utilised in a pilot study to assess the feasibility of day case treatment. Inpatient (n=29) and day-case (n=26) unicompartmental knee arthroplasty (UKA) patients completed the two measures, and the results confirmed that day case treatment and discharge is a valid option.
The work completed in this thesis will now enable these newly developed scores to be used to define and assess an optimal-recovery protocol for lower limb joint replacement.

Keywords: Orthopaedic
Unicompartmental knee replacement
Psychometrics
Surgery
Research
Patient-reported outcome measure
Arthroplasty
Factor analysis
Hip replacement
Quantitative
Postoperative
Patient-reported change measure
Early recovery
Systematic review
Questionnaire development
Knee replacement
Health measurement scales
Joint replacement
Qualitative
Recovery
Advisor: Pandit, H
Jenkinson
Murray, D
Electronic and optoelectronic devices based on 2-dimensional heterostructures

Two-dimensional materials, including graphene, h-BN, and monolayer transition metal dichalcogenides such as MoS2 and WS2, have attracted enormous attention due to their unique properties and potential application in electronics. A variety of heterostructures devices can be made based on 2D materials. In this thesis, we investigate the electronic and optoelectronic properties of heterostructures of 2D crystals grown by chemical vapor deposition.
In our study on graphene-MoS2 heterojunction, we show that a rectification ratio over 104 can be achieved in Au-MoS2-graphene device. The rectifying behavior can be tuned by external gating and photo-irradiation. The decrease of rectification ratio under irradiation can be explained by the quick drop of Au-MoS2 Schottky barrier height, which is derived by fitting the output characteristics of Au-MoS2-Au and Gr-MoS2-Gr device as a metal-semiconductor-metal transistor.
The thickness of 2D materials is found to have a great impact on the properties of WS2-graphene heterostructures. Heterojunction based on graphene and bilayer WS2 have much higher conductivity and photoresponsivity compared to monolayer WS2-graphene device. A greater than unity photogain is measured for both devices. The layer-dependent conductivity and photoresponsivity are due to different electron affinities and band gaps of monolayer and bilayer WS2.
The fabrication methods of vertical heterostructures are also explored, including electron-beam lithography, wet transfer of pre-patterned materials, and graphene printing technique. Using graphene printing, a transfer resolution of 10 mm can be achieved, which is promising to be used in both lateral and vertical device making.

Advisor: Warner, J
Kernel-based hypothesis tests: large-scale approximations and Bayesian perspectives

This thesis contributes to the field of nonparametric hypothesis testing (i.e. two-sample and independence testing) by providing a large-scale framework and developing a Bayesian perspective. We focus on nonparametric measures of homogeneity and dependence by considering the Hilbert norms between the embeddings of probability distributions in the reproducing kernel Hilbert space (RKHS). The rich representation provided by the associated kernel feature map enables the use of multivariate or non-Euclidean observations (e.g. strings and graphs) and it leads to powerful tests that are able to solve challenging problems given enough observations. However, the cost of computing the kernel matrix scales at least quadratically in the number of samples and makes it prohibitive to use in modern large-scale datasets. First, we propose three estimators of the well-known kernel dependence measure, the Hilbert Schmidt Independence Criterion (HSIC), namely the block-based estimator, the Nystrom estimator and the random Fourier feature (RFF) estimator, and establish the corresponding linear time independence test for each of the estimators. Secondly, we consider a normalised version of HSIC, the NOrmalised Cross COvariance (NOCCO) statistic, and propose an RFF approximated NOCCO. This results in a distribution free test that is robust to the kernel bandwidth misspecification. Thirdly, we propose a two-step conditional independence test that extends the popular two-step approach REgression with Subsequent Independence Test (RESIT) through RKHS valued regressions. When used as a part of the classical PC algorithm for causal inference, the resulting algorithm is more robust to hidden variables that induce nonfunctional associations. Finally, we utilise the classical Bayes factor formalism for model comparison and propose a Bayesian two-sample test by modelling the witness function of the well-known kernel measure of homogeneity, the Maximum Mean Discrepancy (MMD), with a Gaussian Process.

Keywords: Bayes Factor
Hilbert Schmidt Independence Criterion
Kernel Methods
Large-Scale
Hypothesis Testing
Advisor: Sejdinovic, D
Filippi, S
Teh, Y
Functional study of waist-hip ratio associated loci and the WARS2 gene as modulators of fat distribution.

Waist-hip ratio (WHR) is a risk factor for diabetes and cardiovascular disease. Genome-wide association studies identified 346 loci linked to increased WHR adjusted for Body Mass Index (WHRadjBMI) (Shungin et al., 2015; Pulit et al., 2018). To elucidate the genetic underpinning of WHRadjBMI, I aimed to identify causal SNPs in 4 of these loci and test the tryptophanyl-tRNA synthetase 2 (WARS2) gene, previously shown to severely affect adipose mass, as modulators of fat distribution and browning.
To prioritise real signals, with colleagues, I selected 3 SNPs in EMILIN2, VEGFA, C5orf67 loci with posterior probability analysis (PPA) scores > 0.95 for functional analysis. In the more complex TBX15-WARS2 locus, we filtered 61 SNPs and selected 5 SNPs with a PPA score > 0.2 and further 8 top-scoring SNPs according to the epi-Phylogenetic Module Complexity Analysis (epi-PMCA). Using electrophoretic mobility shift assays (EMSAs) and luciferase assays in a differentiating human white adipose cell line, I showed that rs3936510 in the C5orf67 locus and rs3810068 in the EMILIN2 affected DNA-protein binding and identified enhancer/promoter activities in these loci. I demonstrated that rs3810068 altered the binding of CCAAT/enhancer-binding protein beta (CEBP/β). In the TBX15-WARS2 locus, I used luciferase assays, RNA degradation analysis and allele-specific qPCR to show that the rs2645294, lead SNP in the 3’UTR of WARS2, did not impact RNA stability.
Wars2 (Wars2V117L/V117L) mice showed previously progressive tissue-specific pathologies including reduced adiposity and browning of white adipose tissue (GTEx-Consortium, 2013; Civelek et al., 2017; Agnew et al., 2018). I show that whilst heterozygous female mice (Wars2+/V117L and Wars2+/-) were unaffected, Wars2V117L/V117L mice failed to gain fat mass on a high-fat diet (HFD) in both sexes, had increased visceral:subcutaneous adipose ratio specifically in males on HFD and showed lower food intake in males. In both sexes, brown adipose tissue (BAT) showed loss of browning markers and mitochondrial dysfunction. In white adipose tissue (WAT), browning markers were upregulated, with a greater difference in the subcutaneous inguinal WAT compared to visceral gonadal WAT. In differentiated primary preadipocytes no difference in browning was observed. Plasma showed elevated levels of Fibroblast growth factor-21 (FGF21) and Growth/differentiation factor 15 (GDF15) In summary, a hypomorphic mutation in the mitochondrial gene WARS2 reduced fat mass irrespective of diet and altered fat distribution in a diet and sex-specific manner, likely due to differences in depot-specific browning and elevation of mitokines FGF21 and GDF15 from other affected tissues.

Keywords: Epigenetics
TBX15
Obesity
Waist-hip ratio
GWAS
WARS2
Advisor: Rodriguez, B
Minchole, A
Multiscale human-based computer modelling and simulation for investigations of arrhythmic risk in acute ischemia

Acute myocardial ischemia is a major cause of sudden arrhythmic death. Variability in ischemic extent and location hampers the understanding of arrhythmic mechanisms and challenges risk diagnosis, stratification and treatment. Moreover, co-existent alterations in ionic channels have been proven to affect ischemia-induced arrhythmogenesis. Ischemic patients with alterations in the sodium (Na+) current availability due to SCN5A mutations, such as Brugada syndrome, are particularly prone to develop cardiac events. Low Na+ current availability can also be acquired with the use of pharmacological treatments. For instance, flecainide is a Na+ channel blocker commonly used for treating atrial fibrillation, but its effects have been proven to increase mortality among ischemic patients, as observed in the CAST trials.
Although electrophysiological abnormalities caused by ischemia have been extensively investigated, the mechanisms linking such changes to high arrhythmic risk remain poorly understood. The use of in silico trials provides an alternative and high-resolution method to investigate ischemia-induced arrhythmogenesis, which overcomes ethical and technological restrictions linked to experiments. Computer simulations also allow considering variability both in ionic conditions and ischemic regions, providing a comprehensive and controlled approach for the investigations on arrhythmogenesis in acute myocardial ischemia. Thereby, I aim to investigate variability in arrhythmic risk and ECG abnormalities using a modelling and simulation framework constructed using extensive clinical and experimental data. Firstly, I present the construction and validation process of the computational framework for simulating acute myocardial ischemia. Secondly, I analyse the effects of size, transmural extent and location of myocardial ischemia on arrhythmogenesis and ECG. Then, I investigate the effects of changes in Na+ current variability on ischemia-induced arrhythmic risk.
In this thesis, I construct a computational framework for simulating acute myocardial ischemia. The simulation pipeline is used for providing mechanistic evidence on ischemia-induced arrhythmogenesis in the context of clinical findings reported in the literature. A thorough analysis of the pro-arrhythmic mechanisms induced by ischemia is expected to provide new insights for formulating effective new anti-arrhythmic therapies.

Advisor: Rodriguez, B
Bueno-Orovio, A