VictorJuiz/thesis huggingface dataset:
Transcriptional mechanisms influencing glycaemic traits and risk of type 2 diabetes
Keywords: islet
lncRNA
RNA-seq
eQTL
T2D

Genome-wide association studies (GWASs) have identifified many genetic variants associated with type 2 diabetes (T2D) risk and glycaemic traits, most of which are noncoding. Although existing islet RNA sequencing (RNA-seq) studies have identified genes regulated by T2D-associated variants, sample sizes are small, and most known regulatory targets are messenger RNAs RNAs). The work presented in this thesis aims to characterise long noncoding RNA (lncRNA) expression in islets, identify candidate lncRNA regulatory mechanisms, and through incorporation of genetic data, identify genes with potential causal mediation of T2D-associated genetic variation.
Using data from 43 GTEx tissues, I first showed that lncRNAs are more tissue specific than mRNAs. Using 38 human islet samples with paired ribosomal rRNA depletion (RD) and poly-A-tailed RNA selection (PA) RNA-seq, I then showed that RD more comprehensively isolates lncRNAs, but the relative effective sequencing depth is approximately half that of PA. Using RD RNA-seq from 54 islet samples, I identified previously unannotated expressed regions, but comparison to lncRNAs from recently published islet-specific annotations showed high discordance between studies. Thus, although RD better captures lncRNAs, its use in transcriptome-wide islet analyses is not practical until sample sizes increase.
By analysing differential expression (DE) by T2D status in islets (n = 207) and 48 tissues from GTEx, I found 89 unique lncRNAs with DE in at least one GTEx tissue, and 75 with DE in islets. To give these functional context, co-expression modules were constructed in each tissue with lncRNAs and mRNAs. One common gene module between pancreas and islet was enriched for lncRNAs with DE, and contained mRNAs associated with insulin secretion regulation, ultimately pointing to lncRNA CTB-12O2.1 as a candidate regulator of T2D-relevant gene expression.
I next incorporated genetic data with islet RNA-seq (n = 426) to demonstrate a modelling approach for identifying sparse, robust genetic models of gene expression. My approach is replicable, robust, and provides models that are sparser and explain more expression variation than LASSO or elastic net models.
Using these models along with expression quantitative trait locus models, I identified 33 candidate expression mediators of genetic associations with T2D and glycaemic traits. Amongst these were two lncRNAs that were transcriptionally associated with biologically relevant mRNAs, making them candidate regulatory targets of corresponding T2D-associated noncoding genetic variants.
The data presented throughout has therefore implicated previously unstudied lncRNAs in T2D risk and the regulation of insulin secretion, and has demonstrated how integration of disease-focussed islet RNA-seq and large-scale public datasets such as GTEx and GWAS meta-analyses can effectively identify novel regulatory mechanisms underlying genetic associations with T2D.
Nanostructured molybdenum disulfide thin film based electrocatalysts for hydrogen evolution reaction
Keywords: Molybdenum disulfide
Water splitting
Nanostructure
Hydrogen evolution reaction
Catalysis

2H-Molybdenum disulfide (2H-MoS2) with catalytically active edges has emerged as a promising catalyst for the hydrogen evolution reaction (HER), 2H+ + 2e− → H2. Towards designing highly active MoS2 catalyst with maximized edge density and activated basal surfaces, this DPhil project focused on the synthesis of nanostructured MoS2 thin film based HER electrocatalysts, using chemical vapor deposition (CVD), gas phase treatments and thermal annealing (TA) methods, followed by characterisation and electrochemical testing of their structural and catalytic properties.
Firstly, a reproducible and scalable synthesis method for high-quality 3D edge rich (3D-ER) MoS2 nanoplatelets utilizing single-step CVD approach was developed. Tailoring CVD parameters resulted in the optimized structure for HER that consists of larger MoS2 platelets with smaller layered MoS2 sheets growing perpendicularly, which increases the total number of edge sites within a given geometric area. By systematically controlling the growth temperature, tunable film thickness and surface morphology were achieved, enabling the optimized combination of edge density, inter-planar charge transport and sufficient binding with the substrate as well as fast removal of gas bubbles via a superaerophobic surface.
Subsequently, gas phase treatments for post-growth modification was applied to activate the catalytically inactive basal plane sites of 3D-ER-MoS2. Hydrogen (H2) annealing and oxygen (O2) plasma etching were utilized to generate defects (cracks, pits, holes, and vacancies) that can catalyze HER in the basal surfaces. By controlling O2 plasma exposure time and H2 annealing temperature, tunable defect density, surface area, and catalytic activity enhancement can be obtained. Optimum treatment conditions led to dramatic improvements in electrocatalytic activity.
Lastly, a hybrid electrocatalyst was prepared by growing Pt nanocrystals on the surface of 3D-ER-MoS2 via TA of Pt precursor. By varying synthesis conditions – precursor loading and TA temperature – average size and specific surface area of Pt nanoparticles can be precisely controlled. Results show that higher Pt loading yields better HER performance despite a smaller specific surface area; higher TA temperature delivers a larger average particle size of the Pt crystals and lowers HER activity. Larger average size led to fast sintering and thus poor durability of the catalyst. The outstanding HER activity of Pt/MoS2 is attributed to highly-dispersed Pt nanoparticles grown on MoS2 basal surfaces, large MoS2 edge density and Pt – S bonding effect induced activity improvement of MoS2 as well as 3D porous network assisted superaerophobic surface.
Mathematical modelling of cell cycle network motifs controlling M-Phase progression
Keywords: Mathematical Modelling
APC/C
Bistability
Cyclins
Cell Cycle

Eukaryotic cells must coordinate growth, replication of their genetic material, and cell division in order to generate two progeny cells from a single progenitor. M-phase is a critical phase of this process during which newly replicated DNA is precisely segregated into two distinct fractions, followed by cell division to produce two new daughter cells. M-phase is a component of both the mitotic cell cycle, during which each daughter cell should inherit an exact copy of the genetic material from the parent cell, and of meiosis, during which each daughter should receive only half of the genetic material from the parent cell to generate a haploid gamete. Despite these differences, both mitotic and meiotic M-phases share many of the same regulatory components.
In this thesis we present work from four different studies in which mathematical modelling is used to analyse the behaviour of the biochemical reaction networks controlling M-phase progression in mitosis and meiosis. We firstly present a theoretical analysis of a conserved network motif (termed here the Feedback-amplified Domineering Substrate or FADS motif), which is responsible for creating bistable switches controlling cell cycle progression at multiple points, including progression through and exit from mitotic M-phase.
We then present three sets of work using mathematical models in combination with data provided by experimental collaborators to examine the regulation of M-phase progression in mitosis and meiosis. We present evidence for how variations on common regulatory themes can generate the distinct outcomes required in each case.
Molecular flexibility of DNA as a major determinant of RAD51 recruitment
Keywords: polymerisation
ssDNA
dsDNA
RAD51
surface plasmon resonance (SPR)
mathematical model
homologous recombination

The timely activation of homologous recombination (HR) is essential for the maintenance of genome stability, in which the RAD51 recombinase plays a central role. In vivo, RAD51 polymerises on single-stranded DNA (ssDNA) at double-strand breaks (DSBs) to catalyse HR-dependent DSB repair. Biochemically, human RAD51 polymerises faster on ssDNA compared to double-stranded DNA (dsDNA), raising a key conceptual question: how does it discriminate between them? Throughout this thesis, I tackled this problem by systematically assessing RAD51 binding kinetics on ssDNA and dsDNA differing in length and flexibility using surface plasmon resonance. By fitting detailed polymerisation models informed by the experimental datasets, I suggest that RAD51 is a mechano-sensor that polymerises faster on flexible ssDNA compared to rigid ssDNA or dsDNA. Furthermore, I suggest that the energy released during RAD51 polymerisation is sufficient to overcome any entropic penalty to binding flexible ssDNA. This model presents a new general framework suggesting that the flexibility of DNA, which may increase locally as a result of DNA damage, plays an important role in recruiting repair factors that multimerise at sites of DNA damage.
Neolithic occupation and stone working on the Yorkshire Wolds
Keywords: Yorkshire Wolds
Lithic analysis
Surface scatters
Mobility

This thesis explores the evidence for Neolithic occupation and stone working on the Yorkshire Wolds based on stray finds and lithic scatters from surface contexts. Traditional models for Neolithic occupation are based largely on evidence from excavated contexts, in particular the groups of Neolithic pits at Rudston, and Neolithic houses on the Holderness coast. Extensive scatters of worked flint, however, have been identified on the Yorkshire Wolds. These scatters have not been incorporated into accounts of Neolithic occupation for two reasons: 1) the lithic scatters are typically characterised by low-densities of artefacts, and; 2) the scatters typically contain few artefacts which are typologically diagnostic. A methodology that addresses both of these problems was developed, using: 1) an implementation of Tobler’s resel-based GIS to apply focal functions/spatial filters to polygon features in order to identify spatial patterning in survey data characterised by low-densities of artefacts, and; 2) a method for assigning dates to stone tools and lithic debitage using artefact scores based on diagnostic traits identified through the analysis of lithic assemblages from excavated contexts. The methodology was developed using case studies drawn from a study area centred on the parish of Fimber that had previously been investigated in the nineteenth century by J.R. Mortimer. Analysis of lithic assemblages from sixteen of the Neolithic burial mounds excavated by Mortimer and a surface scatter at Wharram-le-Street close to the former source of the Gypsey Race was carried out. This analysis indicates that traditional models of Neolithic occupation based on a distinction between the High Wolds and Low Wolds cannot be sustained on the basis of evidence from surface contexts and that Neolithic stone working traditions on the Yorkshire Wolds were constrained by the nature of the raw materials available to local communities.
The cusp of capacity: empowering and protecting people in decisions about treatment and care
Keywords: Autonomy
Decision-making
Mental capacity
Best interests
Mental health

The law’s cliff-edge approach to mental capacity denies those who lack capacity any right to determine what will happen to them. Consequently, the test for capacity (contained in section 3 of the Mental Capacity Act 2005) must accurately distinguish between those who can and cannot make autonomous decisions.
However, the test relies on too narrow a conception of autonomy, preventing it from capturing impairments in the content of the person’s beliefs or values, rather than their decision-making processes. Moreover, whether a decision is autonomous is rarely as clear-cut as the threshold approach presupposes, and there is substantial ambiguity on the cusp of capacity, exacerbated by the realities of assessing capacity in practice. Faced with this uncertainty, decision-makers have sought to manipulate the test through straining the ‘use or weigh’ criterion in section 3, and more readily rebutting the presumption of capacity where the person wishes to do something that will harm them. This thesis therefore advocates introducing a new authenticity limb to the test that asks whether the person’s values or beliefs are the product of an illness or disorder, as well as greater guidance to enhance the consistency with which the test is applied.
Even so, as no test can infallibly distinguish autonomous from non-autonomous decisions, the law’s cliff-edge approach needs softening. To address concerns that the best interests provisions currently facilitate risk aversion and paternalism, a new framework is proposed to encourage decision-makers to prioritise the wishes of the individual, through a rebuttable presumption that their wishes be determinative of their best interests unless giving effect to them would expose the person to a serious risk of significant harm. If this is rebutted, the weight accorded to the person’s wishes ought to be proportionate to the strength of those wishes when determining what is in their best interests.
Oxonium ions, rearrangements, and natural products
Keywords: Oxonium Ions

This thesis focuses on the studies of a set of biologically relevant oxonium ions pertinent to the natural product biosynthesis of the red algae of the genus Laurencia. The total synthesis of these oxonium ions is reported along with their structural elucidation supported by extensive NMR spectroscopic analysis and DFT computations. The biosynthetic significance of these oxonium ions is demonstrated by their direct derivatisation into 12 natural products, namely (Z/E)-bromofucins, (Z/E)-chlorofucins, (Z/E)-elatenynes, laurendecumenyne B, laurefurenyne E, laurefurenyne F, ent-(Z/E)-laurefucins and ent-acetyllaurefucin.
Furthermore, 6 additional natural products are synthesised indirectly from the oxonium ions, namely (Z/E)-notoryne, laurefurenyne C, laurefurenyne D, ent-deacetyllaurencin and ent-laurencin. The total synthesis of laurefurenynes C-F also enabled their structural reassignment.
Chapters 1-3 of this thesis introduce the project, provide a brief summary of the chemistry of oxonium ions, and an overview of the proposed biosyntheses of Laurencia natural products.
Chapters 4-6 report the total synthesis of the oxonium ions, their characterisation and their direct derivatisation into various natural products.
Chapters 7-8 concerns the total synthesis of ent-deacetyllaurencin, ent-laurencin and the total synthesis of laurefurenyne C-F and their structural reassignment.
Eating disorders and compulsivity: neural, computational, and psychopharmacological approaches
Keywords: Computational Modelling
Compulsivity
N-Acetyl Cysteine
Eating Disorders
MRI

This DPhil thesis takes the transdiagnostic construct of compulsivity as a basis for investigation into eating disorders, which are severe psychiatric disorders with high mortality rates.
This thesis includes three experimental studies (discussed in Chapters 3 to 5), which investigate different aspects of eating disorders and compulsivity.
The first experimental study (Chapter 3) is a multimodal magnetic resonance imaging study, in which the neural basis of compulsivity was investigated in participants who had recovered from anorexia nervosa and control participants. We used a task with functional magnetic resonance imaging which incorporated key elements of compulsivity, performed a resting-state analysis with frontostriatal seeds, and analysed glutamate levels using magnetic resonance spectroscopy. We neither found evidence of the hypothesised frontostriatal differences, nor of a difference in glutamate levels in participants, but did find parietal differences in both the resting-state and task-based analyses.
The next study, discussed in Chapter 4, aimed to investigate adaptive learning in eating disorders. We predicted that participants in two clinically-relevant groups (those who had recovered from anorexia nervosa, and those who had elevated eating disorder symptoms) would show diminished adaptation of their learning rates in a task which manipulated environmental volatility, and that this would correspond to a reduction in pupil dilation to volatile outcomes in these groups compared to control participants. However, we found elevated adaptation of learning rates in those who had recovered from anorexia nervosa, which may be attributed to heightened learning rates in this group in particular in the first block.
The final experimental study is discussed in Chapter 5, and investigated whether a dietary supplement, N-acetylcysteine, would improve performance of those with elevated eating disorder symptoms on tasks which measure compulsive and impulsive responding. However, this did not seem to be the case, though N-acetylcysteine was well-tolerated.
Hypoxia-activated small molecule-induced gene expression
Keywords: Hypoxia
Bioreduction
Prodrugs
Gene Expression

Hypoxia, conditions of insufficient oxygen, can occur in a wide variety of biological environments, including solid tumours, bacterial biofilms, and plants. Hypoxic tumours are associated with aggressive tumour phenotypes, increased resistance to radio- and chemotherapy, and poor patient prognosis. In biofilms, low oxygen delivery to cells causes significant reduction in bacterial growth rates, which increases resistance to antibiotics. Plants most commonly become hypoxic through flooding, which negatively impacts crop yields. Consequently, tools to study hypoxia are crucial. Hypoxia-activated prodrugs offer the ability to deliver compounds selectively to regions of hypoxia, through attachment of bioreductive groups, (e.g. 4 nitrobenzyl moiety). Oxygen-dependent nitroreductase enzymes catalyse reduction of the nitro group to form a radical nitro anion, which is re-oxidised back to the nitro group in the presence of oxygen. Under hypoxic conditions, this futile REDOX cycling cannot occur. The nitro anion radical is further reduced to form a hydroxylamine or amine; subsequent fragmentation releases the drug.
This work combines the concept of hypoxia-activated prodrugs with an IPTG-inducible gene expression system in BL21 (DE3) E. coli bacteria. We hypothesised that protecting IPTG 76 with a bioreductive group would inhibit IPTG-induced expression. Only under hypoxic conditions will reduction of the bioreductive group, release of IPTG 76 and induction of gene expression occur.
First, a hypoxia-activated resorufin-based fluorophore was employed to determine whether hypoxia-dependent bioreduction of a nitroaryl group would take place in bacteria using the BL21 (DE3) strain of E. coli. Then a range of derivatives of IPTG, protected with a bioreductive group were synthesised and analysed for their ability to undergo reduction and fragmentation to release IPTG 76. Using, sfGFP as a reporter gene, these were then tested for their ability to induce hypoxia-dependent gene expression in BL21 (DE3) E. coli. Through fluorescence and western blot analysis, compound 94 was shown to induce expression of sfGFP in a hypoxia-dependent manner. This work represents a proof-of-concept system for hypoxia- activated small molecule-induced gene expression.
Behavioural adaptations to breeding in a long-lived pelagic seabird
Keywords: Bio-logging
Manx Shearwater
Seabirds
Tracking
Skomer

The traits of organisms evolve by natural selection to maximise fitness; however, we do not observe Darwinian Demons. This is because all organisms face various types of constraint, which ultimately limit fitness. Reproduction is inextricably linked with fitness, and constraints on reproduction have extensive implications for evolution and adaptation.
Two broad types of constraints on breeding are treated here. Firstly, breeding may be constrained by life-history trade-offs, perhaps most fundamentally in that current reproductive effort is constrained by its costs to future reproduction. Secondly, breeding may be constrained by the physical and ecological conditions and finite resources that are accessible from the breeding site, to which organisms may be tied to varying extents. The life-history and behaviour of animals are profoundly affected by these constraints, and they are especially influential in long-lived species.
This thesis examines behavioural adaptations to each of these types of constraint in a long-lived pelagic seabird: the Manx Shearwater, Puffinus puffinus. Firstly, I investigate how patterns of behaviour vary between sexes and populations in preparation for breeding and how this variation is related to the ecological and physiological constraints faced by the groups during breeding. Secondly, I test the responsiveness of parents to changes in offspring hunger during food provisioning and discuss the influence of constraint by costs to future reproduction. I tackle these questions using well-established biologging methods to remotely monitor behaviour in a natural and experimental setting.
Quantifying brain maturation in the preterm baby from EEG sleep analyses
Keywords: Bayesian machine learning
Brain maturation
Electroencephalogram (EEG)
Neonatal sleep
Preterm baby

The preterm (premature) baby, born before term-age of 37 weeks Postmenstrual Age (PMA, the age since the last menstrual cycle of the mother) remains vulnerable and is admitted to the Neonatal Intensive Care Unit (NICU). Continual improvement of care in the NICU has limited their lifelong impact. However, clinical interventions and other environmental stresses can facilitate delays in brain maturation resulting in abnormal neurodevelopmental outcomes (mental and motor disabilities) by school-age. This is not easily detected by existing methods in the NICU, though Electroencephalography (EEG) is emerging as a promising modality to capture such deviations through the maturation of sleep. Due to a shortage of trained clinicians and the infeasibility of continually labelling EEG, developing fully automated methods is crucial.
Current methods are either not fully automated, do not consider the maturational effects across multiple sleep states, or have limited to no clinical validation on abnormal outcome data. Consequently, the aim of this research is to develop fully automated methods to quantify brain maturation from EEG sleep, through (i) robust automated sleep staging, (ii) tracking sleep-dependent developmental trajectories over PMA, (iii) assessing the quality of sleep-wake cycling with PMA, and (iv) validating these methods using both normal and abnormal outcome data.
This thesis first presents a robust algorithm for detecting the Quiet Sleep (QS) and non-QS sleep states from EEG over a wide PMA range, with median sensitivity and specificity of 0.82 and 0.92, respectively. With this method, sleep states are then estimated from abnormal outcome data and a data-driven feature extraction applied to identify maturational ‘biomarkers’ and derive sleep-dependent trajectories over PMA. Developmental deviations are detected that identify abnormal outcome patients early.
Probabilistic models are next developed to assess sleep-wake cycling by performing the first multi-state classification of sleep at term-age (with median sensitivity and specificity of 0.72 and 0.91, respectively). At this age, EEG differentiates into more complex states and the timing of this differentiation is also an important indicator of brain maturation. Finally, these models are expanded to novel, end-to- end solutions (employing Bayesian non-parametrics) that incorporate both age and sleep dependencies. These methods additionally classify severely delayed sleep-wake cycling behaviours, known as ‘dysmaturity’.