VictorJuiz/thesis huggingface dataset:
A novel glycoconjugation method and unexpected photo-induced site-selective protein cleavage reaction

Homogenous glycoforms of glycoproteins are one of the primary targets in glycobiology to allow for the determination of glycoprotein function and to create glycoprotein mimetics for use as therapeutic agents. Although N- and O-linked glycosylation is preferred in nature, S-linked glycoproteins are attractive synthetic targets due to their enhanced chemical stability and enzymatic resistance. This thesis reports a novel convergent method for the synthesis of S-linked glycoproteins through the site-specific ligation of 1-glycosyl thiols to olefin containing proteins. This strategy employs unnatural amino acid incorporation for the introduction of L-homoallylglycine (L-Hag) into proteins and free-radical addition hydrothiolation chemistry, under conditions mild enough to preserve protein activity. The unique reactivity profile of L-Hag, which has an olefinic side-chain, compared with the natural amino acids characteristically found in proteins, allows for a chemoselective chemical reaction. At the outset, methodology was optimised using Hag as a model system. The reaction was then successfully applied to proteins with different structures, for precise, site-selective glycoconjugation at single and even multiple sites. Whilst investigating the above-mentioned photochemical modification of proteins, an unexpected photo-induced site-selective protein cleavage reaction localised to the TIM-barrel proteins from family 1 of glycosylhydrolases was discovered. Although proteins are known to be affected by UV irradiation, examples of clean, site-selective photocleavage without the use of a cleaving agent are rare. Remarkably, the β-glycosidase from Sulfolobus solfataricus (SsβG) was found to form two daughter fragments following UV irradiation (240–308 nm). Alterations at and alaninescanning of a sphere of residues around the cleavage site were used to establish which residues were essential for the reaction to occur and extensive analysis of the fragments allowed a reaction mechanism to be proposed. The propensity of other proteins to undergo photo-induced cleavage was also investigated. In addition, the biotechnological utility of the aforementioned photocleavage reaction has been applied to the development of a cleaved-tag affinity purification method using a GFPSsβG fusion as the model protein.

Keywords: cleavage
protein
glycoconjugation
Advisor: Davis, B
The heroic cult of the sovereign goddess in mediaeval India

This thesis examines why the cult of the sovereign goddess was considered important for the expression of royal power in mediaeval India. In literature and ritual, the goddess was conceptualized as the sovereign of heaven and earth. Her cult was heroic because it was primarily a cult of warriors: a good hero was one who worshipped the goddess for great powers, foremost among them being sovereignty. Certain ritual practices of the cult such as self-mutilation formed the criteria for a warrior- worshipper’s heroism. By assessing the available epigraphical, literary, scriptural and anthropological material, I will attempt to show that the association between Indic kingship and the cult’s belief-systems, also referred to as heroic Śāktism, was indeed an ancient one. Tracing its roots to non-Aryan religion, the cult of the sovereign goddess became a vital part of the Sanskritic kingdom, particularly from the latter half of the 6th c., when tribal kingdoms began to elevate themselves on the political map. One of the hallmarks of the cult, responsible for its pan-Indic popularity, was its syncretic nature: besides outcastes, its followers were from a number of sects. The goddess at its centre had no ﬁxed identity but was formed of various personalities. The more public and well-attested of these was the martial goddess Durgā/Caṇḍī/Caṇḍikā, although other goddesses were also worshipped as her other aspects. In all these aspects the sovereign goddess was believed to grant the power of the king and the community. This idea was evoked in the mediaeval Indic world in an array of symbols: sacred statues, ritually empowered swords and insignia put on display for all to see, legends circulated throughout the kingdom, festivals where the sacred might of the realm was ritually reinforced. By assessing these symbols, I will attempt to show the vibrant forms whereby the connection of the cult with power was manifested in the mediaeval period.

Keywords: Indian kingship
warrior culture
Candika
royal goddess cults
Advisor: Sanderson, A
Time heals all wounds ?

The mechanisms responsible for the healing of corneal surface wounds are the subject of biological controversy. In particular, the role and source of the regulatory chemical epidermal growth factor (EGF) is an area of intense debate. In the first part of this thesis, we propose a reaction-diffusion model which focuses on the stimulus for increased mitotic and migratory activity due to secretion of EGF. A detailed numerical study of various possible models, with parameter values based on biological data, reveals that, for realistic healing times, EGF must be released by the underlying layers of the cornea, in addition to the tear film source. The model exhibits travelling wave solutions and further analysis elucidates the interaction and role of the parameters in determining the speed of healing. Furthermore, we consider the effect of topical application of EGF and investigate the effect of curvature of the eye. We show that our model is consistent with many of the key features of corneal wound healing.
Adult dermal wounds, in contrast to foetal wounds, heal with the formation of scar tissue. A crucial factor in determining the nature of the healed tissue is the ratio of collagen 1 to collagen 3, which indicates the fibril diameter. We develop a reaction-diffusion model which focuses on the stimulus for collagen synthesis due to the secretion of the different isoforms of the regulatory chemical transforming growth factor β (TGFβ). Numerical simulations of the model without diffusion lead to a value of this ratio consistent with that of healthy tissue for the foetus but corresponding to scarring in the adult. The model equations evolve to waves moving into the wound, but addition of TGFβ only has a transient effect on the final collagen levels. We investigate this effect by developing a caricature model. The model indicates that the main source of the fibroblasts is the underlying subcutaneous tissue and we determine key parameters which explain the difference between adult and foetal wound healing. Furthermore we make clinically testable predictions on the effects that topical application of various chemicals will have on scar formation.

Advisor: Sherratt, J
The synthesis of haemoglobin E

Hb E (α2β226 glu→lys) is one of tne most common haemoglobin variants, found in an estimated 30 million people in South-East Asia. Homozygotes for Hb E are only mildly anaemic but compound heterozygotes with β thalassaemia have a severe clinical disorder which is the commonest form of symptomatic thalassaemia in S.E. Asia. The reasons for the high frequency of the S E gene and the severity of its interaction with β thalassaemia have never been adequately explained. We have studied eight Hb E homozygotes and nine heterozygotes all of S.E. Asian origin.
In peripheral blood reticulocytes of homozygotes there was marked deficit of βE chain synthesis relative to α chain synthesis (α/βE ratio 2.0-3.3) and this was also observed to a lesser degree in the heterozygotes (1.23-2.19). There was no evidence that this was due to rapid destruction of the newly synthesised βE chains, nor that Hb E was preferentially destroyed during the lifespan of the red cell.
Measurement of the ratios of α/β globin mRNA in the reticulocytes of these subjects showed E a deficit of 3 mRNA consistent with the decreased βE chain synthesis in these cells. Assessment of α/β mRNA ratios in bone marrow samples suggested normal transcription of βE mRNA and transport out of the nucleus but that once in the cytoplasm the βE mRNA was relatively unstable. The nature of the mRNA defect is unknown and could result either from the base substitution responsible for the amino acid change or from a second independent mutation in this gene.
Thus the βE gene acts as a mild β thalassaemia gene, the defect acting at a pretranslational level. This explains why on interaction with β thalassaemia there is marked deficit of β chain production leading to a disorder of clinical importance.

Advisor: Wood, W
Wood, B
Imputation aided analysis of the association between autoimmune diseases and the MHC

The Major Histocompatibility Complex (MHC) is a genomic region in chromosome 6 which has been consistently found to be associated with the risk of developing virtually all common autoimmune diseases. Although its importance in disease pathogenesis has been known for decades, efforts to disentangle the roles of the classical human leukocyte antigens (HLA) and other variants responsible for the susceptibility to disease have often met with limited success, owing to the complex structure and extreme heterogeneity of the region.
In this thesis, I interrogate the MHC for association with three common autoimmune diseases, ankylosing spondylitis, psoriasis and multiple sclerosis, with the aim of confirming the previously-reported associations and of identifying novel ones. To do so, I employ a systematic, joint analysis of single nucleotide polymorphism (SNP) and HLA allele data, in a logistic regression framework, using a recently developed algorithm to predict the HLA alleles for samples where such information is unavailable. To ensure the reliability of the analysis, I apply stringent quality control procedures and integrate over the uncertainty of the HLA allele predictions. Moreover, I resolve the haplotype phase of individuals from the HapMap project to create reliable reference panels, used in both HLA prediction and in quality control procedures.
By directly testing HLA subtypes for association with the disease, the power to detect such associations is increased. I present the results of the analysis on the three disease phenotypes and discuss the evidence for important novel findings amongst both SNPs and HLA alleles in two of the diseases.
In the final part of this thesis, I introduce a novel, model-based approach to detect inconsistencies in the data and show how it can be used to flag problematic SNPs which conventional quality control procedures may fail to identify.

Keywords: multiple sclerosis
HLA
Li &amp; Stephens model
ankylosing spondylitis
association studies
autoimmune diseases
statistical genetics
psoriasis
GWAS
MHC
Advisor: McVean, G
Analysis of biological pattern formation models

In this thesis we examine mathematical models which have been suggested as possibile mechanisms for forming certain biological patterns. We analyse them in detail attempting to produce the requisite patterns both analytically and numerically. A reaction diffusion system in two spatial dimensions with anisotropic diffusion is examined in detail and the results compared with certain snakeskin patterns. We examine two other variants to the standard reaction diffusion system: a system where the reaction kinetics and the diffusion coefficients depend upon the cell density suggested as a possible model for the segmentation sequence in Drosophila and a system where the model parameters have one dimensional spatial gradients.
We also analyse a model derived from known cellular processes used to model the branching behaviour in bryozoans and show that, in one dimension, such a model can, in theory, give all the required solution behaviour. A genetic switch model for pattern elements on butterfly wings is also briefly examined to obtain expressions for the solution behaviour under coldshock.

Advisor: Murray, J
Coverage probabilities of edges in a regular graph by a random walk

We investigate the probability that a random walk covers a given edge in a connected regular network. For a complete graph or a circle graph, we obtain an explicit expression of the coverage probability by using the walk generating function. Alternatively, for any fixed connected regular network, we use the largest eigenvalue of the adjacency matrix of the network with the given edge removed from the original network to give a lower bound for the coverage probability. Finally, we give the results by Cooper and Frieze (2013) on the coverage probabilities of nice edges for random regular networks.
The motivation of this project is to obtain properties of a network from a new perspective, which is through primes of a network using random walks. Primes are simple paths and simple cycles in a network, which can be seen as building blocks of a network. A network is uniquely determined by its set of primes.
A network can be explored through a random walk on it, and the random walk can be used to detect primes of the network. A necessary condition for retrieving all the primes in a network is that a random walk visits all edges in the network. The approach of investigating the coverage probability of a given edge serves as a first step to investigate the coverage probabilities of primes.

Keywords: random walk
regular graphs
primes
coverage probability of an edge
accumulative prime factorisation
Advisor: Reinert, G
Jaksch, D
Cracking cribs: representations of burglars and burglary in London, 1860-1939

This thesis explores how burglars and burglary in London were understood in cultural, criminological, legal, political, and economic discourse during the period 1860-1939, demonstrating how the ideas about crime and the criminal circulating in these domains were mutually constitutive. Specifically, it identifies how characterisations of burglary in visual and written forms of media — encompassing legal and criminological documents, as well as those produced by the press and commercial advertising, and in fiction, theatre, and film — cultivated a range of attitudes towards the crime to a greater or lesser extent. Encompassing not only fear-mongering and sympathetic representations, but also those designed to be exciting, to challenge preconceptions, and to entertain, I argue that these conflicting attitudes towards burglary and burglars emerged in response to specific changes in the cultural landscape: the advent of mass literacy and corresponding interest in narratives of crime that reflected the social, cultural, and political concerns of an audience diverse of class, age, and gender; the commercial imperatives of the insurance and entertainment industries as the middle classes expanded, including the development of household insurance and the popularity of the ‘true crime’ genre; debates surrounding women’s increasing social and sexual agency and their alignment with particular crimes; and the evolution of new modes of policing and regulation. The thesis thereby uses the topic of burglary to illuminate a broader range of contemporary preoccupations and experiences with gender relations, class structures and stereotypes, and the moral authority of state and society. By approaching burglary as a focus of interactions not only between police, criminal, and victim, but also between the market, consumers, and the state, this thesis uncovers new terrain upon which crime intersected with everyday lives historically.

Keywords: culture
London
Britain
burglary
crime
history
Advisor: Houlbrook, M
Studies on the effects of N-ethylmaleimide (NEM) in the urinary bladder of Bufo marinus

This thesis sets out a characterisation of the effects of the sulphydryl agent N-ethylmaleimide (NEM) on water flow across the urinary bladder of the toad, Bufo marinus. and compares the effects of NEM with those of vasopressin (VP). This has been done using functional, biochemical, and ultrastructural studies of bladders treated with NEM or VP.
The introduction reviews the action of VP in the toad bladder, and summarises the previous experiments with NEM in this tissue. The results show that NEM causes a specific, irreversible, increase in transepithelial osmotic water flow, but inhibits sodium transport. The increase in water flow does not appear to be mediated by cAMP, or changes of pH or calcium ion concentration, but can be inhibited by low pH, raised calcium, or disruption of the cytoskeleton or cellular metabolism. NEM-induced water flow is additive with that induced by a sub-maximal, but not a maximal, VP dose. NEM treatment leaves the overall epithelial structure intact, while causing changes consistent with increased water flow through the granular cells. Membrane fusion profiles, similar to those seen after VP stimulation, are visible at the apical plasma membrane, and particle aggregates morphologically identical to those believed to mediate the hydrosmotic response to VP can be visualised by freeze-fracture electron microscopy.
These results suggest that NEM induces a specific increase in transepithelial water flow by activating, via one or more sulphydryl reactions, the cellular apparatus stimulated by VP. This activation must occur distal to cAMP production, but proximal to cytoskeletal involvement. NEM may prove valuable in understanding the action of vasopressin, by providing an agonist that acts later in the pathway than others currently available. The implications of the experiments reported here, and suggestions for further work, are discussed.

Advisor: Taylor, A
Vasculature reconstruction from 3D cryomicrotome images

Background: Research in heart disease can be aided by modelling myocardial hemodynamics with knowledge of coronary pressure and vascular resistance measured from the geometry and morphometry of coronary vasculature. This study presents methods to automatically reconstruct accurate detailed coronary vascular anatomical models from high-resolution three-dimensional optical fluorescence cryomicrotomography image volumes for simulating blood flow in coronary arterial trees.
Methods: Images of fluorescent cast and bead particles perfused into the same heart comprise the vasculature and microsphere datasets, employed in a novel combined approach to measure vasculature and simulate a flow model on the extracted coronary vascular tree for estimating regional myocardial perfusion. The microspheres are used in two capacities - as fiducial biomarker point sources for measuring the image formation in order to accurately measure the vasculature dataset and as flowing particles for measuring regional myocardial perfusion through the reconstructed vasculature. A new model-based template-matching method of vascular radius estimation is proposed that incorporates a model of the optical fluorescent image formation measured from the microspheres and a template of the vessels’ tubular geometry.
Results: The new method reduced the error in vessel radius estimation from 42.9% to 0.6% in a 170 micrometer vessel as compared to the Full-Width Half Maximum method. Whole-organ porcine coronary vascular trees, automatically reconstructed with the proposed method, contained on the order of 92,000+ vessel segments in the range 0.03 – 1.9 mm radius. Discrepancy between the microsphere perfusion measurements and regional flow estimated with a 1-D steady state linear static blood flow simulation on the reconstructed vasculature was modelled with daughter-to-parent area ratio and branching angle as the parameters. Correcting the flow simulation by incorporating this model of disproportionate distribution of microspheres reduced the error from 24% to 7.4% in the estimation of fractional microsphere distribution in oblique branches with angles of 100°-120°.

Keywords: Cryomicrotome imaging
three-dimensional (3-D) automatic reconstruction
vascular extraction
whole-organ coronary vasculature
Advisor: Smith, N
Grau, V
On collapsible pushdown automata, their graphs and the power of links

Higher-Order Pushdown Automata (HOPDA) are abstract machines equipped with a nested stacks of stacks... of stacks of stacks. Collapsible pushdown automata (CPDA) enhance these stacks with the addition of ‘links’ emanating from atomic elements to the higher-order stacks below. For trees CPDA are equi-expressive with recursion schemes, which can be viewed as simply-typed λY terms. With vanilla HOPDA, one can only capture schemes satisfying a syntactic constraint called safety.
This dissertation begins with some results concerning the signiﬁcance of links in terms of recursion schemes. We introduce a ﬁne-grained notion of safety that allows us to correlate the need for links of a given order with the imposition of safety on variables of a corresponding order. This generalises some joint work with William Blum that shows we can dispense with homogeneous types when characterising safety. We complement this result with a demonstration that homogeneity by itself does not constrain the expressivity of otherwise unrestricted recursion schemes.
The main results of the dissertation, however, concern the conﬁguration graphs of CPDA. Whilst the conﬁguration graphs of HOPDA are well understood and have decidable MSO theories (they coincide with the Caucal hierarchy), relatively little is known about the transition graphs of CPDA. It is known that they already have undecidable MSO theories at order-2, but Kartzow recently showed that 2-CPDA graphs are tree automatic and hence ﬁrst-order logic is decidable at order-2. We provide a characterisation of the decidability of ﬁrst-order logic on CPDA graphs in terms of quantiﬁer-alternation and the order of CPDA stacks and the links contained within. Whilst this characterisation is fairly comprehensive, we do leave open the question of decidability for some sub-classes of CPDA. It turns out that decidability can be highly sensitive to the order of links in a stack relative to the order of the stack itself.
In addition to some strong and surprising undecidability results, we also develop further Kartzow’s work on 2-CPDA. We introduce preﬁx-rewrite systems for nested-words that characterise the conﬁguration graphs of both 2-CPDA and 2-HOPDA, capturing the power of collapse precisely in terms outside of the language of CPDA. It also formalises and demonstrates the inherent asymmetry of the collapse operation. This generalises the rational preﬁx-rewriting systems characterising conventional pushdown graphs and we believe establishes the 2-CPDA graphs as an interesting and robust class.

Keywords: prefix-rewrite systems
first-order logic
collapsible pushdown automata
Advisor: Ong, C