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    Creation of an artificial Stetterase through the design, synthesis and installation of an organocatalyst into a protein scaffold

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    The application of biocatalysis in industrial synthesis continues to rise at pace, driven by a demand for sustainable synthetic methods. As a result, chemo-enzymatic cascades which merge the use of chemocatalysis and biocatalysis are of growing interest. Whilst the majority of enzymatic reactions take place in water, chemocatalysis is typically performed in organic solvents making solvent-compatibility an issue. One option to overcome this is the use of protein hosted organocatalytic reactions. Proteins are inherently compatible with aqueous solvents, but their internal environment contains hydrophobic pockets and functional groups suited to organocatalysis. Progress in protein engineering has enabled us to design, evolve and select structures which can incorporate and exploit the reactivity of non-proteinogenic components. Whilst modification of existing cofactors has increased organocatalytic reactivity and reaction scope, in some cases modification is not compatible with the native protein host. In this thesis we look to use an alternative protein scaffold covalently functionalised with an organocatalyst. We also consider how the chiral environment of the protein could be utilised to enable an enantioselective reaction. In this work we select, express and purify several protein scaffolds with cysteine (Cys) residues at selected positions to allow for functionalisation with an organocatalyst. For some of the scaffolds (e.g. human steroid carrier protein, hSCP) Cys-containing variants already exist. Whilst for others (e.g. Thermus thermophilus SCP, TTSCP), the placement of Cys residues was guided by structural analysis, docking (AutoDock Vina) and modelling of the constructs using AlphaFold. We functionalised our chosen scaffold with N-heterocyclic carbenes (NHCs), a large group of organocatalysts which have been inspired by the natural cofactor thiamine pyrophosphate (TPP). NHCs catalyses a wide number of reactions including C-C bond formation and other reactions that are not known in nature. We synthesised novel NHCs with appropriate handles to enable bioconjugation to specific positions in a protein scaffold. We went on to screen and select conditions for functionalisation of the protein scaffolds and identify the best-functionalised scaffolds to test as catalysts. We also investigated the use of genetic code expansion (GCE) for the incorporation of an NHC unnatural amino acids (UAAs) into a protein. To do this we synthesised novel NHC based UAAs and screen existing orthogonal translation systems. To test the catalytic activity of our functionalised protein scaffolds (hSCP and TTSCP) we used an intramolecular Stetter reaction as a well-studied model reaction. The Stetter reaction uses a nucleophilic catalyst to catalyse C-C bond formation between an aldehyde and an α,β-unsaturated carbonyl forming a 1,4 dicarbonyl product. This reaction is of interest as the synthesis of enantiopure 1,4 dicarbonyl compounds remains a challenging transformation in synthetic chemistry. Stetter reactions are mostly undertaken in organic solvents with only one, aqueous Stetter catalyst reported to date, which is not enantioselective. The TPPdependant Stetterase enzymes such as PigD and MenD can produce chiral products in water, however, these too have limitations in their substrate scope and soluble recombinant expression. By using a protein hosted organocatalyst we have the opportunity to incorporate NHCs with different core structures and enable more diverse chemistries. Here we show SCP scaffolds covalently functionalised with an NHC catalyse an intramolecular Stetter reaction with modest yields and % e.e. We demonstrate that our functionalised proteins operate under ambient conditions with low catalyst loading. Furthermore, we demonstrate that activity can be increased >20 fold by altering the protein scaffold. This is the first example of an artificial Stetterase constructed from an inactive protein scaffold and a synthetic organocatalyst. This breakthrough discovery lays the foundations to optimise the catalytic activity and improve the enantioselectivity. Furthermore, this proof-of-concept study paves the way for this methodology to be applied to other NHC/protein scaffold combinations

    Assessing Locally-Led Anticipatory Action Options to Counter Climate-induced Humanitarian Crisis in East Africa

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    Summary of ongoing PhD research presented as a poster at the University of Edinburgh Royal (Dick) School of Veterinary Studies Annual PGR Conference, 23 April 202

    Spencer cohomology, supersymmetry and the structure of Killing superalgebras

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    We review and expand upon work from the last decade on the application of Spencer cohomology to the study of supersymmetric bosonic backgrounds of supergravity. The central observation of this project is that the symmetry superalgebras of such backgrounds, known as Killing superalgebras, are filtered subdeformations of the Poincaré superalgebra. Such deformations of Z-graded Lie superalgebras are governed by Spencer cohomology, thus the structure of Killing superalgebras can be determined from the Spencer cohomology of (graded subalgebras of) the Poincaré superalgebra. Moreover, the cohomology calculation often allows one to write down the Killing spinor equation and determine much of the structure of supersymmetric supergravity backgrounds, and in some cases it allows one to generalise the notion of supersymmetric geometry. This thesis contributes to the existing literature on Spencer cohomology and supersymmetry both in terms of general theoretical results and in terms of explicit calculations and examples. We consider the algebraic structure of Killing superalgebras, with particular focus on the highly supersymmetric case, generalising to arbitrary dimension and amount of supersymmetry a number of results previously only proven for 11-dimensional supergravity. We characterise possible obstructions to ``integrating'' infinitesimal filtered deformations ((2,2)-Spencer cohomology classes) of the Poincaré superalgebra to full deformations. We also give a geometric description of backgrounds with gauged R-symmetry, clarifying and improving upon previous treatments in the literature, and generalise the aforementioned results to Killing superalgebras of such backgrounds. Some worked examples in 2 dimensions are presented. We determine the (2,2)-Spencer cohomology of the N-extended Poincaré superalgebra in 5 and 6 spacetime dimensions with gauged R-symmetry. We also show that this cohomology is trivial in Type IIA. We then consider the structure of filtered deformations and maximally supersymmetric backgrounds in the minimal 5-dimensional case with gauged R-symmetry, showing that obstructions to integrating infinitesimal deformations exist and arise in both algebraic and geometric guises. We also classify some sub-classes of the maximally supersymmetric backgrounds and their superalgebras in this case

    Reshaping narratives: women Artists from West Asia and North Africa in Western museums

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    The last three decades saw an increase in the number of group and solo exhibitions of modern and contemporary artists from the West Asia and North Africa (WANA) in western museums. The exhibitions sparked many debates among artists, curators, and art historians. These exhibitions were often presented as part of the growing tendencies of globalism in the art world. However, like many exhibitions featuring non-western artists, they were met with accusations of exoticism and neo-orientalism. The debates surrounding the displays and perception of modern and contemporary art from the region were further amplified by the politically charged climate following the events of September 11. This brought the questions of cultural divergence to the forefront. Applying postcolonial and feminist theories, this study aims to examine these issues, analysing the conflicting viewpoints and the impact of curatorial approaches on the perception of art and artists, with a specific focus on women artists. Women artists from WANA represent the intersection between different groups and identities that have been marginalised and exoticised by art history and its narratives. As nonwestern artists and as women artists, they were excluded from the narratives of modern art. As artists from WANA, the perception of their work is constantly challenged by the politically charged context. As women from WANA, their identity has long been overburdened with stereotypes that were further perpetuated by Orientalist art. In this study, I explore the work of four Abstract women artists whose reception has been hindered by discourses of universality and exclusive narratives of modernism. By examining the politics of display and the associated political discourses, I demonstrate how western museums tend to exhibit the works of artists within the confines of Orientalist narratives, thereby overshadowing the voices of the artists. This is especially true in the case of women artists. Women artists and art addressing gender issues are significantly visible in recent exhibitions. However, this study argues that the spaces dedicated to women artists remain limited risking the construction and perpetuation of stereotypical tropes surrounding women artists and their art. Moreover, the reliance of discourses on controversies and dichotomies overlooks the artistic and aesthetic contributions and the extensive history of women artists’ practices and their impact on art scenes. This study not only emphasises the diverse range of styles, themes, and approaches found in the artworks of women artists, but it also highlights the significant role these artists have played in shaping art scenes in various societies

    Dickens and temporality: reading Dickens's fiction through the lens of Bergson's philosophy

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    This thesis examines the representation of subjective temporal experience in Dickens’s fiction, by reading his fiction through the lens of Henri Bergson’s philosophy of subjective time. This research’s main argument is that Dickens’s fiction anticipates a modern conception of temporal experience, which is rooted in heterogeneity, a coexistence that implies both past and present, memory and re-creation, continuity and change. In the first section, I begin by analysing Bergson’s concepts of memory, interconnectedness and continuous re-creation, which will form the lens through which to read Dickens’s fiction. Following this, I conduct three specific case studies in Dickens’s fiction. I begin by showing that Dickens’s Christmas books represent a turning point in his conception of temporality and subjectivity, before analysing the incorporation of these ideas in Dickens’s construction of narrative voice in David Copperfield, arguing that this novel marks a shift in his perspective on subjective time and memory. Finally, I show that Dickens’s most complex exploration of the human experience of time is found in Great Expectations, as his quintessential novel of time, showing the coexistence of past and present, life and death, memory and re-creation, continuity and change. This research addresses the gap in scholarship surrounding Dickens’s representation of time and temporal experience, showing that his fiction’s unparalleled success in the nineteenth century was tied to his new conception of and particular insight into subjectivity and temporality

    Sequencing B cell receptor repertoires in human disease: applications in myalgic encephalomyelitis/chronic fatigue syndrome and in experimental malaria infection

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    The human adaptive immune system has the capacity to respond to any potential pathogen, to fine-tune the specificity of this response upon encountering an antigen, and commit the effective B or T cells to immune memory. This specificity relies on selecting antigenbinders from a vastly diverse pool of B cell receptors (BCRs) produced by VDJ gene segment recombination and junctional diversification during B cell development, and affinity maturation upon encounter with a cognate antigen. Adaptive Immune Receptor Repertoire sequencing (AIRRseq) enables us to characterise features of B cell populations by sequencing BCRs. In this thesis AIRRseq was used to investigate properties of the human BCR repertoire in two different disease settings. We also attempted to improve on existing methods for BCR-antigen mapping, which would address a major limitation of current AIRRseq analyses. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a common chronic illness with unknown aetiology and characterised uniquely by the exacerbation of symptoms following exertion. Chronic infection and autoimmunity have been proposed as two mechanisms that potentially underlie the pathology of ME/CFS. We compared the BCR repertoires of 25 patients with mild-moderate ME, 36 patients with severe ME, 21 healthy controls and 28 patients with Multiple Sclerosis to see if we could find signatures of infection or autoimmune responses. ME patients did not display increased clonality or differential somatic hypermutation compared to healthy controls and patients with Multiple Sclerosis. One of two V genes reported to be differentially used in ME patients in a previous study, was replicated in patients with mild/moderate disease. There were no obvious differences in affinity maturation in the ME cohort, but we observed skewing of the ratio of IgM to IgG BCRs in a majority of ME patients. The second chapter explores a cohort of seven volunteers undergoing a first and second homologous challenge with Plasmodium falciparum. The BCR repertoires of volunteers infected with malaria displayed clonal expansion and somatic hypermutation of repertoires in a primary challenge but, upon re-challenge, we did not observe any signatures of clonal expansion or recurrence of clones expanded in the first challenge. Twenty-eight days post challenge, volunteers showed a trend towards an enrichment of unmutated IgG B cell receptors in their repertoires and this signature was enhanced in the second infection. This was an unexpected finding that warrants further investigation. Finally, we attempted optimisation of a protocol to pair native B cell receptor heavy and light chains as expression-ready scFv libraries for phage display at high throughput in a user-friendly microfluidics system. While significant progress was made with improving on existing protocols and developing the method, including making a low-cost alternative to a commercially available droplet generator to generate uniform and stable emulsions at high throughput, the full reactions to pair native heavy and light chains in single cell reactions were not achieved. The work described here provides a basis for future lab members to fully optimise the reactions and will allow the lab to interrogate the antigen specificity of sequenced BCR repertoires in future. Taken together, these three chapters explore the uses and limitations of state-of-the-art BCR repertoire sequencing, and generated and analysed two high-quality BCR repertoire datasets

    Estimation and application of Bayesian Hawkes process models

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    In this thesis, we examine various facets of Bayesian approaches to Hawkes Processes. Hawkes Processes are a flexible class of point processes that are used to model events that occur in clusters or bursts, as classic Hawkes processes capture the self-exciting behaviour where one event makes future events more likely. While they are popular in the earthquake literature, they are also successfully used in other applications, such as crime, email or Twitter messaging patterns, or tradings on the stock market. A variety of estimation procedures, both in the frequentist and Bayesian domains, exist to estimate the parameters of the Hawkes process. The goal of this thesis is to enable and improve parameter estimation for different scenarios, such as missing data and inhibition. We use these findings to apply Hawkes processes to product sales analysis, specifically to identify product cannibalisation, and to model data from a group chat setting. We address issues in parameter estimation in the excitation-only case when data from a Hawkes process is missing. This can severely bias the learning of the Hawkes process parameters. As such, we develop a novel estimation approach based on Approximate Bayesian Computation. We then consider an extension of the Hawkes process which incorporates inhibition, where events can decrease the intensity function. This leads to additional complexities in the estimation procedure. We resolve challenges regarding the integration of the intensity function and introduce a new, less restrictive condition for stability as existing conditions are unnecessarily strict under inhibition. Based on these findings, we use the multivariate Hawkes process to model product sales. In particular, we are interested in product cannibalisation, which refers to the decrease in the sales of one product due to competition from another product. We examine this phenomenon in a wholesale data set provided by an international company using a multivariate Hawkes process with inhibition. For this, we design a dimension-independent prior for inhibition based on a reparametrisation. Finally, we propose an extension to the classic multivariate Hawkes model, which permits different influences for immigrant and triggered events subject to the latent branching structure. We showcase this extended model on data from a group chat

    Asset maintenance of thick section fibre-reinforced composite structures

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    Fibre-reinforced polymer (FRP) composites are popular in engineering, because they generally have higher specific strength and stiffness compared to other materials (e.g., some metals, polymers and ceramics). The use of FRPs is most often associated with thin, lightweight structures and components (e.g., aerospace, sporting goods, luxury and high-performance vehicles). As such, the vast majority of FRP research is targeted towards thin laminate structures and components. However, there exist thick-section FRP structures—such as Hunt-class mine countermeasures vessels (MCMVs)—that were designed decades ago (e.g., vessels resembling MCMVs appear in c. 1970s publications). Some of these early designs—or derivatives thereof—entered production, and have been in regular service for many years. Due to the comparatively sparse literature available, these structures now constitute an asset maintenance dilemma. For these reasons, this thesis focuses on the asset maintenance of thick-section FRP structures from multiple perspectives. Firstly, the efficacy of two Non-destructive Testing (NDT) techniques to detect delamination flaws in thick section composites was evaluated. In the first technique, a Full Matrix Capture (FMC) Total Focusing Method (TFM) ultrasound was used. A range of delaminations were generated during manufacturing of six glass FRP blocks, which ranged in total specimen thickness from 20 to 120 mm in 20 mm increments, whilst delamination thickness, delamination in-plane dimensions, and delamination depth location were selected as test variables. For this inspection setup, research indicates that 3 mm thick delaminations are identifiable when embedded at depths up to 74 mm, reducing to 36 mm for surface-to-surface contact delaminations. Regardless of FRP specimen thickness, delaminations were observed when embedded at depths up to 74 % of FRP thickness, beyond which signal decay, noise and mechanically-benign acoustic features limited the success of industrially-representative inspection methods. An inverse relationship was observed between the FRP thickness and the ability to find delaminations. Furthermore, data shows that when delaminations are inserted at greater depths in the FRPs, the accuracy of measuring their depths using this setup increases. Thereafter, in an innovative study, the efficacy of Ground Penetrating Radar (GPR) to detect delaminations in these same FRP composite specimens was evaluated, using a 2000 MHz microwave antenna. Therein, FRP specimen thickness, delamination depth location, antenna orientation and delamination cavity dryness were selected as variables. For perpendicular antenna orientation, research indicates that 3 mm thick dry delaminations are identifiable—after background removal and other post-processes—up to a depth of 87 mm in the 100 mm plate, and 107 mm in the 120 mm plate. These corresponded to the deepest-set delaminations in the test matrix, and furthermore, were deeper set (and in thicker FRP) than could be detected using advanced ultrasonic techniques. Since this is, apparently, the first successful inspection of thick FRP structures using GPR, it is speculated that additional research could unlock the true potential of GPR inspection of FRPs, with respect to the FRP specimen thickness and the characteristics of the damage/defect targets to be identified. When the detection of damage in a structure (e.g., via NDT) is considered, it is logical to subsequently question what the consequences of that damage are, with respect to the original mechanical properties in the undamaged state. During NDT campaigns, the effect of found damage on the mechanical properties can be assessed, if the significance of similar damage has been parametrically quantified. This would empower asset owners/operators with data to determine appropriate next-steps, when these damages are identified during in-service NDT campaigns. To achieve this, a partial-factorial investigation, exploring the effect of delamination flaws on the mechanical properties of glass FRPs in flexure, is presented. Test variables included: the FRP thickness (expressed in number of plies); delamination through-thickness location; and delamination in-plane area (that was determined parametrically). The mean flexural strength and stiffness of each pre-flawed case was normalised using the corresponding reference case (that which had the same thickness but no deliberately inserted delaminations prior to testing). Potential differences in specimen manufacturing quality were accounted for using the respective measured densities. Curves having exponential form were fitted using the mean, normalised specific strength data, such that the relationships could be established between each of the test variables and the normalised specific flexural strength. In this way, the effect of delaminations of various sizes, positioned at various locations within laminates of various thickness, was quantified. Surface plots were created that connect all of the test variables to the normalised specific flexural strength, so that the consequence of an arbitrary delamination in another laminate can be inferred. These results are intended to be used in tandem with in-field NDT techniques, to empower owners and operators to determine design-appropriate limits for permissible damage in FRP structures. Furthermore, it is hoped that this research will inform their asset maintenance and repair procedures in a data-driven manner, such that the occurrence of would-be unnecessary and environmentally harmful repair processes, is minimised. Some theories that relate stresses to strains (in FRP structures) are predicated on assumptions that are difficult to prove mathematically. It is common in the literature for researchers to develop axiomatic Equivalent Single Layer (ESL) theories that describe the behaviour of FRP plates and beams, often intended for use on "thick" FRPs. However, there remains a shortage of literature that defines the properties that a laminate must have for it to qualify as "thick", and therefore, the suitability of the ESL theories described in the literature, is unknown. In the penultimate chapter of this thesis, the definition of the descriptor "thick", with respect to FRP beams, was challenged. The research methodology was based on observing the effect of laminate thickness (expressed in number of plies) on the relationships recorded between through-thickness position and the Digital Imaging Correlation (DIC)-measured in-plane strains. The experimental design and the test matrix were selected on the supposition that the descriptor "thick" (and thereby, the suitability of any ESL theory axioms), could be directly linked to the number of plies used to construct a given laminate. Therefore, changes to the quantity of plies in a given beam would be most likely to result in changes to the characteristics of the resulting through-thickness strain relationships (i.e., strain profiles). The through-thickness strain profiles that were measured using DIC, and their corresponding beam thicknesses appeared to be mostly uncorrelated, with linear strain profiles observed regularly in both the thinnest and thickest specimens, whilst strain profiles that could be described as nonlinear were observed in the middle-thickness beams. Although the data presented does not show any easily extracted trends between the number of plies in a laminate and the nature and distribution of through-thickness measured strain profile, the research remains valuable as a foundation upon which further experiments can be conducted

    An evaluation of the structural, functional, cellular and molecular basis of heart pathophysiology in mouse models of spinal muscular atrophy

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    Spinal Muscular Atrophy (SMA) is a multi-system disorder caused by reduced levels of Survival Motor Neuron (SMN) protein and primarily impacts the motor neurons. Previous studies have reported defects in multiple non-neuronal tissues, and cardiac defects such as thinning of left ventricular wall and interventricular septum, fibrosis, and increased apoptosis. In this thesis, I undertook a detailed morphological and functional study of the heart in the Smn2B/- mouse model which develops motor symptoms from day 10 after birth in order to understand the development and progression of the heart defects caused by reduced Smn levels. Initial analysis of the cardiac structure at disease end stage revealed defects consistent with the literature such as thinning of the left ventricular wall and the interventricular septum. I then considered the impact of the smaller body size and recognized that when the structural measures were normalised to tibia length – a surrogate for body size – many of these defects were no longer significant. Thus, the size of most aspects of the heart were in proportion to the reduced body size. The results also implied that the weight of the hearts of the Smn2B/- mice were significantly reduced even after being accounted for a reduced body size. Furthermore, I established similar corrections in literature-based mouse models with an increased disease severity. I then confirmed the absence of structural changes in the end-stage Smn2B/- mice by in vivo high-resolution echocardiography. The results also implied that the weight of the hearts of the Smn2B/- mice were significantly reduced even after being accounted for a reduced body size. Systolic and diastolic cardiac function were preserved; however, the myocardial longitudinal segments were significantly deformed during systole. Following this, I performed a detailed time course of the proteomic profile of the heart to investigate any molecular perturbations. I observed that there was a high range of variation in protein levels at all timepoints. Further investigation of these dysregulated proteins revealed metabolic pathways such as oxidative phosphorylation, fatty acid metabolism, glycolysis, and all mitochondrial complexes (especially complex 1) to be consistently perturbed. This could have a major impact on energy production and metabolism. Both the LXR/RXR signalling pathway and the PPARs are downregulated, and activation of both these are known to have protective effects on the cardiovascular system. I then performed a comparative proteomic profiling across the three mouse models of SMA to reveal that these metabolic pathways are disturbed consistently since the day of birth when the animals do not show any pathology. Subsequently I investigated the physiological impact of these pathways on the proliferation to hypertrophy transition, collagen deposition and fat deposition in the cardiac tissue. In summary aside from a slight decrease in proliferation at P18, no other significant changes were identified at the disease end-stage in both the Smn2B/- mice and the SMNΔ7 mice. Finally, I show that activation of the LXR/RXR signaling pathway by administration of Pioglitazone from P5 in the Smn2B/- mice is not able to normalize the levels of Mug1, ApoE and Agt. Collectively, my findings emphasize the significance of properly accounting for body size in assessing structural changes in the heart. However, I have uncovered notable functional anomalies that may predispose the heart to subsequent failure. I have identified a consistent molecular signature pointing to dysregulation in oxidative phosphorylation and fatty acid metabolism across multiple mouse models and throughout the progression of the disease. I propose that the manipulation of LXR/RXR and PPARs presents a promising opportunity to intervene in these processes. This work underlines the importance of understanding non-neuronal pathology in SMA, and provides important evidence into how reduced SMN levels have an impact on the heart and mechanistic insights into the metabolic changes underlying the cardiac pathology

    Understanding the role and function of SPOCD1 in piRNA-directed de novo DNA methylation

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    The survival of the germline is essential for the survival of a species. Yet, the integrity of those cells is threatened by transposons during foetal development. In fact, failure to silence transposons results in male infertility in mammals. The PIWI-interacting RNA (piRNA) pathway is the primary germline defence system which places CpG DNA methylation at transposon loci. piRNAs recruit the PIWI protein MIWI2 to nascent transposon transcripts via complementary base pairing and instruct DNA methylation through SPOCD1. In this work, I defined the interaction of SPOCD1 with three downstream factors, SPIN1, C19ORF84 and TPR. C19ORF84 interacts with a c-terminal α-helix of SPOCD1 and TPR interacts with the SPOCD1 TFIIS-M domain. In addition, I solved the structure of the SPOCD1 SPOC domain, whose function remains to be determined, at 1.7 Å. I then focused on the SPOCD1-SPIN1 interaction. I showed that SPOCD1 directly interacts with SPIN1, a chromatin reader that recognises H3K4me3 and H3K9me3. I found that SPIN1 and SPOCD1 are interacting before MIWI2 is expressed which challenges the current view of all molecular events required for piRNA-directed DNA methylation occurring after the engagement of MIWI2. In addition, I saw that young LINE1 transposon copies are marked by the SPIN1-associated chromatin marks before the initiation of piRNA-directed DNA methylation. I then generated a Spocd1 separation-of-function allele in the mouse encoding a SPOCD1 variant that can no longer interact with SPIN1. I showed that the SPOCD1-SPIN1 interaction is in fact essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 transposons. In summary, this work defines the interaction of SPOCD1 with SPIN1, C19ORF84 and TPR, gives an insight into the SPOCD1 SPOC domain structure and defines the importance of the SPOCD1-SPIN1 interaction which challenges the current model and proposes a novel two-factor authentication system to form the basis of precision

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